Starting phenix.real_space_refine
on Wed May  8 23:32:50 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/05_2024/8xln_38454.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/05_2024/8xln_38454.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/05_2024/8xln_38454.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/05_2024/8xln_38454.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/05_2024/8xln_38454.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/05_2024/8xln_38454.pdb"
  }
  resolution = 3.78
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic.
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      37      5.16       5
     C    4211      2.51       5
     N    1073      2.21       5
     O    1272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "D GLU  171": "OE1" <-> "OE2"
    Residue "D TYR  381": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib"
  Total number of atoms: 6593
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "D"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "A"
      Number of atoms: 1533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1533
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 13, 'TRANS': 179}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.18, per 1000 atoms: 0.63
  Number of scatterers: 6593
  At special positions: 0
  Unit cell: (75.375, 102.51, 110.55, 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      37     16.00
     O    1272      8.00
     N    1073      7.00
     C    4211      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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
    ALPHA1-3
      " BMA H   3 " - " MAN H   4 "
    ALPHA1-6
      " BMA H   3 " - " MAN H   5 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG D 701 " - " ASN D 322 "
      " NAG D 702 " - " ASN D 432 "
      " NAG E   1 " - " ASN D  53 "
      " NAG F   1 " - " ASN D 546 "
      " NAG G   1 " - " ASN D  90 "
      " NAG H   1 " - " ASN D 103 "
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 4 sheets defined
      54.6% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.827A  pdb=" N   HIS D  34 " --> pdb=" O   ASP D  30 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU D  39 " --> pdb=" O   GLU D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 80
    Processing helix  chain 'D' and resid 90 through 105
      removed outlier: 3.581A  pdb=" N   LYS D  94 " --> pdb=" O   ASN D  90 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLN D  96 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 129
    Processing helix  chain 'D' and resid 146 through 155
      removed outlier: 4.285A  pdb=" N   GLU D 150 " --> pdb=" O   PRO D 146 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   MET D 152 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 172
      removed outlier: 3.852A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 194
      removed outlier: 4.119A  pdb=" N   LEU D 179 " --> pdb=" O   GLN D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 219 through 252
      removed outlier: 4.449A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 275 through 279
    Processing helix  chain 'D' and resid 293 through 301
      removed outlier: 3.807A  pdb=" N   MET D 297 " --> pdb=" O   VAL D 293 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL D 298 " --> pdb=" O   THR D 294 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 318
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.692A  pdb=" N   GLY D 377 " --> pdb=" O   HIS D 373 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   HIS D 378 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 412
      removed outlier: 4.019A  pdb=" N   GLY D 405 " --> pdb=" O   HIS D 401 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 422
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 4.007A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 466
      removed outlier: 4.326A  pdb=" N   PHE D 452 " --> pdb=" O   GLY D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 485
      removed outlier: 3.756A  pdb=" N   VAL D 485 " --> pdb=" O   LYS D 481 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 3.852A  pdb=" N   THR D 519 " --> pdb=" O   TYR D 515 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 561
      removed outlier: 3.974A  pdb=" N   GLN D 552 " --> pdb=" O   THR D 548 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU D 560 " --> pdb=" O   ASN D 556 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   GLY D 561 " --> pdb=" O   MET D 557 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 599
      Proline residue:  D 590  - end of helix
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 4.074A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 3.776A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.688A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'A' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'D' and resid 347 through 350
      removed outlier: 3.774A  pdb=" N   ARG D 357 " --> pdb=" O   TRP D 349 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.605A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474

    300 hydrogen bonds defined for protein.
