Starting phenix.real_space_refine
on Fri Feb 14 19:03:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pm5_13521/02_2025/7pm5_13521.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pm5_13521/02_2025/7pm5_13521.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pm5_13521/02_2025/7pm5_13521.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pm5_13521/02_2025/7pm5_13521.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pm5_13521/02_2025/7pm5_13521.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pm5_13521/02_2025/7pm5_13521.cif"
  }
  resolution = 3.1
  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=   0.001
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
     P       4      5.49       5
     Mg      2      5.21       5
     S      63      5.16       5
     C    6474      2.51       5
     N    1727      2.21       5
     O    1901      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 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: 10171
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1059
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 6092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 746, 6092
          Classifications: {'peptide': 746}
          Link IDs: {'PTRANS': 27, 'TRANS': 718}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.49, per 1000 atoms: 0.64
  Number of scatterers: 10171
  At special positions: 0
  Unit cell: (108.12, 140.98, 149.46, 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)
     S      63     16.00
     P       4     15.00
     Mg      2     11.99
     O    1901      8.00
     N    1727      7.00
     C    6474      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " TRP H   1 " - " ALA H   7 "
      " DTH H   4 " - " ALA H   3 "
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTH H   4 "
  Number of C-beta restraints generated:  2378

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 15 sheets defined
      54.6% alpha, 12.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.268A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   ASP B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 56 through 63
    Processing helix  chain 'B' and resid 67 through 79
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 87 through 95
    Processing helix  chain 'B' and resid 106 through 116
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 141 through 150
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 3.679A  pdb=" N   LEU A  77 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 95
    Processing helix  chain 'A' and resid 116 through 119
      removed outlier: 4.464A  pdb=" N   TYR A 119 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 116 through 119'
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 3.596A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 184
      removed outlier: 3.543A  pdb=" N   PHE A 180 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 207
      removed outlier: 3.568A  pdb=" N   ASN A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 4.170A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 3.618A  pdb=" N   LYS A 275 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 4.170A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 315
      removed outlier: 3.933A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.870A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 376
      removed outlier: 3.801A  pdb=" N   CYS A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 424
    Processing helix  chain 'A' and resid 448 through 480
    Processing helix  chain 'A' and resid 483 through 487
      removed outlier: 3.676A  pdb=" N   LEU A 486 " --> pdb=" O   PRO A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 506 through 513
    Processing helix  chain 'A' and resid 519 through 532
    Processing helix  chain 'A' and resid 563 through 569
      removed outlier: 3.835A  pdb=" N   LYS A 567 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
      removed outlier: 3.570A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 3.565A  pdb=" N   GLU A 591 " --> pdb=" O   LYS A 587 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 635 through 653
      removed outlier: 3.696A  pdb=" N   ALA A 653 " --> pdb=" O   GLU A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 685
      removed outlier: 3.599A  pdb=" N   GLN A 680 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 697
    Processing helix  chain 'A' and resid 704 through 712
    Processing helix  chain 'A' and resid 713 through 715
      No H-bonds generated for 'chain 'A' and resid 713 through 715'
    Processing helix  chain 'A' and resid 723 through 736
      removed outlier: 3.946A  pdb=" N   GLU A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 754 through 792
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 92
      removed outlier: 3.640A  pdb=" N   MET C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 4.182A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   MET C 123 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 145
      removed outlier: 3.556A  pdb=" N   SER C 141 " --> pdb=" O   GLN C 137 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   TYR C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
      removed outlier: 3.744A  pdb=" N   ILE C 175 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 172 through 175'
    Processing helix  chain 'C' and resid 181 through 195
      removed outlier: 3.840A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.777A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL C 209 " --> pdb=" O   GLU C 205 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASP C 211 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 252 through 257
    Processing helix  chain 'C' and resid 258 through 262
    Processing helix  chain 'C' and resid 263 through 268
    Processing helix  chain 'C' and resid 273 through 283
    Processing helix  chain 'C' and resid 289 through 295
      removed outlier: 3.706A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 305
    Processing helix  chain 'C' and resid 308 through 319
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 349
      removed outlier: 3.542A  pdb=" N   SER C 348 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 3.922A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 368 through 373
      removed outlier: 3.591A  pdb=" N   ARG C 372 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28
    Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105
    Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 16
      removed outlier: 3.540A  pdb=" N   LEU A  38 " --> pdb=" O   TYR A  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103
      removed outlier: 3.534A  pdb=" N   GLN A 157 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLY A 163 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209
    Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344
      removed outlier: 6.257A  pdb=" N   SER A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381
    Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703
    Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.856A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 8.614A  pdb=" N   THR C 106 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   CYS C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170
      removed outlier: 6.173A  pdb=" N   ASN C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241

    520 hydrogen bonds defined for protein.
    1461 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: 3.40

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1741
        1.32 -     1.45: 2708
        1.45 -     1.57: 5830
        1.57 -     1.69: 6
        1.69 -     1.82: 102
  Bond restraints: 10387
  Sorted by residual:
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.450  0.122 2.00e-02 2.50e+03 3.71e+01
  bond pdb=" C   EEP H   2 "
       pdb=" O   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.263  1.202  0.061 2.00e-02 2.50e+03 9.41e+00
  bond pdb=" CA  TRP H   1 "
       pdb=" C   TRP H   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.463  0.062 2.10e-02 2.27e+03 8.64e+00
  bond pdb=" C   HYP H   6 "
       pdb=" N   ALA H   7 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.40e-02 5.10e+03 8.53e+00
  bond pdb=" CE1 HIC C  73 "
       pdb=" NE2 HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.347  1.400 -0.053 2.00e-02 2.50e+03 7.02e+00
  ... (remaining 10382 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 13743
        2.38 -     4.75: 245
        4.75 -     7.13: 33
        7.13 -     9.51: 6
        9.51 -    11.88: 5
  Bond angle restraints: 14032
  Sorted by residual:
  angle pdb=" C   HYP H   6 "
        pdb=" N   ALA H   7 "
        pdb=" CA  ALA H   7 "
      ideal   model   delta    sigma   weight residual
     121.70  109.82   11.88 1.80e+00 3.09e-01 4.36e+01
  angle pdb=" N   HYP H   6 "
        pdb=" CA  HYP H   6 "
        pdb=" CB  HYP H   6 "
      ideal   model   delta    sigma   weight residual
     103.00  107.78   -4.78 1.10e+00 8.26e-01 1.89e+01
  angle pdb=" C   TRP H   1 "
        pdb=" CA  TRP H   1 "
        pdb=" CB  TRP H   1 "
      ideal   model   delta    sigma   weight residual
     110.10  102.06    8.04 1.90e+00 2.77e-01 1.79e+01
  angle pdb=" CD2 TRP H   1 "
        pdb=" CE2 TRP H   1 "
        pdb=" CZ2 TRP H   1 "
      ideal   model   delta    sigma   weight residual
     122.40  118.26    4.14 1.00e+00 1.00e+00 1.72e+01
  angle pdb=" N   TYR A 113 "
        pdb=" CA  TYR A 113 "
        pdb=" CB  TYR A 113 "
      ideal   model   delta    sigma   weight residual
     113.15  106.47    6.68 1.63e+00 3.76e-01 1.68e+01
  ... (remaining 14027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.90: 6048
       27.90 -    55.80: 181
       55.80 -    83.71: 29
       83.71 -   111.61: 6
      111.61 -   139.51: 4
  Dihedral angle restraints: 6268
    sinusoidal: 2578
      harmonic: 3690
  Sorted by residual:
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   79.51 -139.51     1      2.00e+01 2.50e-03 4.23e+01
  dihedral pdb=" O2A ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" PB  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   70.90 -130.90     1      2.00e+01 2.50e-03 3.97e+01
  dihedral pdb=" O1B ADP A1902 "
           pdb=" O3A ADP A1902 "
           pdb=" PB  ADP A1902 "
           pdb=" PA  ADP A1902 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   68.66 -128.66     1      2.00e+01 2.50e-03 3.90e+01
  ... (remaining 6265 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1162
       0.053 -    0.105: 295
       0.105 -    0.158: 63
       0.158 -    0.211: 9
       0.211 -    0.264: 3
  Chirality restraints: 1532
  Sorted by residual:
  chirality pdb=" CG  LEU A 782 "
            pdb=" CB  LEU A 782 "
            pdb=" CD1 LEU A 782 "
            pdb=" CD2 LEU A 782 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  PHE B  19 "
            pdb=" N   PHE B  19 "
            pdb=" C   PHE B  19 "
            pdb=" CB  PHE B  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  CYS C 257 "
            pdb=" N   CYS C 257 "
            pdb=" C   CYS C 257 "
            pdb=" CB  CYS C 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 1529 not shown)

  Planarity restraints: 1793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 113 "   -0.037 2.00e-02 2.50e+03   3.28e-02 2.15e+01
        pdb=" CG  TYR A 113 "    0.069 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 113 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 113 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 113 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 113 "    0.019 2.00e-02 2.50e+03
        pdb=" OH  TYR A 113 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 677 "    0.086 9.50e-02 1.11e+02   5.14e-02 1.54e+01
        pdb=" NE  ARG A 677 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 677 "    0.065 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 677 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 677 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C  88 "   -0.018 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   HIS C  88 "    0.064 2.00e-02 2.50e+03
        pdb=" O   HIS C  88 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   THR C  89 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1790 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 11
        2.37 -     3.00: 5345
        3.00 -     3.63: 15039
        3.63 -     4.27: 23012
        4.27 -     4.90: 38725
  Nonbonded interactions: 82132
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.732 3.620
  nonbonded pdb="MG    MG A1901 "
            pdb=" O1B ADP A1902 "
     model   vdw
     2.037 2.170
  nonbonded pdb=" OH  TYR A 456 "
            pdb=" OE1 GLU A 500 "
     model   vdw
     2.056 3.040
  nonbonded pdb=" O2B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     2.182 2.170
  nonbonded pdb=" OD1 ASN C 128 "
            pdb=" NZ  LYS C 359 "
     model   vdw
     2.194 3.120
  ... (remaining 82127 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.000
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.122  10387  Z= 0.292
  Angle     :  0.832  11.883  14032  Z= 0.481
  Chirality :  0.050   0.264   1532
  Planarity :  0.007   0.053   1791
  Dihedral  : 14.893 139.511   3884
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.28 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.21), residues: 1236
  helix: -1.48 (0.17), residues: 590
  sheet: -0.25 (0.40), residues: 150
  loop :  0.27 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP C  79 
 HIS   0.010   0.001   HIS B 147 
 PHE   0.033   0.002   PHE B  19 
 TYR   0.069   0.006   TYR A 113 
 ARG   0.066   0.010   ARG A 677 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.7943 (mmp) cc_final: 0.7232 (ttt)
REVERT: A  305 MET cc_start: 0.8785 (tpp) cc_final: 0.8037 (tpp)
REVERT: C  299 MET cc_start: 0.9064 (mmp) cc_final: 0.8834 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 133
  average time/residue: 0.2724
  time to fit residues: 50.0136
Evaluate side-chains
  80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0370
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
A 191 ASN
A 264 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  40 HIS
C  59 GLN
C 162 ASN
C 225 ASN
C 280 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.093952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.058647 restraints weight = 24926.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.40
r_work: 0.2723 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10387  Z= 0.230
  Angle     :  0.650  14.254  14032  Z= 0.333
  Chirality :  0.045   0.300   1532
  Planarity :  0.005   0.084   1791
  Dihedral  :  9.701 136.104   1408
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  3.79 %
    Favored  : 95.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.24), residues: 1236
  helix:  0.53 (0.21), residues: 605
  sheet:  0.17 (0.39), residues: 159
  loop :  0.88 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  79 
 HIS   0.018   0.001   HIS B 147 
 PHE   0.024   0.001   PHE C 255 
 TYR   0.029   0.002   TYR A 113 
 ARG   0.005   0.001   ARG A 542 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.6819 (m-80) cc_final: 0.6456 (m-80)
REVERT: B   96 PHE cc_start: 0.7545 (m-80) cc_final: 0.7125 (m-10)
REVERT: B  105 MET cc_start: 0.7739 (mmp) cc_final: 0.7124 (ttt)
REVERT: A  305 MET cc_start: 0.8965 (tpp) cc_final: 0.8369 (tpp)
REVERT: A  788 MET cc_start: 0.5469 (mtt) cc_final: 0.4785 (tpt)
  outliers start: 13
  outliers final: 5
  residues processed: 94
  average time/residue: 0.2128
  time to fit residues: 29.8140
Evaluate side-chains
  78 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain B residue   89 TYR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 418 HIS
A 463 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.091306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.055806 restraints weight = 25420.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 3.37
r_work: 0.2671 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10387  Z= 0.343
  Angle     :  0.624  12.643  14032  Z= 0.319
  Chirality :  0.045   0.253   1532
  Planarity :  0.004   0.049   1791
  Dihedral  :  9.018 139.018   1407
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  5.54 %
    Favored  : 93.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.24), residues: 1236
  helix:  1.09 (0.21), residues: 603
  sheet:  0.49 (0.40), residues: 151
  loop :  0.64 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  79 
 HIS   0.011   0.001   HIS B 147 
 PHE   0.019   0.001   PHE A 708 
 TYR   0.021   0.001   TYR A 113 
 ARG   0.010   0.001   ARG A 343 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.6851 (m-80) cc_final: 0.6537 (m-80)
REVERT: B  105 MET cc_start: 0.7917 (mmp) cc_final: 0.7289 (ttt)
REVERT: A  135 MET cc_start: 0.9342 (mmm) cc_final: 0.8802 (mmm)
REVERT: A  194 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8353 (pt0)
REVERT: A  305 MET cc_start: 0.8953 (tpp) cc_final: 0.8446 (tpp)
REVERT: A  503 MET cc_start: 0.8933 (mmm) cc_final: 0.8616 (mmm)
REVERT: A  767 LEU cc_start: 0.9114 (tp) cc_final: 0.8812 (pp)
REVERT: A  788 MET cc_start: 0.5349 (mtt) cc_final: 0.4857 (tpt)
REVERT: C  227 MET cc_start: 0.8562 (tpp) cc_final: 0.8323 (tpp)
REVERT: C  283 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8865 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1955
  time to fit residues: 25.4588
Evaluate side-chains
  78 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  283 MET
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   chunk 94 optimal weight:    0.8980
   chunk 117 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.091323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.055997 restraints weight = 25204.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 3.37
r_work: 0.2673 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10387  Z= 0.273
  Angle     :  0.579  12.874  14032  Z= 0.294
  Chirality :  0.043   0.263   1532
  Planarity :  0.004   0.061   1791
  Dihedral  :  8.517 137.392   1407
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  6.09 %
    Favored  : 92.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.24), residues: 1236
  helix:  1.40 (0.22), residues: 604
  sheet:  0.65 (0.41), residues: 149
  loop :  0.52 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  79 
 HIS   0.010   0.001   HIS B 147 
 PHE   0.015   0.001   PHE A 708 
 TYR   0.016   0.001   TYR A 113 
 ARG   0.004   0.000   ARG A 779 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.7958 (mmp) cc_final: 0.7282 (ttt)
REVERT: A  132 MET cc_start: 0.8662 (ttm) cc_final: 0.8320 (tpp)
REVERT: A  135 MET cc_start: 0.9361 (mmm) cc_final: 0.8877 (mmm)
REVERT: A  194 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8339 (pt0)
REVERT: A  305 MET cc_start: 0.8945 (tpp) cc_final: 0.8470 (tpp)
REVERT: A  503 MET cc_start: 0.8907 (mmm) cc_final: 0.8469 (mmm)
REVERT: A  788 MET cc_start: 0.5125 (mtt) cc_final: 0.4814 (tpt)
  outliers start: 17
  outliers final: 6
  residues processed: 81
  average time/residue: 0.1990
  time to fit residues: 25.7048
Evaluate side-chains
  73 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 775 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 = 0.3592 r_free = 0.3592 target = 0.091347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.056296 restraints weight = 24944.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 3.35
r_work: 0.2677 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10387  Z= 0.245
  Angle     :  0.556  11.061  14032  Z= 0.279
  Chirality :  0.043   0.267   1532
  Planarity :  0.004   0.060   1791
  Dihedral  :  8.135 136.325   1407
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.11 %
    Favored  : 91.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.24), residues: 1236
  helix:  1.59 (0.22), residues: 603
  sheet:  0.70 (0.41), residues: 149
  loop :  0.48 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 340 
 HIS   0.007   0.001   HIS B 147 
 PHE   0.013   0.001   PHE C 255 
 TYR   0.012   0.001   TYR A 113 
 ARG   0.003   0.000   ARG C 335 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 VAL cc_start: 0.2797 (OUTLIER) cc_final: 0.2590 (t)
REVERT: B  105 MET cc_start: 0.7990 (mmp) cc_final: 0.7239 (ttt)
REVERT: A  132 MET cc_start: 0.8701 (ttm) cc_final: 0.8361 (tpp)
REVERT: A  194 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8330 (pt0)
REVERT: A  305 MET cc_start: 0.8933 (tpp) cc_final: 0.8507 (tpp)
REVERT: A  503 MET cc_start: 0.8872 (mmm) cc_final: 0.8619 (mmm)
REVERT: A  767 LEU cc_start: 0.9161 (tp) cc_final: 0.8873 (pp)
REVERT: A  788 MET cc_start: 0.5311 (mtt) cc_final: 0.5056 (tpt)
REVERT: C  176 MET cc_start: 0.9125 (mmt) cc_final: 0.8775 (mmt)
  outliers start: 12
  outliers final: 7
  residues processed: 84
  average time/residue: 0.2035
  time to fit residues: 26.0350
Evaluate side-chains
  75 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  424 HIS
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 122 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9990
   chunk 120 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 775 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 = 0.3599 r_free = 0.3599 target = 0.091701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.056437 restraints weight = 25263.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 3.37
r_work: 0.2684 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10387  Z= 0.221
  Angle     :  0.550  10.481  14032  Z= 0.274
  Chirality :  0.042   0.240   1532
  Planarity :  0.004   0.053   1791
  Dihedral  :  7.790 136.035   1407
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  7.48 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.24), residues: 1236
  helix:  1.76 (0.22), residues: 597
  sheet:  0.71 (0.42), residues: 149
  loop :  0.45 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 340 
 HIS   0.009   0.001   HIS B 147 
 PHE   0.013   0.001   PHE C 255 
 TYR   0.010   0.001   TYR A 787 
 ARG   0.006   0.000   ARG A 779 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.7942 (mmp) cc_final: 0.7217 (ttt)
REVERT: B  148 ILE cc_start: 0.5986 (tt) cc_final: 0.5777 (pt)
REVERT: A  102 TYR cc_start: 0.8340 (m-80) cc_final: 0.7796 (m-80)
REVERT: A  132 MET cc_start: 0.8689 (ttm) cc_final: 0.8398 (tpp)
REVERT: A  135 MET cc_start: 0.9357 (mmm) cc_final: 0.8980 (ttm)
REVERT: A  194 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8331 (pt0)
REVERT: A  305 MET cc_start: 0.8949 (tpp) cc_final: 0.8574 (tpp)
REVERT: A  503 MET cc_start: 0.8886 (mmm) cc_final: 0.8630 (mmm)
REVERT: A  767 LEU cc_start: 0.9167 (tp) cc_final: 0.8868 (pp)
REVERT: A  788 MET cc_start: 0.5392 (mtt) cc_final: 0.5160 (tpt)
REVERT: C  176 MET cc_start: 0.9155 (mmt) cc_final: 0.8841 (mmt)
  outliers start: 15
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1932
  time to fit residues: 25.4003
Evaluate side-chains
  75 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  424 HIS
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 110 optimal weight:    0.4980
   chunk 16 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 115 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.090627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.055334 restraints weight = 25481.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 3.37
r_work: 0.2654 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10387  Z= 0.302
  Angle     :  0.585   9.436  14032  Z= 0.292
  Chirality :  0.043   0.198   1532
  Planarity :  0.004   0.047   1791
  Dihedral  :  7.717 133.320   1407
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.40 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.24), residues: 1236
  helix:  1.69 (0.22), residues: 605
  sheet:  0.67 (0.42), residues: 149
  loop :  0.34 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 340 
 HIS   0.008   0.001   HIS B 147 
 PHE   0.015   0.001   PHE C 255 
 TYR   0.011   0.001   TYR A 787 
 ARG   0.003   0.000   ARG A 724 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.5443 (m-30)
REVERT: B  105 MET cc_start: 0.7984 (mmp) cc_final: 0.7277 (ttt)
REVERT: A  102 TYR cc_start: 0.8446 (m-80) cc_final: 0.7948 (m-80)
REVERT: A  132 MET cc_start: 0.8727 (ttm) cc_final: 0.8496 (tpp)
REVERT: A  135 MET cc_start: 0.9380 (mmm) cc_final: 0.9014 (ttm)
REVERT: A  194 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8340 (pt0)
REVERT: A  305 MET cc_start: 0.8969 (tpp) cc_final: 0.8544 (tpp)
REVERT: A  503 MET cc_start: 0.8923 (mmm) cc_final: 0.8663 (mmm)
REVERT: A  767 LEU cc_start: 0.9167 (tp) cc_final: 0.8873 (pp)
REVERT: C  176 MET cc_start: 0.9152 (mmt) cc_final: 0.8859 (mmt)
  outliers start: 13
  outliers final: 10
  residues processed: 82
  average time/residue: 0.2014
  time to fit residues: 25.3196
Evaluate side-chains
  81 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  424 HIS
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0060
   chunk 74 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0870
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.7976

-------------------------------------------------------------------------------
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 = 0.3595 r_free = 0.3595 target = 0.091518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.056182 restraints weight = 25252.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.38
r_work: 0.2676 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10387  Z= 0.216
  Angle     :  0.571  11.024  14032  Z= 0.283
  Chirality :  0.042   0.189   1532
  Planarity :  0.003   0.047   1791
  Dihedral  :  7.435 132.863   1407
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.86 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.24), residues: 1236
  helix:  1.84 (0.22), residues: 598
  sheet:  0.74 (0.42), residues: 148
  loop :  0.36 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 781 
 HIS   0.007   0.001   HIS B 147 
 PHE   0.012   0.001   PHE C 255 
 TYR   0.009   0.001   TYR A 456 
 ARG   0.002   0.000   ARG A 724 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.8007 (mmp) cc_final: 0.7300 (ttt)
REVERT: A   62 LEU cc_start: 0.8705 (tp) cc_final: 0.8476 (tt)
REVERT: A  102 TYR cc_start: 0.8391 (m-80) cc_final: 0.7832 (m-80)
REVERT: A  135 MET cc_start: 0.9373 (mmm) cc_final: 0.9001 (ttm)
REVERT: A  194 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8297 (pt0)
REVERT: A  305 MET cc_start: 0.8950 (tpp) cc_final: 0.8579 (tpp)
REVERT: A  503 MET cc_start: 0.8883 (mmm) cc_final: 0.8626 (mmm)
REVERT: A  767 LEU cc_start: 0.9174 (tp) cc_final: 0.8886 (pp)
REVERT: C  176 MET cc_start: 0.9152 (mmt) cc_final: 0.8864 (mmt)
REVERT: C  283 MET cc_start: 0.8671 (mmm) cc_final: 0.8422 (mmp)
  outliers start: 11
  outliers final: 8
  residues processed: 91
  average time/residue: 0.1931
  time to fit residues: 27.2594
Evaluate side-chains
  81 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 98 optimal weight:    0.2980
   chunk 59 optimal weight:    5.9990
   chunk 103 optimal weight:    0.4980
   chunk 49 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 39 optimal weight:    0.3980
   chunk 68 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.092181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.056979 restraints weight = 25035.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 3.37
r_work: 0.2696 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10387  Z= 0.178
  Angle     :  0.581  11.091  14032  Z= 0.284
  Chirality :  0.041   0.179   1532
  Planarity :  0.003   0.046   1791
  Dihedral  :  7.235 130.380   1407
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  9.97 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1236
  helix:  1.92 (0.22), residues: 597
  sheet:  0.77 (0.42), residues: 148
  loop :  0.35 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 781 
 HIS   0.005   0.001   HIS B 147 
 PHE   0.013   0.001   PHE B  19 
 TYR   0.009   0.001   TYR A 787 
 ARG   0.002   0.000   ARG A 724 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.8008 (mmp) cc_final: 0.7297 (ttt)
REVERT: A   62 LEU cc_start: 0.8691 (tp) cc_final: 0.8462 (tt)
REVERT: A  135 MET cc_start: 0.9371 (mmm) cc_final: 0.8996 (ttm)
REVERT: A  194 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8298 (pt0)
REVERT: A  305 MET cc_start: 0.8964 (tpp) cc_final: 0.8595 (tpp)
REVERT: A  503 MET cc_start: 0.8871 (mmm) cc_final: 0.8609 (mmm)
REVERT: A  751 PHE cc_start: 0.8186 (m-10) cc_final: 0.7887 (m-10)
REVERT: A  767 LEU cc_start: 0.9176 (tp) cc_final: 0.8888 (pp)
REVERT: C  176 MET cc_start: 0.9137 (mmt) cc_final: 0.8863 (mmt)
  outliers start: 7
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1877
  time to fit residues: 24.4560
Evaluate side-chains
  80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0570
   chunk 92 optimal weight:    0.0770
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 98 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.4256

-------------------------------------------------------------------------------
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 = 0.3621 r_free = 0.3621 target = 0.092975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.057813 restraints weight = 25275.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 3.39
r_work: 0.2718 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10387  Z= 0.164
  Angle     :  0.564   8.960  14032  Z= 0.278
  Chirality :  0.041   0.175   1532
  Planarity :  0.003   0.046   1791
  Dihedral  :  6.938 125.370   1407
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  9.79 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.24), residues: 1236
  helix:  1.99 (0.22), residues: 597
  sheet:  0.78 (0.42), residues: 147
  loop :  0.35 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 781 
 HIS   0.005   0.001   HIS B 147 
 PHE   0.011   0.001   PHE C 255 
 TYR   0.010   0.001   TYR A 787 
 ARG   0.002   0.000   ARG A 724 

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.8075 (mmp) cc_final: 0.7386 (ttt)
REVERT: A  132 MET cc_start: 0.8626 (tpp) cc_final: 0.8406 (tpt)
REVERT: A  135 MET cc_start: 0.9356 (mmm) cc_final: 0.8990 (ttm)
REVERT: A  194 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8324 (pt0)
REVERT: A  305 MET cc_start: 0.8948 (tpp) cc_final: 0.8620 (tpp)
REVERT: A  503 MET cc_start: 0.8858 (mmm) cc_final: 0.8615 (mmm)
REVERT: A  751 PHE cc_start: 0.8177 (m-10) cc_final: 0.7869 (m-10)
REVERT: A  767 LEU cc_start: 0.9188 (tp) cc_final: 0.8896 (pp)
REVERT: C  176 MET cc_start: 0.9154 (mmt) cc_final: 0.8857 (mmt)
  outliers start: 7
  outliers final: 6
  residues processed: 84
  average time/residue: 0.2035
  time to fit residues: 26.2193
Evaluate side-chains
  79 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0980
   chunk 112 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 123 optimal weight:    0.2980
   chunk 61 optimal weight:    0.0970
   chunk 49 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0670
   chunk 57 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.2716

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.094267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.059073 restraints weight = 25031.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 3.39
r_work: 0.2749 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10387  Z= 0.145
  Angle     :  0.560  11.714  14032  Z= 0.271
  Chirality :  0.040   0.170   1532
  Planarity :  0.004   0.048   1791
  Dihedral  :  6.634 118.330   1407
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.97 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.25), residues: 1236
  helix:  2.08 (0.22), residues: 595
  sheet:  0.77 (0.43), residues: 147
  loop :  0.46 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 781 
 HIS   0.005   0.001   HIS B 147 
 PHE   0.011   0.001   PHE C 255 
 TYR   0.019   0.001   TYR B 141 
 ARG   0.004   0.000   ARG A 712 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6399.52 seconds
wall clock time: 113 minutes 54.42 seconds (6834.42 seconds total)