Starting phenix.real_space_refine
on Fri Mar 14 02:48:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dw2_27749/03_2025/8dw2_27749.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dw2_27749/03_2025/8dw2_27749.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2025/8dw2_27749.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2025/8dw2_27749.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2025/8dw2_27749.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2025/8dw2_27749.cif"
  }
  resolution = 4.11
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    5906      2.51       5
     N    1565      2.21       5
     O    1858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 9364
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1153
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 4, 'TRANS': 150}
    Chain: "B"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1521
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 10, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1624
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1715
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
    Chain: "H"
      Number of atoms: 1609
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1646
    Chain: "L"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1703
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 6.22, per 1000 atoms: 0.66
  Number of scatterers: 9364
  At special positions: 0
  Unit cell: (79.443, 129.204, 173.727, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    1858      8.00
     N    1565      7.00
     C    5906      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 134 " - pdb=" SG  CYS C 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 154 " - pdb=" SG  CYS D 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG E   1 " - " ASN B 343 "
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2236

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 22 sheets defined
      14.2% alpha, 33.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 25
      removed outlier: 3.917A  pdb=" N   GLU A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 36
    Processing helix  chain 'A' and resid 49 through 58
    Processing helix  chain 'A' and resid 59 through 69
      removed outlier: 3.658A  pdb=" N   TYR A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 91
    Processing helix  chain 'A' and resid 92 through 103
      removed outlier: 4.045A  pdb=" N   VAL A  96 " --> pdb=" O   HIS A  92 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLU A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 123
    Processing helix  chain 'A' and resid 126 through 135
      removed outlier: 3.608A  pdb=" N   GLU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ASN A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 156
      removed outlier: 3.972A  pdb=" N   ILE A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 168
      removed outlier: 3.520A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.978A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 353
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.605A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.585A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE B 410 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'C' and resid 121 through 126
      removed outlier: 3.695A  pdb=" N   LEU C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 187
      removed outlier: 3.746A  pdb=" N   GLU C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 187'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 4.081A  pdb=" N   THR D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 203
      No H-bonds generated for 'chain 'D' and resid 201 through 203'
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 4.127A  pdb=" N   VAL L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 127 through 134
      removed outlier: 3.550A  pdb=" N   GLY L 134 " --> pdb=" O   GLN L 130 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 189 through 194
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.544A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA B 397 " --> pdb=" O   LYS B 356 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5
      removed outlier: 3.876A  pdb=" N   ARG C  24 " --> pdb=" O   THR C   5 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 55
      removed outlier: 3.711A  pdb=" N   TYR C  50 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   LEU C  47 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   GLN C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55
      removed outlier: 3.711A  pdb=" N   TYR C  50 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   LEU C  47 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   GLN C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 118
      removed outlier: 6.373A  pdb=" N   TYR C 173 " --> pdb=" O   ASN C 138 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 150
    Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.346A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 134 through 138
    Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 168
    Processing sheet with id=AB4, first strand: chain 'H' and resid 2 through 6
    Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.623A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.623A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 124 through 128
      removed outlier: 6.227A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 124 through 128
      removed outlier: 6.227A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER H 181 " --> pdb=" O   VAL H 173 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 158
      removed outlier: 3.847A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AC2, first strand: chain 'L' and resid 59 through 60
      removed outlier: 6.617A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 120 through 124
      removed outlier: 5.447A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 150 through 156

