Starting phenix.real_space_refine
on Fri Mar 14 02:08:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zlh_14780/03_2025/7zlh_14780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zlh_14780/03_2025/7zlh_14780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zlh_14780/03_2025/7zlh_14780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zlh_14780/03_2025/7zlh_14780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zlh_14780/03_2025/7zlh_14780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zlh_14780/03_2025/7zlh_14780.cif"
  }
  resolution = 2.75
  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=   0.002
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      44      5.16       5
     C    6106      2.51       5
     N    1570      2.21       5
     O    1761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9481
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1680
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "K"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 921
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 1598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1598
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "A"
      Number of atoms: 5278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 654, 5278
          Classifications: {'peptide': 654}
          Link IDs: {'PTRANS': 24, 'TRANS': 629}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 6.35, per 1000 atoms: 0.67
  Number of scatterers: 9481
  At special positions: 0
  Unit cell: (100.98, 161.04, 99, 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      44     16.00
     O    1761      8.00
     N    1570      7.00
     C    6106      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 156 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 397 " - pdb=" SG  CYS A 630 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 621 " - pdb=" SG  CYS A 650 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.50
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 13 sheets defined
      39.8% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'H' and resid 104 through 108
    Processing helix  chain 'H' and resid 171 through 173
      No H-bonds generated for 'chain 'H' and resid 171 through 173'
    Processing helix  chain 'H' and resid 203 through 207
      removed outlier: 4.094A  pdb=" N   GLN H 207 " --> pdb=" O   LEU H 204 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 62 through 65
      removed outlier: 3.788A  pdb=" N   GLN K  65 " --> pdb=" O   ASP K  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 62 through 65'
    Processing helix  chain 'A' and resid 24 through 55
    Processing helix  chain 'A' and resid 56 through 59
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 70 through 85
      removed outlier: 3.972A  pdb=" N   LEU A  74 " --> pdb=" O   THR A  70 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TYR A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   TYR A  79 " --> pdb=" O   TYR A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 97
    Processing helix  chain 'A' and resid 115 through 136
      Proline residue:  A 127  - end of helix
      removed outlier: 3.614A  pdb=" N   SER A 134 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 175
    Processing helix  chain 'A' and resid 175 through 190
      removed outlier: 4.279A  pdb=" N   SER A 179 " --> pdb=" O   GLY A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 205
      removed outlier: 3.734A  pdb=" N   GLY A 195 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 210
      removed outlier: 3.625A  pdb=" N   THR A 210 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 240
      removed outlier: 3.912A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      Proline residue:  A 225  - end of helix
    Processing helix  chain 'A' and resid 244 through 261
      removed outlier: 3.502A  pdb=" N   ILE A 248 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
      Proline residue:  A 257  - end of helix
    Processing helix  chain 'A' and resid 264 through 281
    Processing helix  chain 'A' and resid 286 through 308
    Processing helix  chain 'A' and resid 318 through 332
    Processing helix  chain 'A' and resid 333 through 337
    Processing helix  chain 'A' and resid 341 through 366
    Processing helix  chain 'A' and resid 375 through 385
      removed outlier: 3.608A  pdb=" N   PHE A 384 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 397
