Starting phenix.real_space_refine
on Tue Feb 11 12:54:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sde_23517/02_2025/7sde_23517_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sde_23517/02_2025/7sde_23517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sde_23517/02_2025/7sde_23517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sde_23517/02_2025/7sde_23517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sde_23517/02_2025/7sde_23517_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sde_23517/02_2025/7sde_23517_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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    3748      2.51       5
     N     943      2.21       5
     O    1011      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5734
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 488, 3856
          Classifications: {'peptide': 488}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 20, 'TRANS': 467}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 115
          Unresolved non-hydrogen angles: 148
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      Number of atoms: 1878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1878
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 5, 'TRANS': 232}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 209
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 119
  Time building chain proxies: 3.87, per 1000 atoms: 0.67
  Number of scatterers: 5734
  At special positions: 0
  Unit cell: (68.096, 80.864, 105.336, 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    1011      8.00
     N     943      7.00
     C    3748      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 650.6 milliseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1414

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      61.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 41
      removed outlier: 3.660A  pdb=" N   LEU A  30 " --> pdb=" O   GLU A  26 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA A  31 " --> pdb=" O   LYS A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 53
      removed outlier: 3.793A  pdb=" N   LEU A  51 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 76
      removed outlier: 3.971A  pdb=" N   VAL A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
      removed outlier: 4.030A  pdb=" N   LEU A  87 " --> pdb=" O   LYS A  83 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 116
    Processing helix  chain 'A' and resid 126 through 140
      removed outlier: 3.775A  pdb=" N   ALA A 138 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP A 140 " --> pdb=" O   PHE A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 209
    Processing helix  chain 'A' and resid 215 through 220
    Processing helix  chain 'A' and resid 229 through 239
      removed outlier: 3.502A  pdb=" N   ILE A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 261
      removed outlier: 3.920A  pdb=" N   CYS A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASP A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 276
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 287 through 289
      No H-bonds generated for 'chain 'A' and resid 287 through 289'
    Processing helix  chain 'A' and resid 292 through 302
      removed outlier: 4.036A  pdb=" N   SER A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   PHE A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 363
      removed outlier: 4.481A  pdb=" N   LEU A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A 362 " --> pdb=" O   CYS A 358 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 363 " --> pdb=" O   PHE A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 391
    Processing helix  chain 'A' and resid 394 through 403
      removed outlier: 3.936A  pdb=" N   PHE A 402 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 426
      removed outlier: 3.565A  pdb=" N   THR A 421 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU A 424 " --> pdb=" O   GLY A 420 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LEU A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 442
      removed outlier: 3.918A  pdb=" N   LEU A 442 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.540A  pdb=" N   PHE A 448 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 457
      removed outlier: 3.950A  pdb=" N   LEU A 455 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 496
      removed outlier: 4.087A  pdb=" N   ILE A 479 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   CYS A 482 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 484 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 518
    Processing helix  chain 'A' and resid 518 through 529
      removed outlier: 4.073A  pdb=" N   ARG A 522 " --> pdb=" O   ASN A 518 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 529 " --> pdb=" O   TRP A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
      removed outlier: 3.505A  pdb=" N   GLN A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   MET A 545 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 217
    Processing helix  chain 'B' and resid 219 through 225
    Processing helix  chain 'B' and resid 245 through 253
    Processing helix  chain 'B' and resid 283 through 292
      removed outlier: 3.513A  pdb=" N   MET B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 317
      removed outlier: 3.541A  pdb=" N   ARG B 304 " --> pdb=" O   ASN B 300 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   PHE B 306 " --> pdb=" O   ASP B 302 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASP B 317 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 322
    Processing helix  chain 'B' and resid 329 through 336
    Processing helix  chain 'B' and resid 339 through 346
    Processing helix  chain 'B' and resid 354 through 366
      removed outlier: 4.065A  pdb=" N   LEU B 358 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG B 361 " --> pdb=" O   PHE B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 378
      removed outlier: 3.663A  pdb=" N   ARG B 375 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   ARG B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG B 377 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 397
    Processing helix  chain 'B' and resid 404 through 416
    Processing helix  chain 'B' and resid 432 through 441
      removed outlier: 3.753A  pdb=" N   CYS B 436 " --> pdb=" O   TYR B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 462
      removed outlier: 4.018A  pdb=" N   LEU B 453 " --> pdb=" O   GLU B 449 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    738 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: 1.34

  Time building geometry restraints manager: 1.53 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: 1785
        1.34 -     1.46: 1133
        1.46 -     1.58: 2893
        1.58 -     1.70: 0
        1.70 -     1.82: 45
  Bond restraints: 5856
  Sorted by residual:
  bond pdb=" CA  GLU A 193 "
       pdb=" C   GLU A 193 "
    ideal  model  delta    sigma   weight residual
    1.524  1.556 -0.032 1.24e-02 6.50e+03 6.64e+00
  bond pdb=" CA  LEU A 192 "
       pdb=" C   LEU A 192 "
    ideal  model  delta    sigma   weight residual
    1.522  1.545 -0.023 1.25e-02 6.40e+03 3.33e+00
  bond pdb=" N   TYR A  20 "
       pdb=" CA  TYR A  20 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.023 1.29e-02 6.01e+03 3.31e+00
  bond pdb=" C   MET A 241 "
       pdb=" O   MET A 241 "
    ideal  model  delta    sigma   weight residual
    1.244  1.226  0.018 1.00e-02 1.00e+04 3.15e+00
  bond pdb=" CA  ALA B 323 "
       pdb=" C   ALA B 323 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.020 1.23e-02 6.61e+03 2.58e+00
  ... (remaining 5851 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 7720
        2.64 -     5.28: 174
        5.28 -     7.92: 23
        7.92 -    10.57: 2
       10.57 -    13.21: 1
  Bond angle restraints: 7920
  Sorted by residual:
  angle pdb=" N   LYS A 146 "
        pdb=" CA  LYS A 146 "
        pdb=" C   LYS A 146 "
      ideal   model   delta    sigma   weight residual
     110.24  123.45  -13.21 1.47e+00 4.63e-01 8.07e+01
  angle pdb=" N   GLN A 194 "
        pdb=" CA  GLN A 194 "
        pdb=" C   GLN A 194 "
      ideal   model   delta    sigma   weight residual
     112.57  119.12   -6.55 1.13e+00 7.83e-01 3.36e+01
  angle pdb=" N   ARG A 364 "
        pdb=" CA  ARG A 364 "
        pdb=" C   ARG A 364 "
      ideal   model   delta    sigma   weight residual
     113.12  106.11    7.01 1.25e+00 6.40e-01 3.15e+01
  angle pdb=" C   ASP A  91 "
        pdb=" N   PRO A  92 "
        pdb=" CA  PRO A  92 "
      ideal   model   delta    sigma   weight residual
     119.24  124.34   -5.10 1.04e+00 9.25e-01 2.40e+01
  angle pdb=" N   LYS A 146 "
        pdb=" CA  LYS A 146 "
        pdb=" CB  LYS A 146 "
      ideal   model   delta    sigma   weight residual
     109.48  102.06    7.42 1.55e+00 4.16e-01 2.29e+01
  ... (remaining 7915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 3072
       17.64 -    35.28: 307
       35.28 -    52.92: 102
       52.92 -    70.56: 28
       70.56 -    88.20: 7
  Dihedral angle restraints: 3516
    sinusoidal: 1356
      harmonic: 2160
  Sorted by residual:
  dihedral pdb=" N   TYR A  20 "
           pdb=" C   TYR A  20 "
           pdb=" CA  TYR A  20 "
           pdb=" CB  TYR A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.03  -12.23     0      2.50e+00 1.60e-01 2.39e+01
  dihedral pdb=" C   TYR A  20 "
           pdb=" N   TYR A  20 "
           pdb=" CA  TYR A  20 "
           pdb=" CB  TYR A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.70   12.10     0      2.50e+00 1.60e-01 2.34e+01
  dihedral pdb=" CA  GLU B 398 "
           pdb=" C   GLU B 398 "
           pdb=" N   PHE B 399 "
           pdb=" CA  PHE B 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.12   17.88     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 3513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 847
       0.098 -    0.195: 52
       0.195 -    0.293: 9
       0.293 -    0.390: 2
       0.390 -    0.488: 1
  Chirality restraints: 911
  Sorted by residual:
  chirality pdb=" CA  TYR A  20 "
            pdb=" N   TYR A  20 "
            pdb=" C   TYR A  20 "
            pdb=" CB  TYR A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 5.95e+00
  chirality pdb=" CA  ILE A 435 "
            pdb=" N   ILE A 435 "
            pdb=" C   ILE A 435 "
            pdb=" CB  ILE A 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.80   -0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" CA  TRP A 240 "
            pdb=" N   TRP A 240 "
            pdb=" C   TRP A 240 "
            pdb=" CB  TRP A 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 908 not shown)

  Planarity restraints: 993
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 279 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   SER A 279 "    0.040 2.00e-02 2.50e+03
        pdb=" O   SER A 279 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PRO A 280 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 193 "    0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   GLU A 193 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLU A 193 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLN A 194 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 411 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.75e+00
        pdb=" C   SER A 411 "    0.029 2.00e-02 2.50e+03
        pdb=" O   SER A 411 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TYR A 412 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 990 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 591
        2.74 -     3.28: 5984
        3.28 -     3.82: 8827
        3.82 -     4.36: 11087
        4.36 -     4.90: 18709
  Nonbonded interactions: 45198
  Sorted by model distance:
  nonbonded pdb=" O   SER A 458 "
            pdb=" OG  SER A 458 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   PHE A 461 "
            pdb=" NH2 ARG A 522 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" N   GLU A 473 "
            pdb=" OE1 GLU A 473 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O   PHE A  50 "
            pdb=" NE2 GLN A  54 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" CD2 LEU A 438 "
            pdb=" OE1 GLU A 451 "
     model   vdw
     2.278 3.460
  ... (remaining 45193 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:             1.140
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     16.460
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
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      :  0.004   0.032   5856  Z= 0.239
  Angle     :  0.918  13.208   7920  Z= 0.621
  Chirality :  0.057   0.488    911
  Planarity :  0.003   0.037    993
  Dihedral  : 17.029  88.204   2102
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 25.84
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 10.62 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  8.60 %
    Allowed  : 16.69 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.65 (0.25), residues: 706
  helix: -2.68 (0.21), residues: 412
  sheet:  None (None), residues: 0
  loop : -3.61 (0.29), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 200 
 HIS   0.002   0.001   HIS A  46 
 PHE   0.011   0.001   PHE A 413 
 TYR   0.009   0.001   TYR A  82 
 ARG   0.001   0.000   ARG A 387 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 116
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 LYS cc_start: 0.7399 (pttt) cc_final: 0.7085 (mtmm)
REVERT: A  300 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6979 (m-10)
REVERT: A  451 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6616 (tt0)
REVERT: A  507 GLU cc_start: 0.7163 (mp0) cc_final: 0.6827 (mp0)
REVERT: A  508 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7159 (pt0)
REVERT: A  545 MET cc_start: 0.7802 (mtp) cc_final: 0.7542 (mtp)
  outliers start: 52
  outliers final: 29
  residues processed: 157
  average time/residue: 0.1839
  time to fit residues: 36.9086
Evaluate side-chains
  121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  440 GLU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  497 ILE
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  511 MET
Chi-restraints excluded: chain A residue  523 ARG
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0070
   chunk 55 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0010
   chunk 33 optimal weight:    0.0870
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.2782

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 HIS
A  90 ASN
A  94 ASN
A 134 GLN
A 227 GLN
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
A 345 GLN
A 383 GLN
A 495 HIS
B 201 HIS
B 206 ASN
B 211 GLN
** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 364 GLN
B 389 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.181188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.153290 restraints weight = 7352.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 1.88
r_work: 0.3788 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3660 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5856  Z= 0.163
  Angle     :  0.598   8.484   7920  Z= 0.304
  Chirality :  0.040   0.170    911
  Planarity :  0.004   0.051    993
  Dihedral  :  8.546  58.944    837
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 17.52 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.68 (0.29), residues: 706
  helix: -0.91 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -3.18 (0.30), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 200 
 HIS   0.008   0.001   HIS A 495 
 PHE   0.012   0.001   PHE A  55 
 TYR   0.027   0.002   TYR A 257 
 ARG   0.007   0.000   ARG A 186 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   51 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6993 (mm)
REVERT: A  227 GLN cc_start: 0.8365 (tp40) cc_final: 0.8121 (mm-40)
REVERT: A  441 ASN cc_start: 0.6630 (m-40) cc_final: 0.3687 (m110)
REVERT: A  447 SER cc_start: 0.7416 (m) cc_final: 0.7118 (t)
REVERT: A  451 GLU cc_start: 0.7643 (tt0) cc_final: 0.7292 (mt-10)
REVERT: A  516 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7552 (tt0)
REVERT: A  545 MET cc_start: 0.7974 (mtp) cc_final: 0.7743 (mtp)
REVERT: B  389 GLN cc_start: 0.7541 (mt0) cc_final: 0.7317 (mt0)
  outliers start: 25
  outliers final: 11
  residues processed: 140
  average time/residue: 0.1705
  time to fit residues: 31.5999
Evaluate side-chains
  112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0170
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
B 407 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.177676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.149216 restraints weight = 7383.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 1.91
r_work: 0.3761 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3634 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5856  Z= 0.182
  Angle     :  0.572   8.804   7920  Z= 0.285
  Chirality :  0.040   0.132    911
  Planarity :  0.004   0.044    993
  Dihedral  :  6.060  51.088    788
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.83 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.72 (0.31), residues: 706
  helix: -0.12 (0.25), residues: 439
  sheet:  None (None), residues: 0
  loop : -2.92 (0.31), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 240 
 HIS   0.004   0.001   HIS A 261 
 PHE   0.019   0.002   PHE B 396 
 TYR   0.019   0.001   TYR A  20 
 ARG   0.002   0.000   ARG B 304 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.8374 (tp40) cc_final: 0.8142 (mm-40)
REVERT: A  363 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7732 (tt)
REVERT: A  447 SER cc_start: 0.7485 (m) cc_final: 0.6843 (t)
REVERT: B  369 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8466 (pp)
REVERT: B  450 ILE cc_start: 0.7340 (mp) cc_final: 0.6818 (mp)
  outliers start: 18
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1712
  time to fit residues: 26.8837
Evaluate side-chains
  107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  304 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  369 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 389 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.177444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.150339 restraints weight = 7535.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.96
r_work: 0.3757 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5856  Z= 0.199
  Angle     :  0.593  14.497   7920  Z= 0.288
  Chirality :  0.040   0.126    911
  Planarity :  0.004   0.045    993
  Dihedral  :  5.381  50.256    782
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.34 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.31), residues: 706
  helix:  0.17 (0.26), residues: 437
  sheet:  None (None), residues: 0
  loop : -2.68 (0.33), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 200 
 HIS   0.003   0.001   HIS A 261 
 PHE   0.014   0.001   PHE B 348 
 TYR   0.019   0.001   TYR B 432 
 ARG   0.005   0.000   ARG A 387 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.8412 (tp40) cc_final: 0.8202 (mm-40)
REVERT: A  300 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7434 (m-10)
REVERT: A  363 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7747 (tt)
REVERT: A  447 SER cc_start: 0.7703 (m) cc_final: 0.7276 (t)
REVERT: A  525 TRP cc_start: 0.6492 (t-100) cc_final: 0.6289 (t-100)
REVERT: B  369 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8489 (pp)
REVERT: B  450 ILE cc_start: 0.7462 (mp) cc_final: 0.6885 (mp)
  outliers start: 20
  outliers final: 13
  residues processed: 120
  average time/residue: 0.1624
  time to fit residues: 26.0660
Evaluate side-chains
  109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  304 ASN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 69 optimal weight:    0.2980
   chunk 43 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 ASN
B 389 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.179156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.151775 restraints weight = 7355.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 1.77
r_work: 0.3777 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3648 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5856  Z= 0.160
  Angle     :  0.558  11.522   7920  Z= 0.274
  Chirality :  0.039   0.123    911
  Planarity :  0.004   0.045    993
  Dihedral  :  5.049  47.444    780
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.83 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.32), residues: 706
  helix:  0.51 (0.26), residues: 433
  sheet:  None (None), residues: 0
  loop : -2.52 (0.33), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 200 
 HIS   0.003   0.000   HIS A 261 
 PHE   0.012   0.001   PHE B 307 
 TYR   0.018   0.001   TYR A  20 
 ARG   0.004   0.000   ARG A 275 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.8368 (tp40) cc_final: 0.8165 (mm-40)
REVERT: A  457 LYS cc_start: 0.7105 (ptpt) cc_final: 0.6810 (pttm)
REVERT: A  477 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7029 (tp)
REVERT: A  525 TRP cc_start: 0.6304 (t-100) cc_final: 0.6088 (t-100)
REVERT: A  545 MET cc_start: 0.7602 (mtp) cc_final: 0.7246 (mtp)