    846 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: 1.38

  Time building geometry restraints manager: 3.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.35: 2079
        1.35 -     1.47: 1780
        1.47 -     1.59: 2860
        1.59 -     1.71: 0
        1.71 -     1.83: 58
  Bond restraints: 6777
  Sorted by residual:
  bond pdb=" C   HIS D 265 "
       pdb=" N   LEU D 266 "
    ideal  model  delta    sigma   weight residual
    1.334  1.311  0.024 1.52e-02 4.33e+03 2.43e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" C1  BMA H   3 "
       pdb=" C2  BMA H   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.18e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.14e+00
  ... (remaining 6772 not shown)

  Histogram of bond angle deviations from ideal:
       98.32 -   105.46: 148
      105.46 -   112.61: 3497
      112.61 -   119.75: 2236
      119.75 -   126.90: 3216
      126.90 -   134.05: 118
  Bond angle restraints: 9215
  Sorted by residual:
  angle pdb=" C   CYS D 133 "
        pdb=" CA  CYS D 133 "
        pdb=" CB  CYS D 133 "
      ideal   model   delta    sigma   weight residual
     110.42  116.59   -6.17 1.99e+00 2.53e-01 9.62e+00
  angle pdb=" C   ALA D 264 "
        pdb=" N   HIS D 265 "
        pdb=" CA  HIS D 265 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.54e+00
  angle pdb=" CA  LEU D 162 "
        pdb=" CB  LEU D 162 "
        pdb=" CG  LEU D 162 "
      ideal   model   delta    sigma   weight residual
     116.30  124.64   -8.34 3.50e+00 8.16e-02 5.68e+00
  angle pdb=" C   ALA D 384 "
        pdb=" N   TYR D 385 "
        pdb=" CA  TYR D 385 "
      ideal   model   delta    sigma   weight residual
     122.65  118.78    3.87 1.66e+00 3.63e-01 5.42e+00
  angle pdb=" C   GLN D 102 "
        pdb=" N   ASN D 103 "
        pdb=" CA  ASN D 103 "
      ideal   model   delta    sigma   weight residual
     122.31  117.77    4.54 2.00e+00 2.50e-01 5.15e+00
  ... (remaining 9210 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.62: 3821
       21.62 -    43.23: 293
       43.23 -    64.85: 42
       64.85 -    86.46: 29
       86.46 -   108.08: 11
  Dihedral angle restraints: 4196
    sinusoidal: 1876
      harmonic: 2320
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.25   89.25     1      1.00e+01 1.00e-02 9.47e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.32   85.32     1      1.00e+01 1.00e-02 8.82e+01
  dihedral pdb=" CA  ARG A 403 "
           pdb=" C   ARG A 403 "
           pdb=" N   GLY A 404 "
           pdb=" CA  GLY A 404 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.56   20.44     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 4193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 827
       0.054 -    0.107: 170
       0.107 -    0.161: 12
       0.161 -    0.215: 0
       0.215 -    0.268: 2
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C5  BMA H   3 "
            pdb=" C4  BMA H   3 "
            pdb=" C6  BMA H   3 "
            pdb=" O5  BMA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ASN D 103 "
            pdb=" N   ASN D 103 "
            pdb=" C   ASN D 103 "
            pdb=" CB  ASN D 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.25e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 234 "    0.040 5.00e-02 4.00e+02   6.09e-02 5.93e+00
        pdb=" N   PRO D 235 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO D 235 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 235 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 145 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO D 146 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO D 146 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D 146 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 103 "    0.020 2.00e-02 2.50e+03   1.94e-02 4.69e+00
        pdb=" CG  ASN D 103 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 103 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 103 "   -0.014 2.00e-02 2.50e+03
        pdb=" C1  NAG H   1 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 201
        2.71 -     3.26: 6861
        3.26 -     3.80: 10402
        3.80 -     4.35: 12276
        4.35 -     4.90: 21018
  Nonbonded interactions: 50758
  Sorted by model distance:
  nonbonded pdb=" O   ILE D 151 "
            pdb=" OG  SER D 155 "
     model   vdw
     2.162 2.440
  nonbonded pdb=" OG  SER D 317 "
            pdb=" O   SER D 545 "
     model   vdw
     2.258 2.440
  nonbonded pdb=" O   ASN A 334 "
            pdb=" N   VAL A 362 "
     model   vdw
     2.276 2.520
  nonbonded pdb=" O   PHE D 327 "
            pdb=" OG  SER D 331 "