      removed outlier: 3.630A  pdb=" N   TYR A 395 " --> pdb=" O   HIS A 391 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   CYS A 397 " --> pdb=" O   ARG A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 415
      removed outlier: 3.723A  pdb=" N   THR A 415 " --> pdb=" O   LYS A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 434
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 3.748A  pdb=" N   LEU A 453 " --> pdb=" O   ASN A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 485
      removed outlier: 3.607A  pdb=" N   MET A 476 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
      Proline residue:  A 478  - end of helix
    Processing helix  chain 'A' and resid 486 through 489
    Processing helix  chain 'A' and resid 500 through 517
      removed outlier: 3.686A  pdb=" N   GLY A 509 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 527
    Processing helix  chain 'A' and resid 534 through 548
      removed outlier: 4.680A  pdb=" N   GLU A 538 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 548 " --> pdb=" O   ILE A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 567
      removed outlier: 3.673A  pdb=" N   ALA A 562 " --> pdb=" O   MET A 558 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ASN A 563 " --> pdb=" O   PRO A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 591
    Processing helix  chain 'A' and resid 592 through 595
    Processing helix  chain 'A' and resid 598 through 610
    Processing helix  chain 'A' and resid 619 through 621
      No H-bonds generated for 'chain 'A' and resid 619 through 621'
    Processing helix  chain 'A' and resid 631 through 636
    Processing helix  chain 'A' and resid 640 through 644
      removed outlier: 3.633A  pdb=" N   SER A 644 " --> pdb=" O   PRO A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 657
      removed outlier: 4.185A  pdb=" N   LEU A 655 " --> pdb=" O   ASP A 651 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15
      removed outlier: 6.752A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 139
      removed outlier: 3.660A  pdb=" N   ALA H 151 " --> pdb=" O   VAL H 199 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 166 through 169
    Processing sheet with id=AA5, first strand: chain 'K' and resid 3 through 7
      removed outlier: 3.800A  pdb=" N   GLN K   3 " --> pdb=" O   SER K  25 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   SER K  21 " --> pdb=" O   SER K   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 59 through 60
      removed outlier: 5.508A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ILE K  98 " --> pdb=" O   ASP K 109 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP K 109 " --> pdb=" O   ILE K  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 59 through 60
      removed outlier: 5.508A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14
      removed outlier: 3.588A  pdb=" N   ILE L  49 " --> pdb=" O   TRP L  36 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119
    Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 150
    Processing sheet with id=AB3, first strand: chain 'A' and resid 140 through 145
      removed outlier: 3.981A  pdb=" N   TRP A 143 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   SER A 155 " --> pdb=" O   TRP A 143 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 554 through 556
      removed outlier: 6.709A  pdb=" N   ALA A 555 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
      removed outlier: 9.083A  pdb=" N   GLN A 617 " --> pdb=" O   ALA A 555 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   TYR A 678 " --> pdb=" O   ASN A 673 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ASN A 673 " --> pdb=" O   TYR A 678 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL A 680 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LYS A 669 " --> pdb=" O   LYS A 682 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1305 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: 2.74

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1487
        1.30 -     1.43: 2724
        1.43 -     1.56: 5438
        1.56 -     1.69: 0
        1.69 -     1.82: 66
  Bond restraints: 9715
  Sorted by residual:
  bond pdb=" C   PRO A 216 "
       pdb=" O   PRO A 216 "
    ideal  model  delta    sigma   weight residual
    1.240  1.169  0.071 1.12e-02 7.97e+03 4.04e+01
  bond pdb=" C   THR A 215 "