REVERT: B  369 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8480 (pp)
REVERT: B  450 ILE cc_start: 0.7430 (mp) cc_final: 0.6849 (mp)
  outliers start: 19
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1605
  time to fit residues: 26.6324
Evaluate side-chains
  117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  304 ASN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 36 optimal weight:    0.0470
   chunk 63 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0040
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0030
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.2700

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 ASN
B 389 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.188027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.161776 restraints weight = 7396.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.4017 rms_B_bonded: 1.71
r_work: 0.3899 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5856  Z= 0.140
  Angle     :  0.566  16.382   7920  Z= 0.273
  Chirality :  0.039   0.121    911
  Planarity :  0.003   0.045    993
  Dihedral  :  4.739  44.573    780
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.50 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.32), residues: 706
  helix:  0.77 (0.26), residues: 437
  sheet:  None (None), residues: 0
  loop : -2.42 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 200 
 HIS   0.002   0.000   HIS A 261 
 PHE   0.010   0.001   PHE B 294 
 TYR   0.020   0.001   TYR B 432 
 ARG   0.003   0.000   ARG A 275 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.8213 (tp40) cc_final: 0.8000 (mm-40)
REVERT: A  363 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7843 (tt)
REVERT: A  477 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7267 (mp)
REVERT: B  270 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7842 (mttt)
REVERT: B  292 MET cc_start: 0.7700 (ttp) cc_final: 0.7454 (ttt)
REVERT: B  369 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8468 (pp)
REVERT: B  450 ILE cc_start: 0.7418 (mp) cc_final: 0.6862 (mp)
  outliers start: 17
  outliers final: 12
  residues processed: 121
  average time/residue: 0.1637
  time to fit residues: 26.1991
Evaluate side-chains
  117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.181658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.154477 restraints weight = 7470.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 1.71
r_work: 0.3818 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3695 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5856  Z= 0.286
  Angle     :  0.669  15.793   7920  Z= 0.323
  Chirality :  0.043   0.128    911
  Planarity :  0.004   0.045    993
  Dihedral  :  4.928  39.028    778
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.82 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.32), residues: 706
  helix:  0.55 (0.26), residues: 435
  sheet:  None (None), residues: 0
  loop : -2.47 (0.33), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 240 
 HIS   0.003   0.001   HIS A 261 
 PHE   0.020   0.002   PHE B 348 
 TYR   0.021   0.002   TYR A  20 
 ARG   0.003   0.000   ARG A 275 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8669 (mt)
REVERT: A  118 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7134 (m-80)
REVERT: A  300 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7396 (m-10)
REVERT: A  363 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7841 (tt)
REVERT: A  477 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7260 (mp)
REVERT: A  545 MET cc_start: 0.7596 (mtp) cc_final: 0.7188 (mtm)
REVERT: B  336 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7861 (mt-10)
REVERT: B  369 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8514 (pp)
REVERT: B  450 ILE cc_start: 0.7389 (mp) cc_final: 0.6852 (mp)
  outliers start: 22
  outliers final: 11
  residues processed: 107
  average time/residue: 0.1751
  time to fit residues: 24.5759
Evaluate side-chains
  110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  304 ASN
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 46 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.184982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.158179 restraints weight = 7323.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 1.71
r_work: 0.3867 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3745 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5856  Z= 0.177
  Angle     :  0.610  14.604   7920  Z= 0.292
  Chirality :  0.040   0.122    911
  Planarity :  0.003   0.045    993
  Dihedral  :  4.668  33.822    778
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.31 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.32), residues: 706
  helix:  0.80 (0.26), residues: 434
  sheet:  None (None), residues: 0
  loop : -2.37 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 200 
 HIS   0.002   0.001   HIS A 261 
 PHE   0.011   0.001   PHE B 348 
 TYR   0.020   0.001   TYR B 432 
 ARG   0.006   0.000   ARG A 387 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7250 (m-80)
REVERT: A  300 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7403 (m-10)
REVERT: A  363 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7852 (tt)
REVERT: A  447 SER cc_start: 0.7596 (m) cc_final: 0.7308 (t)
REVERT: A  477 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7315 (mp)