     model   vdw
     2.329 2.440
  nonbonded pdb=" O   MET D 152 "
            pdb=" NH2 ARG D 161 "
     model   vdw
     2.355 2.520
  ... (remaining 50753 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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 group one per residue
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:             2.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          11.740
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.240
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
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   0.039   6777  Z= 0.237
  Angle     :  0.647   8.339   9215  Z= 0.317
  Chirality :  0.043   0.268   1011
  Planarity :  0.005   0.061   1171
  Dihedral  : 17.143 108.077   2685
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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:  0.46 (0.31), residues: 785
  helix:  1.78 (0.27), residues: 377
  sheet:  0.15 (0.80), residues: 50
  loop : -1.34 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 477 
 HIS   0.005   0.001   HIS D 265 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.027   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 460 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  194 ASN cc_start: 0.7537 (m-40) cc_final: 0.7149 (m110)
REVERT: D  270 MET cc_start: 0.8346 (tpp) cc_final: 0.7723 (tpp)
REVERT: A  467 ASP cc_start: 0.6564 (m-30) cc_final: 0.6347 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2045
  time to fit residues: 23.5886
Evaluate side-chains
  51 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.3980
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  51 ASN
D  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.0838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6777  Z= 0.183
  Angle     :  0.586  10.243   9215  Z= 0.293
  Chirality :  0.040   0.151   1011
  Planarity :  0.004   0.053   1171
  Dihedral  :  9.922  74.475   1163
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.65 %
    Favored  : 91.20 %
  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 (0.31), residues: 785
  helix:  1.82 (0.27), residues: 380
  sheet: -0.20 (0.73), residues: 53
  loop : -1.36 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.023   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 559 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  249 MET cc_start: 0.8421 (tpp) cc_final: 0.7955 (ttt)
REVERT: D  270 MET cc_start: 0.8107 (tpp) cc_final: 0.7639 (tpp)
REVERT: A  467 ASP cc_start: 0.6621 (m-30) cc_final: 0.6363 (m-30)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.1700
  time to fit residues: 15.8015
Evaluate side-chains
  58 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  442 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 70 optimal weight:    0.2980
   chunk 76 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0370
   chunk 24 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0470
   overall best weight:    0.4356

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6777  Z= 0.148
  Angle     :  0.543   6.795   9215  Z= 0.270
  Chirality :  0.040   0.173   1011
  Planarity :  0.004   0.051   1171
  Dihedral  :  8.000  62.936   1163
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.97 %
    Favored  : 87.88 %
  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:  0.59 (0.31), residues: 785
  helix:  2.02 (0.27), residues: 374
  sheet: -0.19 (0.73), residues: 54
  loop : -1.35 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.010   0.001   PHE A 400 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.004   0.000   ARG D 306 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  270 MET cc_start: 0.8088 (tpp) cc_final: 0.7637 (tpp)
REVERT: D  332 MET cc_start: 0.8581 (tpt) cc_final: 0.8324 (tpt)
REVERT: A  391 CYS cc_start: 0.4482 (p) cc_final: 0.3657 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 69
  average time/residue: 0.1503
  time to fit residues: 15.4662
Evaluate side-chains
  59 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
D  49 ASN
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   6777  Z= 0.197
  Angle     :  0.575  15.014   9215  Z= 0.288
  Chirality :  0.041   0.272   1011
  Planarity :  0.004   0.050   1171
  Dihedral  :  7.381  57.969   1163
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.13 %
    Favored  : 85.14 %
  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:  0.60 (0.31), residues: 785
  helix:  2.06 (0.27), residues: 374
  sheet: -0.70 (0.68), residues: 63
  loop : -1.31 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 378 
 PHE   0.011   0.001   PHE D 369 