       pdb=" O   THR A 215 "
    ideal  model  delta    sigma   weight residual
    1.237  1.167  0.070 1.17e-02 7.31e+03 3.61e+01
  bond pdb=" C   PRO A 576 "
       pdb=" O   PRO A 576 "
    ideal  model  delta    sigma   weight residual
    1.238  1.168  0.069 1.24e-02 6.50e+03 3.10e+01
  bond pdb=" C   MET A 470 "
       pdb=" O   MET A 470 "
    ideal  model  delta    sigma   weight residual
    1.234  1.167  0.067 1.24e-02 6.50e+03 2.96e+01
  bond pdb=" C   PRO A 628 "
       pdb=" O   PRO A 628 "
    ideal  model  delta    sigma   weight residual
    1.235  1.169  0.066 1.30e-02 5.92e+03 2.55e+01
  ... (remaining 9710 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.86: 12993
        2.86 -     5.72: 179
        5.72 -     8.58: 20
        8.58 -    11.44: 6
       11.44 -    14.30: 1
  Bond angle restraints: 13199
  Sorted by residual:
  angle pdb=" C   TYR A 578 "
        pdb=" CA  TYR A 578 "
        pdb=" CB  TYR A 578 "
      ideal   model   delta    sigma   weight residual
     110.78  125.08  -14.30 1.60e+00 3.91e-01 7.99e+01
  angle pdb=" CA  MET A 470 "
        pdb=" C   MET A 470 "
        pdb=" O   MET A 470 "
      ideal   model   delta    sigma   weight residual
     121.55  114.18    7.37 1.06e+00 8.90e-01 4.84e+01
  angle pdb=" N   PHE A 401 "
        pdb=" CA  PHE A 401 "
        pdb=" C   PHE A 401 "
      ideal   model   delta    sigma   weight residual
     111.87  102.25    9.62 1.41e+00 5.03e-01 4.65e+01
  angle pdb=" N   PRO A 216 "
        pdb=" CA  PRO A 216 "
        pdb=" C   PRO A 216 "
      ideal   model   delta    sigma   weight residual
     110.70  118.73   -8.03 1.22e+00 6.72e-01 4.33e+01
  angle pdb=" CA  PRO A 216 "
        pdb=" C   PRO A 216 "
        pdb=" N   PRO A 217 "
      ideal   model   delta    sigma   weight residual
     117.93  124.64   -6.71 1.20e+00 6.94e-01 3.13e+01
  ... (remaining 13194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 5218
       17.95 -    35.89: 412
       35.89 -    53.84: 65
       53.84 -    71.78: 11
       71.78 -    89.73: 15
  Dihedral angle restraints: 5721
    sinusoidal: 2194
      harmonic: 3527
  Sorted by residual:
  dihedral pdb=" CB  CYS L 135 "
           pdb=" SG  CYS L 135 "
           pdb=" SG  CYS L 195 "
           pdb=" CB  CYS L 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.90  -76.90     1      1.00e+01 1.00e-02 7.42e+01
  dihedral pdb=" C   THR A  70 "
           pdb=" N   THR A  70 "
           pdb=" CA  THR A  70 "
           pdb=" CB  THR A  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -143.17   21.17     0      2.50e+00 1.60e-01 7.17e+01
  dihedral pdb=" C   GLU A 579 "
           pdb=" N   GLU A 579 "
           pdb=" CA  GLU A 579 "
           pdb=" CB  GLU A 579 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.25  -18.35     0      2.50e+00 1.60e-01 5.39e+01
  ... (remaining 5718 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1467
       0.151 -    0.302: 14
       0.302 -    0.454: 3
       0.454 -    0.605: 1
       0.605 -    0.756: 1
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CA  THR A  70 "
            pdb=" N   THR A  70 "
            pdb=" C   THR A  70 "
            pdb=" CB  THR A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.77    0.76 2.00e-01 2.50e+01 1.43e+01
  chirality pdb=" CA  GLU A 579 "
            pdb=" N   GLU A 579 "
            pdb=" C   GLU A 579 "
            pdb=" CB  GLU A 579 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.02   -0.51 2.00e-01 2.50e+01 6.39e+00
  chirality pdb=" CA  PRO A 216 "
            pdb=" N   PRO A 216 "
            pdb=" C   PRO A 216 "
            pdb=" CB  PRO A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.34 2.00e-01 2.50e+01 2.91e+00
  ... (remaining 1483 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 261 "   -0.023 2.00e-02 2.50e+03   4.56e-02 2.08e+01
        pdb=" C   PHE A 261 "    0.079 2.00e-02 2.50e+03
        pdb=" O   PHE A 261 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   TRP A 262 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 262 "   -0.017 2.00e-02 2.50e+03   3.38e-02 1.14e+01
        pdb=" C   TRP A 262 "    0.058 2.00e-02 2.50e+03
        pdb=" O   TRP A 262 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLN A 263 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  56 "    0.024 2.00e-02 2.50e+03   2.38e-02 9.93e+00
        pdb=" CG  PHE A  56 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  56 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  56 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  56 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  56 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 382
        2.72 -     3.26: 9411
        3.26 -     3.81: 15221
        3.81 -     4.35: 18868
        4.35 -     4.90: 31957
  Nonbonded interactions: 75839
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 116 "
            pdb=" O   LEU A 307 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   ALA A 388 "
            pdb=" OG1 THR A 392 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ILE A 315 "
            pdb=" OG1 THR A 316 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NH1 ARG A 342 "
            pdb=" O   ASN A 437 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" NE2 GLN H 186 "
            pdb=" OG  SER H 188 "
     model   vdw
     2.226 3.120
  ... (remaining 75834 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:             4.590
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.740
  Find NCS groups from input model:        0.090
  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:11.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
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      :  0.005   0.071   9715  Z= 0.340
  Angle     :  0.808  14.300  13199  Z= 0.476
  Chirality :  0.057   0.756   1486
  Planarity :  0.005   0.046   1662
  Dihedral  : 13.853  89.729   3433
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.42 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.86 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.68 (0.24), residues: 1199
  helix:  0.36 (0.25), residues: 436
  sheet:  0.49 (0.33), residues: 265
  loop : -1.72 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 262 
 HIS   0.015   0.002   HIS A 580 
 PHE   0.055   0.002   PHE A  56 
 TYR   0.018   0.002   TYR A  75 
 ARG   0.004   0.001   ARG A  69 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: H   65 ASP cc_start: 0.7586 (p0) cc_final: 0.7284 (m-30)
REVERT: L    6 THR cc_start: 0.6669 (t) cc_final: 0.6356 (p)
REVERT: L   37 TYR cc_start: 0.5852 (m-80) cc_final: 0.5627 (m-80)
REVERT: L   46 LYS cc_start: 0.6902 (tmmt) cc_final: 0.6535 (tmtt)
REVERT: L  208 LYS cc_start: 0.3030 (mmtp) cc_final: 0.2803 (ttpt)
REVERT: A  640 ASP cc_start: 0.7591 (t0) cc_final: 0.7314 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 1.1665
  time to fit residues: 134.4121
Evaluate side-chains
  82 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  578 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 90 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 ASN
A 545 GLN
A 550 GLN
A 643 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.216813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.127769 restraints weight = 10354.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.24
r_work: 0.3350 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.0973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9715  Z= 0.251
  Angle     :  0.654  10.542  13199  Z= 0.346
  Chirality :  0.047   0.268   1486
  Planarity :  0.005   0.039   1662
  Dihedral  :  5.126  59.061   1314
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  7.10 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.37 (0.24), residues: 1199
  helix:  0.88 (0.25), residues: 440
  sheet:  0.38 (0.32), residues: 266
  loop : -1.67 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 440 
 HIS   0.005   0.001   HIS A 391 
 PHE   0.032   0.002   PHE A  56 
 TYR   0.023   0.002   TYR A 578 
 ARG   0.003   0.000   ARG A 570 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: H   65 ASP cc_start: 0.7825 (p0) cc_final: 0.7502 (m-30)
REVERT: L   37 TYR cc_start: 0.6201 (m-80) cc_final: 0.5975 (m-80)
REVERT: L   46 LYS cc_start: 0.7013 (tmmt) cc_final: 0.6689 (tmtt)
REVERT: L  208 LYS cc_start: 0.3123 (mmtp) cc_final: 0.2923 (ttpt)
REVERT: A  585 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5930 (pm20)
REVERT: A  593 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8475 (mtm)
REVERT: A  640 ASP cc_start: 0.8039 (t0) cc_final: 0.7351 (t0)
  outliers start: 17
  outliers final: 6
  residues processed: 92
  average time/residue: 1.1511
  time to fit residues: 114.3821
Evaluate side-chains
  88 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Chi-restraints excluded: chain A residue  593 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 68 optimal weight:    0.0060
   chunk 88 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 92 optimal weight:    0.1980
   chunk 8 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0870
   chunk 56 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 105 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0370
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.2652

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 ASN
A 550 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.221689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.134136 restraints weight = 10531.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.17
r_work: 0.3484 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9715  Z= 0.143
  Angle     :  0.554   7.922  13199  Z= 0.291
  Chirality :  0.043   0.234   1486
  Planarity :  0.004   0.040   1662
  Dihedral  :  4.612  59.662   1314
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.60 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.07 (0.25), residues: 1199
  helix:  1.45 (0.26), residues: 445
  sheet:  0.53 (0.32), residues: 266
  loop : -1.61 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 262 
 HIS   0.005   0.001   HIS A 391 
 PHE   0.015   0.001   PHE A 387 
 TYR   0.023   0.001   TYR L  50 
 ARG   0.003   0.000   ARG L  25 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 2.048 
Fit side-chains
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.5392 (mmm-85) cc_final: 0.4683 (mmt180)
REVERT: L   37 TYR cc_start: 0.6026 (m-80) cc_final: 0.5785 (m-80)
REVERT: L   46 LYS cc_start: 0.7002 (tmmt) cc_final: 0.6623 (tmtt)
REVERT: A  434 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.4710 (mttm)
REVERT: A  471 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7405 (ttt180)
REVERT: A  585 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5821 (pp20)
REVERT: A  626 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.5024 (ppt170)
REVERT: A  640 ASP cc_start: 0.7835 (t0) cc_final: 0.7300 (t0)
  outliers start: 19
  outliers final: 5
  residues processed: 105
  average time/residue: 1.4968
  time to fit residues: 170.1822
Evaluate side-chains
  97 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  626 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:   50.0000
   chunk 12 optimal weight:   20.0000
   chunk 93 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
H  31 ASN
A  42 ASN
A 272 GLN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 ASN
A 550 GLN
A 677 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.212358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.122376 restraints weight = 10432.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.34
r_work: 0.3302 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.082   9715  Z= 0.530
  Angle     :  0.803  10.128  13199  Z= 0.425
  Chirality :  0.056   0.276   1486
  Planarity :  0.006   0.043   1662
  Dihedral  :  5.187  57.814   1312
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.34 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.09 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.68 (0.24), residues: 1199
  helix:  0.37 (0.24), residues: 437
  sheet:  0.44 (0.32), residues: 259
  loop : -1.68 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP H 109 
 HIS   0.008   0.002   HIS A 546 
 PHE   0.026   0.003   PHE A  56 
 TYR   0.023   0.003   TYR A 345 
 ARG   0.005   0.001   ARG A 570 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
REVERT: H   65 ASP cc_start: 0.7843 (p0) cc_final: 0.7480 (m-30)
REVERT: L   37 TYR cc_start: 0.6298 (m-80) cc_final: 0.6053 (m-80)
REVERT: L   46 LYS cc_start: 0.7030 (tmmt) cc_final: 0.6766 (ttpt)
REVERT: A  434 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5262 (mttm)
REVERT: A  471 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7620 (ttt180)
REVERT: A  585 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5951 (pm20)
REVERT: A  626 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.3980 (ppt170)
REVERT: A  640 ASP cc_start: 0.8219 (t0) cc_final: 0.7409 (t0)
  outliers start: 30
  outliers final: 12
  residues processed: 105
  average time/residue: 1.2083
  time to fit residues: 136.9114
Evaluate side-chains
  99 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain L residue  127 LYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Chi-restraints excluded: chain A residue  626 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 41 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H  31 ASN
A  42 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.217333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.130163 restraints weight = 10446.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.34
r_work: 0.3366 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9715  Z= 0.182
  Angle     :  0.591   9.731  13199  Z= 0.310
  Chirality :  0.045   0.240   1486
  Planarity :  0.004   0.043   1662
  Dihedral  :  4.720  57.258   1312
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.20 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.19 (0.25), residues: 1199
  helix:  1.07 (0.25), residues: 445
  sheet:  0.44 (0.32), residues: 261
  loop : -1.58 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 110 
 HIS   0.005   0.001   HIS A 391 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.018   0.001   TYR L  50 
 ARG   0.002   0.000   ARG A 676 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: H   65 ASP cc_start: 0.7842 (p0) cc_final: 0.7551 (m-30)
REVERT: H   68 LYS cc_start: 0.7716 (tppt) cc_final: 0.7513 (tptm)
REVERT: H  175 THR cc_start: 0.3664 (OUTLIER) cc_final: 0.3418 (t)
REVERT: L   37 TYR cc_start: 0.6095 (m-80) cc_final: 0.5835 (m-80)
REVERT: L   46 LYS cc_start: 0.7020 (tmmt) cc_final: 0.6706 (ttpt)
REVERT: L  136 LEU cc_start: 0.3121 (mm) cc_final: 0.2889 (tp)
REVERT: A  422 LEU cc_start: 0.7871 (mp) cc_final: 0.7619 (mt)
REVERT: A  434 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5033 (mttm)
REVERT: A  471 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7415 (ttt180)
REVERT: A  585 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5732 (pp20)
REVERT: A  640 ASP cc_start: 0.8011 (t0) cc_final: 0.7355 (t0)
  outliers start: 20
  outliers final: 6
  residues processed: 100
  average time/residue: 1.2015
  time to fit residues: 130.0000
Evaluate side-chains
  93 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   chunk 9 optimal weight:   30.0000
   chunk 117 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.215107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.129261 restraints weight = 10423.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.39
r_work: 0.3317 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9715  Z= 0.285
  Angle     :  0.644  10.167  13199  Z= 0.339
  Chirality :  0.047   0.212   1486
  Planarity :  0.004   0.041   1662
  Dihedral  :  4.815  56.932   1312
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.84 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.59 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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 (0.24), residues: 1199
  helix:  0.82 (0.25), residues: 447
  sheet:  0.36 (0.32), residues: 263
  loop : -1.61 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H 109 
 HIS   0.006   0.002   HIS A 580 
 PHE   0.020   0.002   PHE A 390 
 TYR   0.016   0.002   TYR L  50 
 ARG   0.004   0.000   ARG A 676 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: H   65 ASP cc_start: 0.7803 (p0) cc_final: 0.7508 (m-30)
REVERT: H   68 LYS cc_start: 0.7751 (tppt) cc_final: 0.7543 (tptm)
REVERT: H  175 THR cc_start: 0.3659 (OUTLIER) cc_final: 0.3411 (t)
REVERT: L   37 TYR cc_start: 0.6174 (m-80) cc_final: 0.5922 (m-80)
REVERT: L   46 LYS cc_start: 0.7029 (tmmt) cc_final: 0.6711 (ttpt)
REVERT: L  136 LEU cc_start: 0.3116 (mm) cc_final: 0.2894 (tp)
REVERT: A  434 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5225 (mttm)
REVERT: A  471 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7480 (ttt180)
REVERT: A  585 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5784 (pp20)
REVERT: A  640 ASP cc_start: 0.8109 (t0) cc_final: 0.7384 (t0)
  outliers start: 27
  outliers final: 12
  residues processed: 103
  average time/residue: 1.1731
  time to fit residues: 130.3493
Evaluate side-chains
  98 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain L residue  127 LYS
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 22 optimal weight:   30.0000
   chunk 85 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 50 optimal weight:   30.0000
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
H  31 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.214465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128413 restraints weight = 10514.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.49
