Starting phenix.real_space_refine
on Wed Mar 12 04:30:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tcf_41153/03_2025/8tcf_41153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tcf_41153/03_2025/8tcf_41153.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tcf_41153/03_2025/8tcf_41153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tcf_41153/03_2025/8tcf_41153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tcf_41153/03_2025/8tcf_41153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tcf_41153/03_2025/8tcf_41153.cif"
  }
  resolution = 2.9
  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=   0.048
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      5      9.91       5
     Mg      1      5.21       5
     S      35      5.16       5
     C    4443      2.51       5
     N    1179      2.21       5
     O    1387      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7050
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3406
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 21, 'TRANS': 422}
    Chain: "B"
      Number of atoms: 2823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2823
          Classifications: {'peptide': 359}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "D"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 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: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 44
          Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.22, per 1000 atoms: 0.74
  Number of scatterers: 7050
  At special positions: 0
  Unit cell: (72.93, 98.736, 107.712, 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      5     19.99
     S      35     16.00
     Mg      1     11.99
     O    1387      8.00
     N    1179      7.00
     C    4443      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  67 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 108 " - pdb=" SG  CYS A 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 155 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 401 " - pdb=" SG  CYS B 259 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 224 " - pdb=" SG  CYS B 265 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 377 " distance=2.09
    Simple disulfide: pdb=" SG  CYS B 397 " - pdb=" SG  CYS B 425 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C   3 " - pdb=" SG  CYS C  74 " distance=2.04

  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
    ALPHA1-2
      " MAN D   4 " - " MAN D   5 "
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
    ALPHA1-6
      " BMA D   3 " - " MAN D   6 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A 505 " - " ASN A 260 "
      " NAG B2003 " - " ASN B 191 "
      " NAG B2004 " - " ASN B 360 "
      " NAG B2005 " - " ASN B 379 "
      " NAG D   1 " - " ASN A 266 "
      " NAG E   1 " - " ASN A  44 "
      " NAG F   1 " - " ASN B 389 "
      " NAG G   1 " - " ASN B 414 "
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1606

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 14 sheets defined
      18.5% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 188 through 194
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 428 through 430
      No H-bonds generated for 'chain 'A' and resid 428 through 430'
    Processing helix  chain 'B' and resid 114 through 118
    Processing helix  chain 'B' and resid 120 through 127
      removed outlier: 4.007A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 135
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 191 through 201
    Processing helix  chain 'B' and resid 213 through 224
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 250 through 256
    Processing helix  chain 'B' and resid 282 through 293
    Processing helix  chain 'B' and resid 305 through 311
    Processing helix  chain 'B' and resid 312 through 316
    Processing helix  chain 'B' and resid 330 through 343
    Processing helix  chain 'C' and resid 13 through 29
    Processing helix  chain 'C' and resid 51 through 63
      removed outlier: 4.094A  pdb=" N   LYS C  55 " --> pdb=" O   GLU C  51 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12
      removed outlier: 4.236A  pdb=" N   THR A 413 " --> pdb=" O   ASP A 422 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE A 424 " --> pdb=" O   GLY A 411 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   GLY A 411 " --> pdb=" O   ILE A 424 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY A 426 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   MET A 409 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26
    Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81
      removed outlier: 7.089A  pdb=" N   ASP A  84 " --> pdb=" O   TYR A  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88
      removed outlier: 3.502A  pdb=" N   HIS A 113 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101
      removed outlier: 3.915A  pdb=" N   SER A  97 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164
      removed outlier: 3.516A  pdb=" N   SER A 160 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229
      removed outlier: 6.618A  pdb=" N   VAL A 253 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ASN A 266 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ILE A 255 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283
    Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303
    Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348
      removed outlier: 6.297A  pdb=" N   ILE A 344 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   ALA A 361 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   ALA A 359 " --> pdb=" O   PRO A 346 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A 348 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLN A 389 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 63 through 65
      removed outlier: 6.588A  pdb=" N   VAL B  81 " --> pdb=" O   HIS B 420 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   HIS B 422 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ILE B  83 " --> pdb=" O   HIS B 422 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 76 through 77
    Processing sheet with id=AB4, first strand: chain 'B' and resid 182 through 189
      removed outlier: 5.343A  pdb=" N   HIS B 184 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   SER B 148 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   LEU B 188 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LEU B 144 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   TYR B 103 " --> pdb=" O   SER B 139 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ASP B 141 " --> pdb=" O   TYR B 103 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU B 237 " --> pdb=" O   PRO B 104 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ASP B 106 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   LEU B 239 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   TYR B 108 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   MET B 241 " --> pdb=" O   TYR B 108 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   LEU B 110 " --> pdb=" O   MET B 241 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   ILE B 320 " --> pdb=" O   ILE B 295 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   VAL B 297 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   GLY B 322 " --> pdb=" O   VAL B 297 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   PHE B 299 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 37
      removed outlier: 3.870A  pdb=" N   ASN C  33 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL C  42 " --> pdb=" O   PHE C   9 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   CYS C   3 " --> pdb=" O   GLY C  48 " (cutoff:3.500A)

    246 hydrogen bonds defined for protein.
