Starting phenix.real_space_refine
on Wed Feb 12 22:38:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7la4_23245/02_2025/7la4_23245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7la4_23245/02_2025/7la4_23245.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7la4_23245/02_2025/7la4_23245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7la4_23245/02_2025/7la4_23245.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7la4_23245/02_2025/7la4_23245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7la4_23245/02_2025/7la4_23245.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    5213      2.51       5
     N    1386      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8281
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "H"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 911
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 3467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3467
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 27, 'TRANS': 424}
    Chain: "B"
      Number of atoms: 2940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2940
          Classifications: {'peptide': 377}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 357}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      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: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 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: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 18
          Unusual residues: {' CA': 4, 'NAG': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' MG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 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: 5.38, per 1000 atoms: 0.65
  Number of scatterers: 8281
  At special positions: 0
  Unit cell: (102, 110, 100, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      33     16.00
     Mg      1     11.99
     O    1642      8.00
     N    1386      7.00
     C    5213      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 167 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 386 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " MAN D   3 " - " MAN D   4 "
    ALPHA1-4
      " NAG D   2 " - " MAN D   3 "
      " NAG E   2 " - " MAN E   3 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1105 " - " ASN A  15 "
      " NAG C   1 " - " ASN B  99 "
      " NAG D   1 " - " ASN B 320 "
      " NAG E   1 " - " ASN B 371 "
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 932.2 milliseconds
  

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1912

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 19 sheets defined
      11.6% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.940A  pdb=" N   SER H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.955A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.605A  pdb=" N   ASP L  82 " --> pdb=" O   GLU L  79 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE L  83 " --> pdb=" O   GLN L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing helix  chain 'A' and resid 151 through 156
      removed outlier: 3.575A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'B' and resid 121 through 125
    Processing helix  chain 'B' and resid 130 through 134
    Processing helix  chain 'B' and resid 135 through 143
    Processing helix  chain 'B' and resid 170 through 175
      removed outlier: 4.058A  pdb=" N   GLU B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 203
      removed outlier: 3.760A  pdb=" N   ARG B 202 " --> pdb=" O   GLN B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 232
      removed outlier: 3.889A  pdb=" N   ALA B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 259 through 264
      removed outlier: 3.794A  pdb=" N   LEU B 262 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 302
      removed outlier: 3.865A  pdb=" N   LYS B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
      removed outlier: 3.775A  pdb=" N   ASN B 320 " --> pdb=" O   ASN B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 349
      removed outlier: 3.916A  pdb=" N   VAL B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 23
    Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 47
    Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 14
      removed outlier: 3.733A  pdb=" N   GLN L  89 " --> pdb=" O   ASN L  34 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 9 through 12
      removed outlier: 3.551A  pdb=" N   THR A   9 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 23 through 27
    Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 77
      removed outlier: 3.502A  pdb=" N   PHE A  87 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99
    Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117
      removed outlier: 3.738A  pdb=" N   GLU A 120 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AB2, first strand: chain 'A' and resid 241 through 242
      removed outlier: 3.569A  pdb=" N   GLU A 252 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 256 through 257
      removed outlier: 6.323A  pdb=" N   VAL A 267 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   ARG A 279 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ILE A 269 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 293 through 295
      removed outlier: 3.535A  pdb=" N   VAL A 308 " --> pdb=" O   TYR A 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AB6, first strand: chain 'A' and resid 360 through 362
      removed outlier: 3.691A  pdb=" N   GLN A 405 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 87 through 88
    Processing sheet with id=AB8, first strand: chain 'B' and resid 97 through 102
      removed outlier: 3.784A  pdb=" N   LYS B  98 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B 401 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 102
      removed outlier: 3.784A  pdb=" N   LYS B  98 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B 401 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 197
      removed outlier: 4.655A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   ILE B 151 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL B 112 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   GLY B 152 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE B 114 " --> pdb=" O   GLY B 152 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   GLY B 154 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   TYR B 116 " --> pdb=" O   GLY B 154 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   PHE B 156 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   MET B 118 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL B 247 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR B 250 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)

    182 hydrogen bonds defined for protein.
    432 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: 2.25

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2701
        1.34 -     1.46: 1858
        1.46 -     1.58: 3847
        1.58 -     1.70: 0
        1.70 -     1.82: 49
  Bond restraints: 8455
  Sorted by residual:
  bond pdb=" N   ILE H  72 "
       pdb=" CA  ILE H  72 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.07e-02 8.73e+03 1.03e+01
  bond pdb=" N   TYR H 100 "
       pdb=" CA  TYR H 100 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.29e-02 6.01e+03 8.59e+00
  bond pdb=" N   ILE L 106 "
       pdb=" CA  ILE L 106 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.23e+00
  bond pdb=" N   ARG L  24 "
       pdb=" CA  ARG L  24 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.23e-02 6.61e+03 7.35e+00
  bond pdb=" N   ILE L  29 "
       pdb=" CA  ILE L  29 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.08e+00
  ... (remaining 8450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 10666
        1.49 -     2.98: 677
        2.98 -     4.46: 108
        4.46 -     5.95: 23
        5.95 -     7.44: 12
  Bond angle restraints: 11486
  Sorted by residual:
  angle pdb=" N   PHE H 104 "
        pdb=" CA  PHE H 104 "
        pdb=" C   PHE H 104 "
      ideal   model   delta    sigma   weight residual
     111.71  105.39    6.32 1.34e+00 5.57e-01 2.23e+01
  angle pdb=" N   ASN L  31 "
        pdb=" CA  ASN L  31 "
        pdb=" C   ASN L  31 "
      ideal   model   delta    sigma   weight residual
     112.30  106.45    5.85 1.36e+00 5.41e-01 1.85e+01
  angle pdb=" N   VAL B 314 "
        pdb=" CA  VAL B 314 "
        pdb=" C   VAL B 314 "
      ideal   model   delta    sigma   weight residual
     113.20  109.15    4.05 9.60e-01 1.09e+00 1.78e+01
  angle pdb=" N   MET H  81 "
        pdb=" CA  MET H  81 "
        pdb=" C   MET H  81 "
      ideal   model   delta    sigma   weight residual
     114.64  108.32    6.32 1.52e+00 4.33e-01 1.73e+01
  angle pdb=" CA  ARG H  84 "
        pdb=" C   ARG H  84 "
        pdb=" O   ARG H  84 "
      ideal   model   delta    sigma   weight residual
     121.60  116.89    4.71 1.21e+00 6.83e-01 1.52e+01
  ... (remaining 11481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.14: 4827
       24.14 -    48.28: 262
       48.28 -    72.41: 47
       72.41 -    96.55: 20
       96.55 -   120.69: 4
  Dihedral angle restraints: 5160
    sinusoidal: 2151
      harmonic: 3009
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.51   47.49     1      1.00e+01 1.00e-02 3.11e+01
  dihedral pdb=" CA  ASN B 377 "
           pdb=" C   ASN B 377 "
           pdb=" N   GLU B 378 "
           pdb=" CA  GLU B 378 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.33  -27.67     0      5.00e+00 4.00e-02 3.06e+01
  dihedral pdb=" CA  THR H  28 "
           pdb=" C   THR H  28 "
           pdb=" N   PHE H  29 "
           pdb=" CA  PHE H  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.47  -24.53     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 5157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1242
       0.113 -    0.225: 44
       0.225 -    0.338: 5
       0.338 -    0.450: 0
       0.450 -    0.563: 1
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN B  99 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.84   -0.56 2.00e-01 2.50e+01 7.93e+00
  chirality pdb=" CA  TYR H 106 "
            pdb=" N   TYR H 106 "
            pdb=" C   TYR H 106 "
            pdb=" CB  TYR H 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  LEU A  84 "
            pdb=" N   LEU A  84 "
            pdb=" C   LEU A  84 "
            pdb=" CB  LEU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 1289 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 288 "   -0.026 2.00e-02 2.50e+03   1.85e-02 6.81e+00
        pdb=" CG  TYR A 288 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 288 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 288 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 288 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 288 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 288 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 288 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  99 "   -0.024 2.00e-02 2.50e+03   2.24e-02 6.25e+00
        pdb=" CG  ASN B  99 "    0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  99 "   -0.006 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  99 "    0.024 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "   -0.013 2.00e-02 2.50e+03   1.44e-02 5.16e+00