r_work: 0.3311 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9715  Z= 0.310
  Angle     :  0.664   9.964  13199  Z= 0.350
  Chirality :  0.048   0.220   1486
  Planarity :  0.005   0.042   1662
  Dihedral  :  4.897  55.091   1312
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.26 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.93 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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 (0.24), residues: 1199
  helix:  0.69 (0.25), residues: 444
  sheet:  0.48 (0.32), residues: 255
  loop : -1.66 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H 109 
 HIS   0.006   0.002   HIS A 546 
 PHE   0.020   0.002   PHE A 390 
 TYR   0.017   0.002   TYR A 345 
 ARG   0.003   0.000   ARG A 570 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: H   65 ASP cc_start: 0.7761 (p0) cc_final: 0.7495 (m-30)
REVERT: H   68 LYS cc_start: 0.7746 (tppt) cc_final: 0.7529 (tptm)
REVERT: H  175 THR cc_start: 0.3638 (OUTLIER) cc_final: 0.3380 (t)
REVERT: L   46 LYS cc_start: 0.7009 (tmmt) cc_final: 0.6696 (ttpt)
REVERT: L  136 LEU cc_start: 0.3070 (mm) cc_final: 0.2862 (tp)
REVERT: A  434 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5121 (mttm)
REVERT: A  471 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7423 (ttt180)
REVERT: A  585 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5822 (pp20)
REVERT: A  640 ASP cc_start: 0.8112 (t0) cc_final: 0.7384 (t0)
  outliers start: 26
  outliers final: 16
  residues processed: 105
  average time/residue: 1.2655
  time to fit residues: 144.0384
Evaluate side-chains
  103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain L residue  127 LYS
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0570
   chunk 8 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 99 optimal weight:    0.1980
   chunk 96 optimal weight:    0.0770
   chunk 48 optimal weight:   20.0000
   chunk 30 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
H  31 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.218092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.128946 restraints weight = 10583.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.20
r_work: 0.3380 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9715  Z= 0.182
  Angle     :  0.583  10.053  13199  Z= 0.304
  Chirality :  0.044   0.179   1486
  Planarity :  0.004   0.045   1662
  Dihedral  :  4.611  55.156   1312
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.79 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.16 (0.25), residues: 1199
  helix:  1.16 (0.25), residues: 445
  sheet:  0.43 (0.32), residues: 269
  loop : -1.66 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 110 
 HIS   0.005   0.001   HIS A 391 
 PHE   0.014   0.001   PHE A 390 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.003   0.000   ARG A 676 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
REVERT: H   68 LYS cc_start: 0.7714 (tppt) cc_final: 0.7511 (tptm)
REVERT: H  175 THR cc_start: 0.3651 (OUTLIER) cc_final: 0.3398 (t)
REVERT: L   37 TYR cc_start: 0.5785 (m-80) cc_final: 0.5496 (m-80)
REVERT: L   46 LYS cc_start: 0.7008 (tmmt) cc_final: 0.6761 (ttpt)
REVERT: L  136 LEU cc_start: 0.3125 (mm) cc_final: 0.2914 (tp)
REVERT: A  313 MET cc_start: 0.7224 (tmm) cc_final: 0.6938 (tpp)
REVERT: A  422 LEU cc_start: 0.7855 (mp) cc_final: 0.7587 (mt)
REVERT: A  434 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5090 (mttm)
REVERT: A  471 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7451 (ttt180)
REVERT: A  585 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5800 (pp20)
REVERT: A  640 ASP cc_start: 0.8027 (t0) cc_final: 0.7400 (t0)
  outliers start: 20
  outliers final: 11
  residues processed: 105
  average time/residue: 1.1989
  time to fit residues: 135.6771
Evaluate side-chains
  101 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 20 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0970
   chunk 77 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.218957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.129622 restraints weight = 10504.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.39
r_work: 0.3386 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9715  Z= 0.170
  Angle     :  0.576   9.759  13199  Z= 0.299
  Chirality :  0.043   0.170   1486
  Planarity :  0.004   0.042   1662
  Dihedral  :  4.479  54.560   1312
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.99 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.02 (0.25), residues: 1199
  helix:  1.35 (0.26), residues: 445
  sheet:  0.48 (0.32), residues: 269
  loop : -1.64 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 143 
 HIS   0.005   0.001   HIS A 391 
 PHE   0.014   0.001   PHE A 390 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.004   0.000   ARG A 676 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: H   68 LYS cc_start: 0.7716 (tppt) cc_final: 0.7511 (tptm)
REVERT: H  175 THR cc_start: 0.3675 (OUTLIER) cc_final: 0.3411 (t)
REVERT: L   37 TYR cc_start: 0.5860 (m-80) cc_final: 0.5586 (m-80)
REVERT: L   46 LYS cc_start: 0.7025 (tmmt) cc_final: 0.6779 (ttpt)
REVERT: A  313 MET cc_start: 0.7178 (tmm) cc_final: 0.6892 (tpp)
REVERT: A  471 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7359 (ttt180)
REVERT: A  585 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5813 (pp20)
REVERT: A  640 ASP cc_start: 0.8000 (t0) cc_final: 0.7397 (t0)
  outliers start: 20
  outliers final: 11
  residues processed: 101
  average time/residue: 1.4158
  time to fit residues: 155.5598
Evaluate side-chains
  95 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 39 optimal weight:   30.0000
   chunk 31 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9980
   chunk 119 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 27 optimal weight:    0.4980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
H  31 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.215246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.126565 restraints weight = 10553.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.28
r_work: 0.3309 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9715  Z= 0.324
  Angle     :  0.668   9.841  13199  Z= 0.351
  Chirality :  0.048   0.210   1486
  Planarity :  0.005   0.041   1662
  Dihedral  :  4.785  53.556   1312
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.84 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.60 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.33 (0.24), residues: 1199
  helix:  0.87 (0.25), residues: 444
  sheet:  0.50 (0.33), residues: 259
  loop : -1.66 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H 110 
 HIS   0.006   0.002   HIS A 391 
 PHE   0.022   0.002   PHE A 390 
 TYR   0.017   0.002   TYR A 345 
 ARG   0.004   0.000   ARG A 676 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: H   68 LYS cc_start: 0.7747 (tppt) cc_final: 0.7524 (tptm)
REVERT: H  175 THR cc_start: 0.3553 (OUTLIER) cc_final: 0.3303 (t)
REVERT: L   37 TYR cc_start: 0.5944 (m-80) cc_final: 0.5681 (m-80)
REVERT: L   46 LYS cc_start: 0.7021 (tmmt) cc_final: 0.6716 (ttpt)
REVERT: A  471 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7468 (ttt180)
REVERT: A  585 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5823 (pp20)
REVERT: A  640 ASP cc_start: 0.8099 (t0) cc_final: 0.7386 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 96
  average time/residue: 1.2201
  time to fit residues: 126.2360
Evaluate side-chains
  98 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  585 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 17 optimal weight:    0.0770
   chunk 46 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 104 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.1142

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

Flipped N/Q/H residues before XYZ refinement:
H  31 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.217553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.128847 restraints weight = 10488.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.31
r_work: 0.3356 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9715  Z= 0.209
  Angle     :  0.611  10.597  13199  Z= 0.319
  Chirality :  0.045   0.183   1486
  Planarity :  0.004   0.043   1662
  Dihedral  :  4.669  53.179   1312
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.79 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.20 (0.25), residues: 1199
  helix:  1.07 (0.25), residues: 447
  sheet:  0.50 (0.32), residues: 269
  loop : -1.69 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP H 110 
 HIS   0.006   0.001   HIS A 391 
 PHE   0.017   0.001   PHE A 390 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.004   0.000   ARG A 676 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10049.88 seconds
wall clock time: 176 minutes 43.23 seconds (10603.23 seconds total)