    624 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: 2.18

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1285
        1.32 -     1.45: 1894
        1.45 -     1.58: 3952
        1.58 -     1.71: 15
        1.71 -     1.84: 52
  Bond restraints: 7198
  Sorted by residual:
  bond pdb=" CA  SER B 382 "
       pdb=" CB  SER B 382 "
    ideal  model  delta    sigma   weight residual
    1.527  1.474  0.054 1.49e-02 4.50e+03 1.29e+01
  bond pdb=" CG  PHE A   1 "
       pdb=" CD1 PHE A   1 "
    ideal  model  delta    sigma   weight residual
    1.384  1.456 -0.072 2.10e-02 2.27e+03 1.17e+01
  bond pdb=" CG  PHE A   1 "
       pdb=" CD2 PHE A   1 "
    ideal  model  delta    sigma   weight residual
    1.384  1.453 -0.069 2.10e-02 2.27e+03 1.08e+01
  bond pdb=" C5  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.479 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" CG  ASP B 209 "
       pdb=" OD2 ASP B 209 "
    ideal  model  delta    sigma   weight residual
    1.249  1.188  0.061 1.90e-02 2.77e+03 1.04e+01
  ... (remaining 7193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 8112
        1.70 -     3.41: 1327
        3.41 -     5.11: 227
        5.11 -     6.81: 73
        6.81 -     8.52: 17
  Bond angle restraints: 9756
  Sorted by residual:
  angle pdb=" C   ALA A 362 "
        pdb=" N   PRO A 363 "
        pdb=" CA  PRO A 363 "
      ideal   model   delta    sigma   weight residual
     119.56  128.08   -8.52 1.02e+00 9.61e-01 6.97e+01
  angle pdb=" C   ALA A  40 "
        pdb=" N   PRO A  41 "
        pdb=" CA  PRO A  41 "
      ideal   model   delta    sigma   weight residual
     119.56  127.97   -8.41 1.02e+00 9.61e-01 6.80e+01
  angle pdb=" C   ALA A 297 "
        pdb=" N   PRO A 298 "
        pdb=" CA  PRO A 298 "
      ideal   model   delta    sigma   weight residual
     119.56  127.75   -8.19 1.02e+00 9.61e-01 6.45e+01
  angle pdb=" C   CYS A 401 "
        pdb=" N   PRO A 402 "
        pdb=" CA  PRO A 402 "
      ideal   model   delta    sigma   weight residual
     119.66  125.45   -5.79 7.30e-01 1.88e+00 6.28e+01
  angle pdb=" C   ALA A 109 "
        pdb=" N   PRO A 110 "
        pdb=" CA  PRO A 110 "
      ideal   model   delta    sigma   weight residual
     119.56  127.48   -7.92 1.02e+00 9.61e-01 6.02e+01
  ... (remaining 9751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.32: 4349
       21.32 -    42.63: 104
       42.63 -    63.95: 25
       63.95 -    85.26: 16
       85.26 -   106.58: 8
  Dihedral angle restraints: 4502
    sinusoidal: 1987
      harmonic: 2515
  Sorted by residual:
  dihedral pdb=" CB  CYS A 142 "
           pdb=" SG  CYS A 142 "
           pdb=" SG  CYS A 155 "
           pdb=" CB  CYS A 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   33.56   59.44     1      1.00e+01 1.00e-02 4.72e+01
  dihedral pdb=" CD  ARG B 378 "
           pdb=" NE  ARG B 378 "
           pdb=" CZ  ARG B 378 "
           pdb=" NH1 ARG B 378 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   51.10  -51.10     1      1.00e+01 1.00e-02 3.57e+01
  dihedral pdb=" CB  CYS B 397 "
           pdb=" SG  CYS B 397 "
           pdb=" SG  CYS B 425 "
           pdb=" CB  CYS B 425 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.83   38.83     1      1.00e+01 1.00e-02 2.12e+01
  ... (remaining 4499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 771
       0.078 -    0.157: 256
       0.157 -    0.235: 50
       0.235 -    0.313: 15
       0.313 -    0.392: 15
  Chirality restraints: 1107
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.60e+01
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.53    0.13 2.00e-02 2.50e+03 4.51e+01
  chirality pdb=" C1  NAG G   2 "
            pdb=" O4  NAG G   1 "
            pdb=" C2  NAG G   2 "
            pdb=" O5  NAG G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.52    0.12 2.00e-02 2.50e+03 3.87e+01
  ... (remaining 1104 not shown)

  Planarity restraints: 1268
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 378 "    0.863 9.50e-02 1.11e+02   3.87e-01 9.09e+01
        pdb=" NE  ARG B 378 "   -0.050 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 378 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 378 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 378 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B2005 "    0.079 2.00e-02 2.50e+03   6.51e-02 5.29e+01
        pdb=" C7  NAG B2005 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8  NAG B2005 "    0.060 2.00e-02 2.50e+03
        pdb=" N2  NAG B2005 "   -0.103 2.00e-02 2.50e+03
        pdb=" O7  NAG B2005 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B2003 "    0.071 2.00e-02 2.50e+03   5.86e-02 4.29e+01
        pdb=" C7  NAG B2003 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8  NAG B2003 "    0.054 2.00e-02 2.50e+03
        pdb=" N2  NAG B2003 "   -0.094 2.00e-02 2.50e+03
        pdb=" O7  NAG B2003 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1265 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 29
        2.42 -     3.04: 4416
        3.04 -     3.66: 10012
        3.66 -     4.28: 16815
        4.28 -     4.90: 27099
  Nonbonded interactions: 58371
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  12 "
            pdb="MG    MG B2002 "
     model   vdw
     1.804 2.170
  nonbonded pdb=" OE2 GLU B 212 "
            pdb="MG    MG B2002 "
     model   vdw
     1.809 2.170
  nonbonded pdb=" OG  SER B 114 "
            pdb="MG    MG B2002 "
     model   vdw
     2.033 2.170
  nonbonded pdb=" OD1 ASP A 416 "
            pdb="CA    CA A 503 "
     model   vdw
     2.093 2.510
  nonbonded pdb=" OD1 ASP A 414 "
            pdb="CA    CA A 503 "
     model   vdw
     2.097 2.510
  ... (remaining 58366 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
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             4.210
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     21.460
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
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      :  0.014   0.080   7198  Z= 0.914
  Angle     :  1.405   8.517   9756  Z= 0.948
  Chirality :  0.090   0.392   1107
  Planarity :  0.012   0.387   1260
  Dihedral  : 12.163 106.579   2869
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 0.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.68 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.95 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.27), residues: 870
  helix: -0.59 (0.43), residues: 119
  sheet:  0.85 (0.29), residues: 291
  loop :  0.06 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.006   TRP B 230 
 HIS   0.007   0.001   HIS C  37 
 PHE   0.024   0.004   PHE A 276 
 TYR   0.034   0.006   TYR A 112 
 ARG   0.005   0.001   ARG B 378 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 178
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  162 ASP cc_start: 0.7276 (t0) cc_final: 0.6964 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 179
  average time/residue: 1.1714
  time to fit residues: 220.7901
Evaluate side-chains
  85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  381 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    0.3980
   chunk 34 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0470
   chunk 50 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
A 320 GLN
B 161 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.147000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.120618 restraints weight = 9947.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.54
r_work: 0.3479 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7198  Z= 0.219
  Angle     :  0.660   9.443   9756  Z= 0.346
  Chirality :  0.049   0.216   1107
  Planarity :  0.005   0.040   1260
  Dihedral  :  8.298  81.661   1274
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.64 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.37 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 870
  helix: -0.04 (0.46), residues: 126
  sheet:  0.98 (0.28), residues: 296
  loop :  0.10 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  93 
 HIS   0.010   0.001   HIS B 118 
 PHE   0.019   0.002   PHE A 276 
 TYR   0.021   0.002   TYR A 265 
 ARG   0.006   0.001   ARG A  65 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   34 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (mtt)
REVERT: A  302 ASP cc_start: 0.7890 (t0) cc_final: 0.7646 (t0)
REVERT: A  369 LYS cc_start: 0.7748 (mmpt) cc_final: 0.7148 (mtmt)
REVERT: B  351 GLU cc_start: 0.7093 (mp0) cc_final: 0.6792 (mp0)
REVERT: B  387 LEU cc_start: 0.6212 (mp) cc_final: 0.5973 (mm)
REVERT: B  394 MET cc_start: 0.6113 (tpt) cc_final: 0.5659 (tpt)
  outliers start: 20
  outliers final: 6
  residues processed: 114
  average time/residue: 1.1751
  time to fit residues: 141.7350
Evaluate side-chains
  87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   68 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0040
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
A 206 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.142518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.115917 restraints weight = 9917.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.48
r_work: 0.3418 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7198  Z= 0.233
  Angle     :  0.604   6.324   9756  Z= 0.318
  Chirality :  0.048   0.256   1107
  Planarity :  0.004   0.036   1260
  Dihedral  :  7.628  69.854   1273
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.64 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 13.80 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.28), residues: 870
  helix: -0.24 (0.45), residues: 134
  sheet:  0.84 (0.28), residues: 303
  loop :  0.13 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 179 
 HIS   0.006   0.001   HIS C  37 
 PHE   0.017   0.002   PHE A 276 
 TYR   0.026   0.002   TYR C  43 
 ARG   0.005   0.001   ARG A 248 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.803 
Fit side-chains
REVERT: B  374 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7293 (ttm)
REVERT: B  394 MET cc_start: 0.6326 (tpt) cc_final: 0.5868 (tpt)
REVERT: B  418 LYS cc_start: 0.7476 (mtpm) cc_final: 0.7114 (mmmt)
REVERT: C   13 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8489 (mpp)
  outliers start: 22
  outliers final: 11
  residues processed: 101
  average time/residue: 1.0616
  time to fit residues: 114.1517
Evaluate side-chains
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain B residue   92 ASN
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   70 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0970
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** 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 = 0.3853 r_free = 0.3853 target = 0.140075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.113586 restraints weight = 9877.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.45
r_work: 0.3390 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7198  Z= 0.239
  Angle     :  0.592   6.280   9756  Z= 0.308
  Chirality :  0.049   0.267   1107
  Planarity :  0.004   0.039   1260
  Dihedral  :  7.252  64.794   1273
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.99 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.29 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.28), residues: 870
  helix: -0.28 (0.45), residues: 134
  sheet:  0.96 (0.29), residues: 298
  loop : -0.06 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 179 
 HIS   0.007   0.001   HIS C  37 
 PHE   0.016   0.002   PHE A 276 
 TYR   0.028   0.002   TYR C  43 
 ARG   0.006   0.001   ARG A 437 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.7862 (mmpt) cc_final: 0.7254 (mtpt)
REVERT: B  204 ILE cc_start: 0.8154 (mt) cc_final: 0.7929 (tt)
REVERT: B  374 MET cc_start: 0.7438 (ptp) cc_final: 0.7203 (ttm)
REVERT: B  394 MET cc_start: 0.6289 (tpt) cc_final: 0.5802 (tpt)
REVERT: C   13 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8475 (mpp)
REVERT: C   41 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6604 (mm-30)
REVERT: C   71 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7056 (mt-10)
  outliers start: 19
  outliers final: 10
  residues processed: 92
  average time/residue: 1.2649
  time to fit residues: 123.5820
Evaluate side-chains
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0770
   chunk 43 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114194 restraints weight = 9847.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.52
r_work: 0.3359 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7198  Z= 0.201
  Angle     :  0.563   6.180   9756  Z= 0.292
  Chirality :  0.048   0.261   1107
  Planarity :  0.004   0.037   1260
  Dihedral  :  7.008  60.895   1273
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.76 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.75 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.28), residues: 870
  helix: -0.22 (0.46), residues: 134
  sheet:  1.07 (0.29), residues: 295
  loop : -0.18 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 179 
 HIS   0.006   0.001   HIS C  37 
 PHE   0.014   0.001   PHE A 276 
 TYR   0.028   0.002   TYR C  43 
 ARG   0.004   0.000   ARG A 248 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7974 (mp0)
REVERT: A  369 LYS cc_start: 0.7756 (mmpt) cc_final: 0.7180 (mtpt)
REVERT: B  133 ARG cc_start: 0.7830 (ptp-110) cc_final: 0.7537 (ptp-110)
REVERT: B  196 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6957 (mm-30)
REVERT: B  204 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7907 (tt)
REVERT: B  374 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7194 (ttm)
REVERT: B  394 MET cc_start: 0.6211 (tpt) cc_final: 0.5768 (tpt)
REVERT: C   13 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8467 (mpp)
REVERT: C   41 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6456 (mm-30)
  outliers start: 22
  outliers final: 12
  residues processed: 90
  average time/residue: 0.9951
  time to fit residues: 95.7178
Evaluate side-chains
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   92 ASN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   70 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 50 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 46 optimal weight:    0.3980
   chunk 76 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.140353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.113582 restraints weight = 9986.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.53
r_work: 0.3352 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7198  Z= 0.211
  Angle     :  0.564   6.260   9756  Z= 0.293
  Chirality :  0.048   0.262   1107
  Planarity :  0.004   0.038   1260
  Dihedral  :  6.864  58.418   1273
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.99 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.16 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.28), residues: 870
  helix: -0.24 (0.46), residues: 134
  sheet:  1.06 (0.29), residues: 295
  loop : -0.17 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 179 
 HIS   0.006   0.001   HIS C  37 
 PHE   0.014   0.001   PHE A 276 
 TYR   0.030   0.002   TYR C  43 
 ARG   0.004   0.000   ARG A 437 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8065 (mp0)
REVERT: A  186 ASP cc_start: 0.8030 (t70) cc_final: 0.7650 (m-30)
REVERT: A  203 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8013 (tmmt)
REVERT: B  196 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7078 (mm-30)
REVERT: B  204 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7917 (tt)
REVERT: B  271 VAL cc_start: 0.8474 (p) cc_final: 0.8222 (t)
REVERT: B  394 MET cc_start: 0.6313 (tpt) cc_final: 0.5876 (tpt)
REVERT: C   55 LYS cc_start: 0.7336 (mtmm) cc_final: 0.6824 (mptt)
REVERT: C   71 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7039 (mp0)
  outliers start: 22
  outliers final: 12
  residues processed: 94
  average time/residue: 1.6794
  time to fit residues: 167.4593
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  308 LYS
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain B residue   92 ASN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0020
   chunk 2 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.4988

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.140594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.113684 restraints weight = 9794.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.52
r_work: 0.3357 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7198  Z= 0.187
  Angle     :  0.555   6.748   9756  Z= 0.287
  Chirality :  0.047   0.258   1107
  Planarity :  0.004   0.041   1260
  Dihedral  :  6.668  55.837   1273
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.99 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.56 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.28), residues: 870
  helix: -0.10 (0.47), residues: 134
  sheet:  1.08 (0.29), residues: 290
  loop : -0.12 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 179 
 HIS   0.006   0.001   HIS C  37 
 PHE   0.013   0.001   PHE A 276 
 TYR   0.029   0.002   TYR C  43 
 ARG   0.005   0.000   ARG B 370 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8071 (mp0)
REVERT: A  148 ASP cc_start: 0.7931 (m-30) cc_final: 0.7272 (t70)
REVERT: A  203 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7984 (tmmt)
REVERT: A  369 LYS cc_start: 0.7756 (mmpt) cc_final: 0.7094 (mtpt)
REVERT: B  133 ARG cc_start: 0.7963 (ptp-110) cc_final: 0.7065 (ppp-140)
REVERT: B  204 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7868 (tt)
REVERT: B  271 VAL cc_start: 0.8455 (p) cc_final: 0.8195 (t)
REVERT: B  370 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7750 (mmt90)
REVERT: B  394 MET cc_start: 0.6345 (tpt) cc_final: 0.5915 (tpt)
REVERT: C   46 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8046 (t)
REVERT: C   71 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7056 (mp0)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 1.0499
  time to fit residues: 99.9105
Evaluate side-chains
  87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3819 r_free = 0.3819 target = 0.139164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.112357 restraints weight = 10003.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.55
r_work: 0.3332 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7198  Z= 0.234
  Angle     :  0.588   9.094   9756  Z= 0.303
  Chirality :  0.048   0.260   1107
  Planarity :  0.004   0.038   1260
  Dihedral  :  6.683  54.624   1273
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.45 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.56 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.29), residues: 870
  helix: -0.22 (0.46), residues: 134
  sheet:  1.03 (0.30), residues: 289
  loop : -0.16 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 179 
 HIS   0.007   0.001   HIS C  37 
 PHE   0.015   0.001   PHE A 276 
 TYR   0.030   0.002   TYR C  43 
 ARG   0.003   0.000   ARG B 370 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 1.172 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (mm-30)
REVERT: A  148 ASP cc_start: 0.7988 (m-30) cc_final: 0.7336 (t0)
REVERT: A  203 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8029 (tmmt)
REVERT: A  369 LYS cc_start: 0.7854 (mmpt) cc_final: 0.7322 (mtmt)
REVERT: B  133 ARG cc_start: 0.7938 (ptp-110) cc_final: 0.7051 (ppp-140)
REVERT: B  204 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7905 (tt)
REVERT: B  271 VAL cc_start: 0.8435 (p) cc_final: 0.8189 (t)
REVERT: B  370 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7798 (mmt90)
REVERT: B  394 MET cc_start: 0.6399 (tpt) cc_final: 0.5957 (tpt)
REVERT: C   46 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8061 (t)
REVERT: C   55 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6639 (mptt)
REVERT: C   71 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7058 (mp0)
  outliers start: 18
  outliers final: 12
  residues processed: 84
  average time/residue: 1.4988
  time to fit residues: 134.3621
Evaluate side-chains
  89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain B residue   92 ASN
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0670
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.139443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.112639 restraints weight = 9951.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.52
r_work: 0.3341 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7198  Z= 0.216
  Angle     :  0.595  16.372   9756  Z= 0.303
  Chirality :  0.048   0.258   1107
  Planarity :  0.004   0.037   1260
  Dihedral  :  6.633  53.703   1273
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.99 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.10 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.29), residues: 870
  helix: -0.15 (0.46), residues: 134
  sheet:  1.03 (0.30), residues: 288
  loop : -0.17 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 179 
 HIS   0.006   0.001   HIS C  37 
 PHE   0.026   0.001   PHE B  93 
 TYR   0.017   0.002   TYR A 178 
 ARG   0.005   0.000   ARG A  33 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8092 (mm-30)
REVERT: A  148 ASP cc_start: 0.7934 (m-30) cc_final: 0.7277 (t0)
REVERT: A  203 LYS cc_start: 0.8314 (ttpp) cc_final: 0.8042 (tmmt)
REVERT: A  369 LYS cc_start: 0.7878 (mmpt) cc_final: 0.7277 (mtpt)
REVERT: B  133 ARG cc_start: 0.7974 (ptp-110) cc_final: 0.7080 (ppp-140)
REVERT: B  204 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7899 (tt)
REVERT: B  271 VAL cc_start: 0.8437 (p) cc_final: 0.8191 (t)
REVERT: B  370 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7785 (mmt90)
REVERT: B  394 MET cc_start: 0.6439 (tpt) cc_final: 0.6001 (tpt)
REVERT: C   46 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8059 (t)
REVERT: C   55 LYS cc_start: 0.7248 (mtmm) cc_final: 0.6867 (mptt)
REVERT: C   71 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7102 (mp0)
  outliers start: 17
  outliers final: 10
  residues processed: 84
  average time/residue: 1.4254
  time to fit residues: 127.0111
Evaluate side-chains
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0970
   chunk 5 optimal weight:    0.4980
   chunk 71 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0670
   chunk 49 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0570
   overall best weight:    0.3234

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.141234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.114629 restraints weight = 10075.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.55
r_work: 0.3370 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7198  Z= 0.174
  Angle     :  0.572  13.225   9756  Z= 0.295
  Chirality :  0.047   0.244   1107
  Planarity :  0.004   0.039   1260
  Dihedral  :  6.379  50.685   1273
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.99 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.64 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.29), residues: 870
  helix: -0.01 (0.47), residues: 134
  sheet:  1.03 (0.30), residues: 290
  loop : -0.16 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  60 
 HIS   0.006   0.001   HIS C  37 
 PHE   0.029   0.001   PHE B  93 
 TYR   0.032   0.002   TYR C  43 
 ARG   0.008   0.000   ARG A  33 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8075 (mm-30)
REVERT: A  148 ASP cc_start: 0.7911 (m-30) cc_final: 0.7273 (t70)
REVERT: A  203 LYS cc_start: 0.8266 (ttpp) cc_final: 0.8001 (tmmt)
REVERT: A  369 LYS cc_start: 0.7779 (mmpt) cc_final: 0.7252 (mtpt)
REVERT: B   86 ARG cc_start: 0.7412 (mtm110) cc_final: 0.6369 (ptp-170)
REVERT: B  133 ARG cc_start: 0.8014 (ptp-110) cc_final: 0.7089 (ppp-140)
REVERT: B  204 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7883 (tt)
REVERT: B  271 VAL cc_start: 0.8444 (p) cc_final: 0.8197 (t)
REVERT: B  370 ARG cc_start: 0.8141 (mmt180) cc_final: 0.7669 (mmt90)
REVERT: B  394 MET cc_start: 0.6430 (tpt) cc_final: 0.5995 (tpt)
REVERT: C   41 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6425 (mm-30)
REVERT: C   55 LYS cc_start: 0.7265 (mtmm) cc_final: 0.6885 (mptt)
REVERT: C   71 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7149 (mp0)
  outliers start: 11
  outliers final: 6
  residues processed: 89
  average time/residue: 1.1882
  time to fit residues: 112.5114
Evaluate side-chains
  87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0370
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.140009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113106 restraints weight = 9890.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.53
r_work: 0.3356 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7198  Z= 0.209
  Angle     :  0.580  12.556   9756  Z= 0.299
  Chirality :  0.048   0.248   1107
  Planarity :  0.004   0.036   1260
  Dihedral  :  6.370  49.430   1273
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.33 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.91 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.29), residues: 870
  helix: -0.09 (0.47), residues: 134
  sheet:  1.05 (0.30), residues: 289
  loop : -0.16 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 114 
 HIS   0.006   0.001   HIS C  37 
 PHE   0.012   0.001   PHE A 276 
 TYR   0.033   0.002   TYR C  43 
 ARG   0.003   0.000   ARG C   6 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5339.28 seconds
wall clock time: 96 minutes 13.16 seconds (5773.16 seconds total)