 TYR   0.018   0.001   TYR A 380 
 ARG   0.002   0.000   ARG A 466 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  270 MET cc_start: 0.8083 (tpp) cc_final: 0.7611 (tpp)
  outliers start: 12
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1499
  time to fit residues: 14.5764
Evaluate side-chains
  62 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
D 340 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6777  Z= 0.234
  Angle     :  0.578  13.927   9215  Z= 0.293
  Chirality :  0.040   0.208   1011
  Planarity :  0.004   0.050   1171
  Dihedral  :  6.243  44.468   1163
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.01 %
    Favored  : 82.97 %
  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:  0.48 (0.31), residues: 785
  helix:  1.96 (0.27), residues: 374
  sheet: -0.68 (0.68), residues: 63
  loop : -1.40 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.014   0.001   PHE D 369 
 TYR   0.015   0.001   TYR D 385 
 ARG   0.002   0.000   ARG A 457 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  249 MET cc_start: 0.8431 (tpp) cc_final: 0.8101 (mtm)
  outliers start: 14
  outliers final: 11
  residues processed: 67
  average time/residue: 0.1557
  time to fit residues: 15.2927
Evaluate side-chains
  65 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 72 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   6777  Z= 0.194
  Angle     :  0.567  13.923   9215  Z= 0.285
  Chirality :  0.040   0.191   1011
  Planarity :  0.004   0.051   1171
  Dihedral  :  5.885  43.081   1163
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.02 %
    Favored  : 82.54 %
  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:  0.52 (0.31), residues: 785
  helix:  2.03 (0.27), residues: 372
  sheet: -0.63 (0.70), residues: 61
  loop : -1.40 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.011   0.001   PHE D 369 
 TYR   0.015   0.001   TYR D 385 
 ARG   0.002   0.000   ARG A 466 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  239 HIS cc_start: 0.8096 (t70) cc_final: 0.7755 (t70)
REVERT: D  249 MET cc_start: 0.8440 (tpp) cc_final: 0.8030 (mtm)
  outliers start: 10
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1571
  time to fit residues: 15.3935
Evaluate side-chains
  64 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 47 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0980
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6777  Z= 0.182
  Angle     :  0.569  13.297   9215  Z= 0.284
  Chirality :  0.040   0.193   1011
  Planarity :  0.004   0.048   1171
  Dihedral  :  5.629  41.306   1163
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.59 %
    Favored  : 81.53 %
  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:  0.50 (0.31), residues: 785
  helix:  2.03 (0.27), residues: 372
  sheet: -0.77 (0.70), residues: 62
  loop : -1.41 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 168 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.010   0.001   PHE D 369 
 TYR   0.020   0.001   TYR D  83 
 ARG   0.004   0.000   ARG D 169 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  239 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7692 (t70)
REVERT: D  249 MET cc_start: 0.8416 (tpp) cc_final: 0.8174 (mtp)
  outliers start: 13
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1354
  time to fit residues: 14.0013
Evaluate side-chains
  68 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 59 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0020
   chunk 70 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6777  Z= 0.171
  Angle     :  0.553  12.958   9215  Z= 0.278
  Chirality :  0.039   0.190   1011
  Planarity :  0.004   0.044   1171
  Dihedral  :  5.375  39.254   1163
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.87 %
    Favored  : 81.53 %
  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:  0.52 (0.31), residues: 785
  helix:  2.04 (0.27), residues: 372
  sheet: -0.63 (0.72), residues: 61
  loop : -1.41 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 477 
 HIS   0.002   0.001   HIS D 540 
 PHE   0.016   0.001   PHE A 400 
 TYR   0.019   0.001   TYR D  83 
 ARG   0.003   0.000   ARG D 169 

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  239 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7686 (t70)
REVERT: D  249 MET cc_start: 0.8386 (tpp) cc_final: 0.8033 (mtm)
REVERT: D  332 MET cc_start: 0.8801 (tpt) cc_final: 0.8366 (tpt)
  outliers start: 18
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1042
  time to fit residues: 10.9141
Evaluate side-chains
  69 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: