Starting phenix.real_space_refine
on Tue Mar 11 22:36:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mgw_23830/03_2025/7mgw_23830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mgw_23830/03_2025/7mgw_23830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2025/7mgw_23830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2025/7mgw_23830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2025/7mgw_23830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2025/7mgw_23830.cif"
  }
  resolution = 3.5
  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=   0.001 sd=   0.041
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: 5
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     Cl      1      4.86       5
     C    4140      2.51       5
     N     964      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 6223
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4292
          Classifications: {'peptide': 537}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
    Chain: "B"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 913
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 830
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 160
          Unusual residues: {' CL': 1, 'CLR': 1, 'D10': 1, 'D12': 4, 'HP6': 6, 'LNK': 1, 'SRO': 2}
          Classifications: {'undetermined': 16}
          Link IDs: {None: 15}
  Time building chain proxies: 5.27, per 1000 atoms: 0.85
  Number of scatterers: 6223
  At special positions: 0
  Unit cell: (69.336, 73.224, 121.824, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      34     16.00
     O    1084      8.00
     N     964      7.00
     C    4140      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 931.7 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      54.9% alpha, 10.1% 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 84 through 97
      removed outlier: 3.846A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 113
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 114 through 120
      removed outlier: 3.809A  pdb=" N   LEU A 118 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   LEU A 119 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
      Proline residue:  A 120  - end of helix
    Processing helix  chain 'A' and resid 121 through 144
      Proline residue:  A 131  - end of helix
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.524A  pdb=" N   TRP A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 159
      removed outlier: 3.598A  pdb=" N   LYS A 159 " --> pdb=" O   PRO A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 190
      removed outlier: 4.145A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
      removed outlier: 3.668A  pdb=" N   HIS A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 272
      removed outlier: 4.364A  pdb=" N   LYS A 272 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 284
      removed outlier: 3.642A  pdb=" N   VAL A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 300
      removed outlier: 4.228A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 313
    Processing helix  chain 'A' and resid 325 through 338
    Processing helix  chain 'A' and resid 342 through 349
    Processing helix  chain 'A' and resid 356 through 391
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.783A  pdb=" N   GLU A 396 " --> pdb=" O   ASP A 393 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 397 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 393 through 397'
    Processing helix  chain 'A' and resid 403 through 417
      removed outlier: 4.749A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 454
      removed outlier: 3.807A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ALA A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 461
      removed outlier: 4.511A  pdb=" N   LYS A 460 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 482
      removed outlier: 3.852A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   THR A 480 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 496
      removed outlier: 4.318A  pdb=" N   VAL A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 4.432A  pdb=" N   ASP A 524 " --> pdb=" O   GLN A 520 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   GLU A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
    Processing helix  chain 'A' and resid 543 through 559
    Processing helix  chain 'A' and resid 571 through 585
    Processing helix  chain 'A' and resid 587 through 600
    Processing helix  chain 'A' and resid 603 through 612
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25
      removed outlier: 3.515A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 30
      removed outlier: 5.352A  pdb=" N   GLU B  29 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL B 112 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG B  69 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30
      removed outlier: 5.352A  pdb=" N   GLU B  29 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL B 112 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 25 through 27
      removed outlier: 3.616A  pdb=" N   ALA C  39 " --> pdb=" O   ILE C  99 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   CYS C  43 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   PHE C  95 " --> pdb=" O   CYS C  43 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TYR C  94 " --> pdb=" O   SER C  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 51
      removed outlier: 3.605A  pdb=" N   ASN C  51 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78
      removed outlier: 6.930A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR C 121 " --> pdb=" O   GLN C 114 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    912 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1816
        1.34 -     1.46: 1680
        1.46 -     1.58: 2849
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6394
  Sorted by residual:
  bond pdb=" CD1 SRO A 712 "
       pdb=" NE1 SRO A 712 "
    ideal  model  delta    sigma   weight residual
    1.377  1.324  0.053 2.00e-02 2.50e+03 7.13e+00
  bond pdb=" CD1 SRO A 715 "
       pdb=" NE1 SRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.377  1.324  0.053 2.00e-02 2.50e+03 7.07e+00
  bond pdb=" CD2 SRO A 712 "
       pdb=" CE2 SRO A 712 "
    ideal  model  delta    sigma   weight residual
    1.419  1.370  0.049 2.00e-02 2.50e+03 6.00e+00
  bond pdb=" CD2 SRO A 715 "
       pdb=" CE2 SRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.419  1.370  0.049 2.00e-02 2.50e+03 5.91e+00
  bond pdb=" CB  SRO A 715 "
       pdb=" CG  SRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.498  1.527 -0.029 2.00e-02 2.50e+03 2.14e+00
  ... (remaining 6389 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 8486
        2.07 -     4.13: 161
        4.13 -     6.20: 16
        6.20 -     8.27: 1
        8.27 -    10.34: 1
  Bond angle restraints: 8665
  Sorted by residual:
  angle pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
        pdb=" CA  SER C  48 "
      ideal   model   delta    sigma   weight residual
     121.70  132.04  -10.34 1.80e+00 3.09e-01 3.30e+01
  angle pdb=" C   LEU A 119 "
        pdb=" N   PRO A 120 "
        pdb=" CA  PRO A 120 "
      ideal   model   delta    sigma   weight residual
     121.65  119.11    2.54 1.01e+00 9.80e-01 6.34e+00
  angle pdb=" CA  GLU C  47 "
        pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
      ideal   model   delta    sigma   weight residual
     115.60  118.96   -3.36 1.48e+00 4.57e-01 5.16e+00
  angle pdb=" C20 CLR A 716 "
        pdb=" C22 CLR A 716 "
        pdb=" C23 CLR A 716 "
      ideal   model   delta    sigma   weight residual
     115.57  109.14    6.43 3.00e+00 1.11e-01 4.59e+00
  angle pdb=" N   VAL A 236 "
        pdb=" CA  VAL A 236 "
        pdb=" C   VAL A 236 "
      ideal   model   delta    sigma   weight residual
     113.39  110.26    3.13 1.47e+00 4.63e-01 4.53e+00
  ... (remaining 8660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.03: 3447
       19.03 -    38.06: 230
       38.06 -    57.09: 37
       57.09 -    76.11: 5
       76.11 -    95.14: 10
  Dihedral angle restraints: 3729
    sinusoidal: 1529
      harmonic: 2200
  Sorted by residual:
  dihedral pdb=" C2  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" C5  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -41.36   95.14     1      3.00e+01 1.11e-03 1.16e+01
  dihedral pdb=" C2  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   81.72   93.39     1      3.00e+01 1.11e-03 1.13e+01
  dihedral pdb=" C5  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O3  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -174.13  -81.26  -92.87     1      3.00e+01 1.11e-03 1.12e+01
  ... (remaining 3726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 869
       0.068 -    0.137: 74
       0.137 -    0.205: 2
       0.205 -    0.273: 2
       0.273 -    0.341: 1
  Chirality restraints: 948
  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   -2.22   -0.18 2.00e-02 2.50e+03 7.95e+01
  chirality pdb=" C14 CLR A 716 "
            pdb=" C13 CLR A 716 "
            pdb=" C15 CLR A 716 "
            pdb=" C8  CLR A 716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.66    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" C9  CLR A 716 "
            pdb=" C10 CLR A 716 "
            pdb=" C11 CLR A 716 "
            pdb=" C8  CLR A 716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.68    0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 945 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 570 "    0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 571 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 571 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 571 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 100 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.48e+00
        pdb=" N   PRO C 101 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 101 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 101 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 589 "    0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO A 590 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 590 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 590 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1875
        2.81 -     3.34: 5836
        3.34 -     3.86: 10538
        3.86 -     4.38: 11412
        4.38 -     4.90: 19850
  Nonbonded interactions: 49511
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 106 "
            pdb=" OD1 ASP B 109 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   ILE A 108 "
            pdb=" ND2 ASN A 112 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OG  SER C  76 "
            pdb=" OD1 ASN C  77 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER C  55 "
            pdb=" O   ALA C  74 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   SER A 190 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.323 3.040
  ... (remaining 49506 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.670
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.450
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5007
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      :  0.003   0.053   6394  Z= 0.175
  Angle     :  0.636  10.336   8665  Z= 0.301
  Chirality :  0.041   0.341    948
  Planarity :  0.003   0.031   1049
  Dihedral  : 13.533  95.142   2324
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.66 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.28), residues: 759
  helix: -0.76 (0.23), residues: 354
  sheet: -1.78 (0.51), residues: 93
  loop : -2.62 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP A 317 
 HIS   0.001   0.000   HIS A 143 
 PHE   0.015   0.001   PHE A 474 
 TYR   0.009   0.000   TYR A 176 
 ARG   0.001   0.000   ARG A 564 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 144
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A  144 ARG cc_start: 0.6293 (mtm110) cc_final: 0.6074 (ttm110)
REVERT: A  145 ASN cc_start: 0.6109 (t0) cc_final: 0.5464 (t0)
REVERT: A  243 LYS cc_start: 0.7231 (mtmm) cc_final: 0.7008 (mmtm)
REVERT: A  267 TYR cc_start: 0.5156 (t80) cc_final: 0.4873 (t80)
REVERT: A  370 MET cc_start: 0.6126 (mmp) cc_final: 0.4205 (ttm)
REVERT: A  391 ASN cc_start: 0.7447 (t0) cc_final: 0.7161 (t0)
REVERT: A  430 MET cc_start: 0.6276 (ttm) cc_final: 0.6050 (tmm)
REVERT: A  466 VAL cc_start: 0.3864 (p) cc_final: 0.3450 (t)
REVERT: A  508 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5663 (tm-30)
REVERT: A  572 TYR cc_start: 0.6178 (t80) cc_final: 0.5765 (t80)
REVERT: B   76 ASP cc_start: 0.7630 (t0) cc_final: 0.6898 (t0)
REVERT: C   78 GLN cc_start: 0.7740 (mt0) cc_final: 0.7485 (mt0)
  outliers start: 9
  outliers final: 4
  residues processed: 151
  average time/residue: 0.2151
  time to fit residues: 41.5021
Evaluate side-chains
  101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.0170
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0270
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 ASN
A 205 ASN
A 316 ASN
A 332 GLN
A 355 ASN
B  25 GLN
B  54 ASN
B 101 GLN
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.212375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.178935 restraints weight = 7574.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.184467 restraints weight = 4513.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.188012 restraints weight = 3206.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6394  Z= 0.175
  Angle     :  0.538   9.862   8665  Z= 0.272
  Chirality :  0.040   0.209    948
  Planarity :  0.004   0.029   1049
  Dihedral  :  9.389  77.108   1018
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.67 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.42 (0.30), residues: 759
  helix:  0.30 (0.26), residues: 353
  sheet: -1.24 (0.52), residues: 95
  loop : -2.33 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 326 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.025   0.001   PHE A 428 
 TYR   0.015   0.001   TYR A 358 
 ARG   0.003   0.000   ARG A 564 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A  370 MET cc_start: 0.7371 (mmp) cc_final: 0.5315 (ttm)
REVERT: A  391 ASN cc_start: 0.6378 (t0) cc_final: 0.6159 (t0)
REVERT: A  508 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7228 (tm-30)
REVERT: A  572 TYR cc_start: 0.7195 (t80) cc_final: 0.6990 (t80)
  outliers start: 21
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1776
  time to fit residues: 28.1662
Evaluate side-chains
  107 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0170
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.199680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.162794 restraints weight = 7697.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.168224 restraints weight = 4727.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.171792 restraints weight = 3454.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6394  Z= 0.214
  Angle     :  0.566   9.834   8665  Z= 0.290
  Chirality :  0.041   0.246    948
  Planarity :  0.004   0.038   1049
  Dihedral  :  7.842  65.820   1015
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 18.22 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.24 (0.30), residues: 759
  helix:  0.40 (0.26), residues: 359
  sheet: -1.06 (0.51), residues: 96
  loop : -2.24 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 197 
 HIS   0.004   0.001   HIS A 143 
 PHE   0.017   0.002   PHE A 407 
 TYR   0.023   0.001   TYR A 142 
 ARG   0.008   0.001   ARG A 607 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  145 ASN cc_start: 0.8182 (t0) cc_final: 0.7157 (t0)
REVERT: A  279 LYS cc_start: 0.5321 (tptt) cc_final: 0.4458 (ttpp)
REVERT: A  280 VAL cc_start: 0.4051 (OUTLIER) cc_final: 0.3840 (t)
REVERT: A  391 ASN cc_start: 0.6500 (t0) cc_final: 0.6197 (m-40)
REVERT: A  478 LEU cc_start: 0.7564 (tt) cc_final: 0.7326 (tp)
REVERT: A  508 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7376 (tm-30)
REVERT: A  550 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7795 (tt)
  outliers start: 33
  outliers final: 19
  residues processed: 124
  average time/residue: 0.1552
  time to fit residues: 26.7933
Evaluate side-chains
  112 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 368 ASN
A 416 ASN
A 456 HIS
B  25 GLN
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.185212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146056 restraints weight = 7696.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.151243 restraints weight = 4702.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.154534 restraints weight = 3466.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6394  Z= 0.314
  Angle     :  0.603   9.917   8665  Z= 0.314
  Chirality :  0.043   0.203    948
  Planarity :  0.004   0.035   1049
  Dihedral  :  7.288  59.917   1015
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 20.09 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.34 (0.29), residues: 759
  helix:  0.19 (0.25), residues: 361
  sheet: -0.90 (0.52), residues: 96
  loop : -2.19 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 151 
 HIS   0.007   0.002   HIS A 456 
 PHE   0.021   0.002   PHE A 407 
 TYR   0.012   0.002   TYR A 142 
 ARG   0.008   0.001   ARG A 607 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A  165 ILE cc_start: 0.8796 (tp) cc_final: 0.8595 (tp)
REVERT: A  391 ASN cc_start: 0.6681 (t0) cc_final: 0.6257 (m-40)
REVERT: A  454 PHE cc_start: 0.6604 (m-10) cc_final: 0.6343 (m-10)
REVERT: A  508 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7509 (tm-30)
REVERT: B   74 ASP cc_start: 0.8804 (t0) cc_final: 0.8557 (t0)
  outliers start: 32
  outliers final: 25
  residues processed: 122
  average time/residue: 0.1565
  time to fit residues: 26.4546
Evaluate side-chains
  122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 7 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 43 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0570
   chunk 55 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 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 = 0.4148 r_free = 0.4148 target = 0.186408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.146898 restraints weight = 7709.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.152398 restraints weight = 4628.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.156062 restraints weight = 3363.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6394  Z= 0.214
  Angle     :  0.565  10.000   8665  Z= 0.293
  Chirality :  0.040   0.184    948
  Planarity :  0.004   0.038   1049
  Dihedral  :  6.233  57.859   1015
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.18 %
    Favored  : 74.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.18 (0.30), residues: 759
  helix:  0.31 (0.26), residues: 362
  sheet: -0.87 (0.52), residues: 101
  loop : -2.11 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 456 
 PHE   0.019   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A 142 
 ARG   0.003   0.000   ARG A 144 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.6927 (pttm) cc_final: 0.6129 (ptpt)
REVERT: A  220 TRP cc_start: 0.5805 (m-90) cc_final: 0.5490 (m-90)
REVERT: A  391 ASN cc_start: 0.6774 (t0) cc_final: 0.6323 (m-40)
REVERT: A  508 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7440 (tm-30)
  outliers start: 29
  outliers final: 23
  residues processed: 125
  average time/residue: 0.1555
  time to fit residues: 27.2012
Evaluate side-chains
  120 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 562 GLN
B  25 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.185113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146786 restraints weight = 7528.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.151876 restraints weight = 4664.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.155287 restraints weight = 3446.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6394  Z= 0.213
  Angle     :  0.565   9.878   8665  Z= 0.296
  Chirality :  0.041   0.197    948
  Planarity :  0.004   0.052   1049
  Dihedral  :  5.815  57.004   1015
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.81 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.10 (0.30), residues: 759
  helix:  0.34 (0.26), residues: 363
  sheet: -0.78 (0.53), residues: 101
  loop : -2.04 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.017   0.001   PHE A 407 
 TYR   0.010   0.001   TYR A 110 
 ARG   0.003   0.000   ARG A 144 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.6925 (pttm) cc_final: 0.6139 (ptpt)
REVERT: A  220 TRP cc_start: 0.5802 (m-90) cc_final: 0.5533 (m-90)
REVERT: A  391 ASN cc_start: 0.6741 (t0) cc_final: 0.6250 (m-40)
REVERT: A  508 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7514 (tm-30)
  outliers start: 32
  outliers final: 24
  residues processed: 123
  average time/residue: 0.1690
  time to fit residues: 28.6663
Evaluate side-chains
  121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0070
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 567 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.180347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.141490 restraints weight = 7706.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146780 restraints weight = 4680.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.150304 restraints weight = 3410.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.4816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   6394  Z= 0.245
  Angle     :  0.590   9.908   8665  Z= 0.309
  Chirality :  0.041   0.219    948
  Planarity :  0.004   0.049   1049
  Dihedral  :  5.670  54.359   1015
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 22.27 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.11 (0.30), residues: 759
  helix:  0.21 (0.26), residues: 368
  sheet: -0.80 (0.53), residues: 101
  loop : -1.89 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 326 
 HIS   0.002   0.001   HIS A 235 
 PHE   0.018   0.001   PHE A 407 
 TYR   0.011   0.001   TYR A 110 
 ARG   0.002   0.000   ARG A 144 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.6988 (pttm) cc_final: 0.6228 (ptpt)
REVERT: A  220 TRP cc_start: 0.5848 (m-90) cc_final: 0.5589 (m-90)
REVERT: A  259 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6822 (mm)
REVERT: A  289 TYR cc_start: 0.6776 (m-10) cc_final: 0.6530 (m-80)
REVERT: A  391 ASN cc_start: 0.6819 (t0) cc_final: 0.6284 (m-40)
REVERT: A  508 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7571 (tm-30)
  outliers start: 37
  outliers final: 30
  residues processed: 130
  average time/residue: 0.1637
  time to fit residues: 29.4071
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.1980
   chunk 15 optimal weight:    0.2980
   chunk 2 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 562 GLN
B 101 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.181637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.143207 restraints weight = 7592.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.148225 restraints weight = 4675.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.151573 restraints weight = 3463.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.5012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6394  Z= 0.221
  Angle     :  0.581   9.879   8665  Z= 0.304
  Chirality :  0.041   0.211    948
  Planarity :  0.004   0.049   1049
  Dihedral  :  5.558  53.446   1015
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 23.52 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.04 (0.30), residues: 759
  helix:  0.30 (0.26), residues: 362
  sheet: -0.73 (0.52), residues: 101
  loop : -1.89 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 326 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.016   0.001   PHE A 407 
 TYR   0.017   0.001   TYR A 267 
 ARG   0.003   0.000   ARG A 523 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.7012 (pttm) cc_final: 0.6273 (ptpt)
REVERT: A  220 TRP cc_start: 0.5808 (m-90) cc_final: 0.5559 (m-90)
REVERT: A  259 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.6856 (mm)
REVERT: A  282 TRP cc_start: 0.5698 (OUTLIER) cc_final: 0.4726 (m100)
REVERT: A  289 TYR cc_start: 0.6822 (m-10) cc_final: 0.6611 (m-80)
REVERT: A  391 ASN cc_start: 0.6791 (t0) cc_final: 0.6250 (m-40)
REVERT: A  454 PHE cc_start: 0.6398 (m-10) cc_final: 0.5940 (m-80)
REVERT: A  508 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7667 (tm-30)
REVERT: A  550 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7539 (tt)
  outliers start: 31
  outliers final: 26
  residues processed: 117
  average time/residue: 0.1519
  time to fit residues: 25.2911
Evaluate side-chains
  121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  282 TRP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0870
   chunk 74 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 70 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0570
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.182799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.144276 restraints weight = 7638.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.149293 restraints weight = 4712.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152652 restraints weight = 3473.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6394  Z= 0.220
  Angle     :  0.589   9.876   8665  Z= 0.308
  Chirality :  0.041   0.214    948
  Planarity :  0.004   0.050   1049
  Dihedral  :  5.479  52.566   1015
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 24.30 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.94 (0.30), residues: 759
  helix:  0.29 (0.26), residues: 367
  sheet: -0.64 (0.54), residues: 96
  loop : -1.73 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 326 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.026   0.001   PHE A 407 
 TYR   0.012   0.001   TYR A 267 
 ARG   0.002   0.000   ARG A 564 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.7021 (pttm) cc_final: 0.6282 (ptpt)
REVERT: A  223 HIS cc_start: 0.7766 (m-70) cc_final: 0.7489 (m-70)
REVERT: A  259 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6835 (mm)
REVERT: A  282 TRP cc_start: 0.5731 (OUTLIER) cc_final: 0.4794 (m100)
REVERT: A  391 ASN cc_start: 0.6786 (t0) cc_final: 0.6237 (m-40)
REVERT: A  454 PHE cc_start: 0.6445 (m-10) cc_final: 0.5997 (m-80)
REVERT: A  508 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: A  550 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7524 (tt)
  outliers start: 28
  outliers final: 25
  residues processed: 113
  average time/residue: 0.1479
  time to fit residues: 23.7819
Evaluate side-chains
  121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  282 TRP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 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 = 0.4095 r_free = 0.4095 target = 0.181097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.142872 restraints weight = 7686.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.147818 restraints weight = 4756.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.151084 restraints weight = 3522.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.5293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6394  Z= 0.238
  Angle     :  0.600   9.927   8665  Z= 0.314
  Chirality :  0.042   0.231    948
  Planarity :  0.004   0.051   1049
  Dihedral  :  5.511  51.022   1015
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 24.61 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.99 (0.30), residues: 759
  helix:  0.24 (0.26), residues: 367
  sheet: -0.65 (0.54), residues: 96
  loop : -1.75 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 220 
 HIS   0.003   0.001   HIS A 456 
 PHE   0.031   0.001   PHE A 407 
 TYR   0.012   0.001   TYR A 267 
 ARG   0.003   0.000   ARG A 523 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.7004 (pttm) cc_final: 0.6281 (ptpt)
REVERT: A  223 HIS cc_start: 0.7844 (m-70) cc_final: 0.7561 (m-70)
REVERT: A  259 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6648 (mm)
REVERT: A  282 TRP cc_start: 0.5774 (OUTLIER) cc_final: 0.4909 (m100)
REVERT: A  391 ASN cc_start: 0.6772 (t0) cc_final: 0.6209 (m-40)
REVERT: A  454 PHE cc_start: 0.6477 (m-10) cc_final: 0.6166 (m-10)
REVERT: A  508 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: B  127 MET cc_start: 0.8318 (mtt) cc_final: 0.7992 (mtt)
  outliers start: 27
  outliers final: 24
  residues processed: 114
  average time/residue: 0.1504
  time to fit residues: 24.0942
Evaluate side-chains
  122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  282 TRP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.177585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.139384 restraints weight = 7650.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.144282 restraints weight = 4652.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.147600 restraints weight = 3417.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   6394  Z= 0.257
  Angle     :  0.608  10.073   8665  Z= 0.320
  Chirality :  0.042   0.247    948
  Planarity :  0.004   0.051   1049
  Dihedral  :  5.581  49.749   1015
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 24.14 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.04 (0.30), residues: 759
  helix:  0.19 (0.26), residues: 367
  sheet: -0.62 (0.54), residues: 96
  loop : -1.78 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 220 
 HIS   0.002   0.001   HIS A 235 
 PHE   0.031   0.002   PHE A 407 
 TYR   0.013   0.002   TYR A 121 
 ARG   0.003   0.000   ARG A 523 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2537.55 seconds
wall clock time: 44 minutes 43.12 seconds (2683.12 seconds total)