        pdb=" CG  TRP H  47 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 244
        2.66 -     3.22: 8204
        3.22 -     3.78: 13004
        3.78 -     4.34: 18660
        4.34 -     4.90: 30829
  Nonbonded interactions: 70941
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 220 "
            pdb="MG    MG B2001 "
     model   vdw
     2.100 2.170
  nonbonded pdb=" OD1 ASN A 430 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OH  TYR A 353 "
            pdb=" OE1 GLU B 297 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OG  SER A  22 "
            pdb=" O   GLY A  94 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OE1 GLN A 197 "
            pdb=" OG  SER A 220 "
     model   vdw
     2.159 3.040
  ... (remaining 70936 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.400
  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:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.860
  Find NCS groups from input model:        0.070
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
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      :  0.006   0.046   8455  Z= 0.393
  Angle     :  0.844   7.438  11486  Z= 0.492
  Chirality :  0.056   0.563   1292
  Planarity :  0.004   0.043   1485
  Dihedral  : 16.129 120.689   3224
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.58 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  2.70 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.02 (0.24), residues: 1044
  helix: -3.78 (0.40), residues: 95
  sheet: -2.97 (0.25), residues: 351
  loop : -2.26 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP H  47 
 HIS   0.010   0.001   HIS A 278 
 PHE   0.017   0.002   PHE B 370 
 TYR   0.044   0.002   TYR A 288 
 ARG   0.010   0.001   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   26 SER cc_start: 0.7800 (p) cc_final: 0.7471 (t)
REVERT: A  232 ASP cc_start: 0.8233 (m-30) cc_final: 0.7992 (m-30)
  outliers start: 17
  outliers final: 2
  residues processed: 158
  average time/residue: 0.2177
  time to fit residues: 46.9165
Evaluate side-chains
  121 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue   72 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0370
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0770
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.4416

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.138240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.115001 restraints weight = 11448.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.84
r_work: 0.3268 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8455  Z= 0.211
  Angle     :  0.670   7.425  11486  Z= 0.341
  Chirality :  0.048   0.377   1292
  Planarity :  0.004   0.047   1485
  Dihedral  : 10.569 106.103   1355
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.48 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.11 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    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: -3.77 (0.24), residues: 1044
  helix: -3.48 (0.37), residues: 98
  sheet: -3.00 (0.24), residues: 353
  loop : -1.95 (0.25), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 235 
 HIS   0.007   0.001   HIS A 338 
 PHE   0.013   0.001   PHE B 308 
 TYR   0.025   0.002   TYR A 288 
 ARG   0.005   0.001   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   61 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.8006 (mtm-85)
REVERT: A  285 MET cc_start: 0.8926 (mtp) cc_final: 0.8647 (mtm)
REVERT: B  390 LYS cc_start: 0.6755 (tmtt) cc_final: 0.6335 (mttm)
  outliers start: 19
  outliers final: 8
  residues processed: 153
  average time/residue: 0.2137
  time to fit residues: 45.0406
Evaluate side-chains
  136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 MET
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 99 optimal weight:    0.1980
   chunk 94 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
L  27 GLN
L  31 ASN
L  38 GLN
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.136813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.109862 restraints weight = 11403.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.22
r_work: 0.3226 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8455  Z= 0.243
  Angle     :  0.648   7.596  11486  Z= 0.326
  Chirality :  0.046   0.181   1292
  Planarity :  0.004   0.048   1485
  Dihedral  : 10.033 106.108   1353
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.81 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.82 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    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: -3.56 (0.24), residues: 1044
  helix: -3.11 (0.40), residues: 93
  sheet: -2.78 (0.24), residues: 361
  loop : -1.90 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.007   0.001   HIS A 338 
 PHE   0.013   0.002   PHE B 308 
 TYR   0.024   0.002   TYR A 288 
 ARG   0.005   0.000   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: H   10 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8069 (mm-30)
REVERT: H   23 LYS cc_start: 0.8402 (tppt) cc_final: 0.7827 (tptp)
REVERT: L   61 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7876 (mtm-85)
REVERT: L   79 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8096 (mt-10)
REVERT: A  208 ARG cc_start: 0.8346 (mmt-90) cc_final: 0.8004 (mmt-90)
REVERT: A  285 MET cc_start: 0.8854 (mtp) cc_final: 0.8628 (mtm)
REVERT: B  390 LYS cc_start: 0.6616 (tmtt) cc_final: 0.6143 (mttm)
  outliers start: 19
  outliers final: 13
  residues processed: 144
  average time/residue: 0.2207
  time to fit residues: 43.5154
Evaluate side-chains
  138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 98 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0980
   chunk 39 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
L  31 ASN
L  38 GLN
L  92 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.138247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.111467 restraints weight = 11300.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.21
r_work: 0.3244 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8455  Z= 0.203
  Angle     :  0.645  10.248  11486  Z= 0.322
  Chirality :  0.047   0.353   1292
  Planarity :  0.004   0.047   1485
  Dihedral  :  9.741 104.663   1351
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.96 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    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: -3.33 (0.25), residues: 1044
  helix: -2.91 (0.41), residues: 91
  sheet: -2.58 (0.25), residues: 361
  loop : -1.79 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 107 
 HIS   0.006   0.001   HIS A 338 
 PHE   0.016   0.001   PHE B 100 
 TYR   0.018   0.001   TYR A 288 
 ARG   0.006   0.000   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: H   23 LYS cc_start: 0.8314 (tppt) cc_final: 0.7730 (tptp)
REVERT: H   69 THR cc_start: 0.8159 (m) cc_final: 0.7897 (p)
REVERT: L    6 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7723 (mt0)
REVERT: L   61 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7793 (mtm-85)
REVERT: L   79 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8090 (mt-10)
REVERT: A  208 ARG cc_start: 0.8355 (mmt-90) cc_final: 0.8009 (mmt-90)
REVERT: B  390 LYS cc_start: 0.6666 (tmtt) cc_final: 0.6144 (mttm)
REVERT: B  400 GLU cc_start: 0.7800 (tt0) cc_final: 0.7486 (mm-30)
  outliers start: 20
  outliers final: 13
  residues processed: 147
  average time/residue: 0.2321
  time to fit residues: 46.3323
Evaluate side-chains
  140 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.136748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.109867 restraints weight = 11172.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.20
r_work: 0.3223 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8455  Z= 0.268
  Angle     :  0.639   7.964  11486  Z= 0.319
  Chirality :  0.046   0.179   1292
  Planarity :  0.004   0.045   1485
  Dihedral  : 11.180 118.829   1351
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.74 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.30 (0.25), residues: 1044
  helix: -2.84 (0.41), residues: 91
  sheet: -2.63 (0.25), residues: 367
  loop : -1.70 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.007   0.001   HIS A 338 
 PHE   0.012   0.002   PHE B 308 
 TYR   0.023   0.002   TYR A 288 
 ARG   0.006   0.000   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8587 (tt0)
REVERT: H   10 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8166 (mm-30)
REVERT: H   23 LYS cc_start: 0.8315 (tppt) cc_final: 0.7756 (tptp)
REVERT: H   69 THR cc_start: 0.8236 (m) cc_final: 0.8012 (p)
REVERT: A  208 ARG cc_start: 0.8357 (mmt-90) cc_final: 0.8000 (mmt-90)
REVERT: A  285 MET cc_start: 0.8903 (mtm) cc_final: 0.8635 (mtm)
REVERT: B  124 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7961 (mmt)
REVERT: B  390 LYS cc_start: 0.6624 (tmtt) cc_final: 0.6117 (mttm)
REVERT: B  400 GLU cc_start: 0.7784 (tt0) cc_final: 0.7451 (mm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 141
  average time/residue: 0.2237
  time to fit residues: 43.4412
Evaluate side-chains
  143 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   30 SER
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  227 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.134254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.106940 restraints weight = 11422.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.23
r_work: 0.3185 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   8455  Z= 0.376
  Angle     :  0.683   9.395  11486  Z= 0.337
  Chirality :  0.048   0.371   1292
  Planarity :  0.004   0.044   1485
  Dihedral  : 10.443 102.848   1351
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.51 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    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: -3.27 (0.25), residues: 1044
  helix: -2.80 (0.42), residues: 91
  sheet: -2.63 (0.25), residues: 366
  loop : -1.67 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  47 
 HIS   0.009   0.001   HIS A 338 
 PHE   0.016   0.002   PHE B 100 
 TYR   0.027   0.002   TYR A 288 
 ARG   0.004   0.000   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8588 (tt0)
REVERT: H   23 LYS cc_start: 0.8396 (tppt) cc_final: 0.7838 (tptp)
REVERT: A  285 MET cc_start: 0.8971 (mtm) cc_final: 0.8714 (mtm)
REVERT: B  124 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7946 (mmt)
REVERT: B  390 LYS cc_start: 0.6569 (tmtt) cc_final: 0.6059 (mttm)
  outliers start: 35
  outliers final: 28
  residues processed: 144
  average time/residue: 0.2171
  time to fit residues: 42.7797
Evaluate side-chains
  145 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   30 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0970
   chunk 86 optimal weight:    0.7980
   chunk 43 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
L  31 ASN
B 280 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.111581 restraints weight = 11290.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.17
r_work: 0.3250 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8455  Z= 0.205
  Angle     :  0.635   8.270  11486  Z= 0.315
  Chirality :  0.044   0.178   1292
  Planarity :  0.004   0.046   1485
  Dihedral  : 11.027 122.976   1351
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.64 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.19 (0.25), residues: 1044
  helix: -2.63 (0.43), residues: 91
  sheet: -2.51 (0.25), residues: 370
  loop : -1.68 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 338 
 PHE   0.019   0.001   PHE B 100 
 TYR   0.016   0.001   TYR A 288 
 ARG   0.007   0.000   ARG H  84 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8566 (tt0)
REVERT: H   34 MET cc_start: 0.8516 (tpp) cc_final: 0.8232 (mmm)
REVERT: H   47 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7675 (t60)
REVERT: A  259 THR cc_start: 0.9064 (m) cc_final: 0.8601 (p)
REVERT: B  124 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7917 (mmt)
REVERT: B  390 LYS cc_start: 0.6657 (tmtt) cc_final: 0.6155 (mttm)
REVERT: B  400 GLU cc_start: 0.7799 (tt0) cc_final: 0.7459 (mm-30)
  outliers start: 26
  outliers final: 19
  residues processed: 145
  average time/residue: 0.2175
  time to fit residues: 43.3966
Evaluate side-chains
  143 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   30 SER
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  311 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.136110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.108901 restraints weight = 11533.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.26
r_work: 0.3200 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8455  Z= 0.322
  Angle     :  0.669   8.423  11486  Z= 0.330
  Chirality :  0.047   0.320   1292
  Planarity :  0.004   0.042   1485
  Dihedral  :  9.514 101.460   1351
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.96 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.76 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    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: -3.13 (0.25), residues: 1044
  helix: -2.64 (0.42), residues: 91
  sheet: -2.42 (0.25), residues: 370
  loop : -1.67 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.007   0.001   HIS A 338 
 PHE   0.013   0.002   PHE B 308 
 TYR   0.024   0.002   TYR A 288 
 ARG   0.004   0.000   ARG H  84 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8605 (tpp) cc_final: 0.8327 (mmm)
REVERT: H   47 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.7695 (t60)
REVERT: B  124 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7858 (mmt)
REVERT: B  149 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8220 (pt)
REVERT: B  253 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8401 (mtmm)
REVERT: B  390 LYS cc_start: 0.6543 (tmtt) cc_final: 0.6073 (mttm)
  outliers start: 31
  outliers final: 21
  residues processed: 137
  average time/residue: 0.2102
  time to fit residues: 40.2556
Evaluate side-chains
  140 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   30 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 73 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    0.3980
   chunk 77 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.110943 restraints weight = 11459.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.31
r_work: 0.3237 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8455  Z= 0.205
  Angle     :  0.643   8.826  11486  Z= 0.318
  Chirality :  0.045   0.175   1292
  Planarity :  0.004   0.045   1485
  Dihedral  : 10.646 121.171   1351
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.55 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.03 (0.25), residues: 1044
  helix: -2.44 (0.43), residues: 91
  sheet: -2.37 (0.26), residues: 372
  loop : -1.61 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 338 
 PHE   0.012   0.001   PHE B 100 
 TYR   0.016   0.001   TYR A 288 
 ARG   0.004   0.000   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8552 (tpp) cc_final: 0.8260 (mmm)
REVERT: H   47 TRP cc_start: 0.8037 (OUTLIER) cc_final: 0.7631 (t60)
REVERT: L   61 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7651 (mtm-85)
REVERT: A  259 THR cc_start: 0.9058 (m) cc_final: 0.8611 (p)
REVERT: B  124 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7993 (mmt)
REVERT: B  390 LYS cc_start: 0.6665 (tmtt) cc_final: 0.6153 (mttm)
REVERT: B  400 GLU cc_start: 0.7841 (tt0) cc_final: 0.7428 (mm-30)
  outliers start: 25
  outliers final: 18
  residues processed: 140
  average time/residue: 0.2121
  time to fit residues: 41.1155
Evaluate side-chains
  138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.137317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.111043 restraints weight = 11391.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.13
r_work: 0.3246 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8455  Z= 0.244
  Angle     :  0.646   8.982  11486  Z= 0.319
  Chirality :  0.046   0.240   1292
  Planarity :  0.004   0.048   1485
  Dihedral  :  8.705 100.187   1351
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 20.00 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.25), residues: 1044
  helix: -2.39 (0.43), residues: 91
  sheet: -2.25 (0.27), residues: 346
  loop : -1.68 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 338 
 PHE   0.019   0.001   PHE B 100 
 TYR   0.019   0.001   TYR A 288 
 ARG   0.004   0.000   ARG A  41 

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8537 (tpp) cc_final: 0.8256 (mmm)
REVERT: H   47 TRP cc_start: 0.8023 (OUTLIER) cc_final: 0.7644 (t60)
REVERT: A  259 THR cc_start: 0.9083 (m) cc_final: 0.8662 (p)
REVERT: B  124 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7963 (mmt)
REVERT: B  390 LYS cc_start: 0.6697 (tmtt) cc_final: 0.6210 (mttm)
  outliers start: 22
  outliers final: 20
  residues processed: 134
  average time/residue: 0.2126
  time to fit residues: 39.8646
Evaluate side-chains
  143 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   30 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 36 optimal weight:    0.0170
   chunk 48 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0040
   chunk 38 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0770
   chunk 88 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.2788

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

Flipped N/Q/H residues before XYZ refinement:
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.140006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.113481 restraints weight = 11451.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.16
r_work: 0.3285 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8455  Z= 0.178
  Angle     :  0.649  10.816  11486  Z= 0.317
  Chirality :  0.046   0.284   1292
  Planarity :  0.004   0.047   1485
  Dihedral  : 10.018 115.687   1351
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.55 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.25), residues: 1044
  helix: -2.12 (0.46), residues: 88
  sheet: -2.20 (0.27), residues: 344
  loop : -1.63 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.005   0.001   HIS A 338 
 PHE   0.010   0.001   PHE B 100 
 TYR   0.013   0.001   TYR A 288 
 ARG   0.008   0.000   ARG L  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4598.84 seconds
wall clock time: 82 minutes 34.01 seconds (4954.01 seconds total)