REVERT: A  545 MET cc_start: 0.7546 (mtp) cc_final: 0.7173 (mtm)
REVERT: B  369 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8493 (pp)
REVERT: B  450 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6873 (mp)
  outliers start: 20
  outliers final: 12
  residues processed: 111
  average time/residue: 0.1643
  time to fit residues: 24.5905
Evaluate side-chains
  113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  450 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 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 = 0.4285 r_free = 0.4285 target = 0.184511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.157660 restraints weight = 7388.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.73
r_work: 0.3865 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3740 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5856  Z= 0.185
  Angle     :  0.610  14.124   7920  Z= 0.294
  Chirality :  0.040   0.121    911
  Planarity :  0.004   0.045    993
  Dihedral  :  4.565  32.395    778
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.64 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.32), residues: 706
  helix:  0.83 (0.26), residues: 435
  sheet:  None (None), residues: 0
  loop : -2.29 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 200 
 HIS   0.002   0.001   HIS A 261 
 PHE   0.013   0.001   PHE B 348 
 TYR   0.017   0.001   TYR A  20 
 ARG   0.005   0.000   ARG A 387 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7284 (m-80)
REVERT: A  300 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7369 (m-10)
REVERT: A  363 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7857 (tt)
REVERT: A  477 LEU cc_start: 0.7802 (tp) cc_final: 0.7449 (mp)
REVERT: A  545 MET cc_start: 0.7537 (mtp) cc_final: 0.7185 (mtm)
REVERT: B  336 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7916 (mt-10)
REVERT: B  369 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8448 (pp)
REVERT: B  450 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6889 (mp)
  outliers start: 18
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1800
  time to fit residues: 26.0152
Evaluate side-chains
  112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  450 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    0.0870
   chunk 31 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0770
   chunk 46 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.5916

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.185471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.158558 restraints weight = 7482.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.74
r_work: 0.3864 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5856  Z= 0.177
  Angle     :  0.615  13.805   7920  Z= 0.294
  Chirality :  0.040   0.121    911
  Planarity :  0.004   0.045    993
  Dihedral  :  4.370  32.227    776
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.64 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.33), residues: 706
  helix:  0.88 (0.26), residues: 437
  sheet:  None (None), residues: 0
  loop : -2.21 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 200 
 HIS   0.002   0.001   HIS A 261 
 PHE   0.016   0.001   PHE B 338 
 TYR   0.020   0.001   TYR B 432 
 ARG   0.005   0.000   ARG A 387 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7259 (m-80)
REVERT: A  300 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7483 (m-10)
REVERT: A  363 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: A  477 LEU cc_start: 0.7710 (tp) cc_final: 0.7363 (mp)
REVERT: A  545 MET cc_start: 0.7554 (mtp) cc_final: 0.7200 (mtm)
REVERT: B  369 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8439 (pp)
REVERT: B  450 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6915 (mp)
  outliers start: 18
  outliers final: 13
  residues processed: 108
  average time/residue: 0.1693
  time to fit residues: 24.2401
Evaluate side-chains
  110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  277 ASN
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  450 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 35 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 4 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0470
   overall best weight:    0.2878

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 ASN
B 342 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.187987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.161674 restraints weight = 7424.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.4012 rms_B_bonded: 1.72
r_work: 0.3895 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5856  Z= 0.140
  Angle     :  0.595  13.538   7920  Z= 0.284
  Chirality :  0.039   0.124    911
  Planarity :  0.003   0.046    993
  Dihedral  :  4.186  31.975    776
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.98 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.33), residues: 706
  helix:  1.03 (0.26), residues: 438
  sheet:  None (None), residues: 0
  loop : -2.23 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 200 
 HIS   0.002   0.000   HIS A 261 
 PHE   0.013   0.001   PHE B 396 
 TYR   0.015   0.001   TYR A  20 
 ARG   0.005   0.000   ARG A 387 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3278.51 seconds
wall clock time: 58 minutes 50.39 seconds (3530.39 seconds total)