    366 hydrogen bonds defined for protein.
    948 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3009
        1.34 -     1.46: 2391
        1.46 -     1.59: 4134
        1.59 -     1.71: 1
        1.71 -     1.83: 44
  Bond restraints: 9579
  Sorted by residual:
  bond pdb=" CA  ASN D 211 "
       pdb=" CB  ASN D 211 "
    ideal  model  delta    sigma   weight residual
    1.530  1.565 -0.035 1.55e-02 4.16e+03 5.10e+00
  bond pdb=" CB  PRO C  81 "
       pdb=" CG  PRO C  81 "
    ideal  model  delta    sigma   weight residual
    1.492  1.604 -0.112 5.00e-02 4.00e+02 4.99e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.43e+00
  bond pdb=" CA  ARG L  67 "
       pdb=" C   ARG L  67 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.018 1.34e-02 5.57e+03 1.90e+00
  bond pdb=" CB  PRO B 384 "
       pdb=" CG  PRO B 384 "
    ideal  model  delta    sigma   weight residual
    1.492  1.559 -0.067 5.00e-02 4.00e+02 1.81e+00
  ... (remaining 9574 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 12798
        2.62 -     5.23: 189
        5.23 -     7.85: 36
        7.85 -    10.47: 4
       10.47 -    13.09: 1
  Bond angle restraints: 13028
  Sorted by residual:
  angle pdb=" CA  PRO C  81 "
        pdb=" N   PRO C  81 "
        pdb=" CD  PRO C  81 "
      ideal   model   delta    sigma   weight residual
     112.00  104.54    7.46 1.40e+00 5.10e-01 2.84e+01
  angle pdb=" C   SER C  95 "
        pdb=" CA  SER C  95 "
        pdb=" CB  SER C  95 "
      ideal   model   delta    sigma   weight residual
     116.54  111.33    5.21 1.15e+00 7.56e-01 2.05e+01
  angle pdb=" CB  MET H  40 "
        pdb=" CG  MET H  40 "
        pdb=" SD  MET H  40 "
      ideal   model   delta    sigma   weight residual
     112.70  125.79  -13.09 3.00e+00 1.11e-01 1.90e+01
  angle pdb=" N   ALA D  92 "
        pdb=" CA  ALA D  92 "
        pdb=" C   ALA D  92 "
      ideal   model   delta    sigma   weight residual
     108.24  113.74   -5.50 1.32e+00 5.74e-01 1.74e+01
  angle pdb=" CA  LYS B 444 "
        pdb=" CB  LYS B 444 "
        pdb=" CG  LYS B 444 "
      ideal   model   delta    sigma   weight residual
     114.10  122.22   -8.12 2.00e+00 2.50e-01 1.65e+01
  ... (remaining 13023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.73: 5045
       21.73 -    43.47: 592
       43.47 -    65.20: 79
       65.20 -    86.94: 17
       86.94 -   108.67: 5
  Dihedral angle restraints: 5738
    sinusoidal: 2226
      harmonic: 3512
  Sorted by residual:
  dihedral pdb=" CB  CYS C 134 "
           pdb=" SG  CYS C 134 "
           pdb=" SG  CYS C 194 "
           pdb=" CB  CYS C 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.64  -58.64     1      1.00e+01 1.00e-02 4.60e+01
  dihedral pdb=" CA  CYS B 361 "
           pdb=" C   CYS B 361 "
           pdb=" N   VAL B 362 "
           pdb=" CA  VAL B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.89   31.11     0      5.00e+00 4.00e-02 3.87e+01
  dihedral pdb=" CA  ASP B 420 "
           pdb=" C   ASP B 420 "
           pdb=" N   TYR B 421 "
           pdb=" CA  TYR B 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.38  -28.62     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 5735 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1168
       0.055 -    0.109: 251
       0.109 -    0.164: 42
       0.164 -    0.218: 4
       0.218 -    0.273: 1
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  ASN L 144 "
            pdb=" N   ASN L 144 "
            pdb=" C   ASN L 144 "
            pdb=" CB  ASN L 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.46e-01
  chirality pdb=" CA  VAL H 117 "
            pdb=" N   VAL H 117 "
            pdb=" C   VAL H 117 "
            pdb=" CB  VAL H 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.76e-01
  ... (remaining 1463 not shown)

  Planarity restraints: 1672
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 520 "   -0.062 5.00e-02 4.00e+02   9.55e-02 1.46e+01
        pdb=" N   PRO B 521 "    0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO B 521 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 521 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 158 "   -0.021 2.00e-02 2.50e+03   2.02e-02 1.02e+01
        pdb=" CG  TRP H 158 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 158 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 158 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 158 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 158 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 158 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 158 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 158 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 158 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 150 "   -0.047 5.00e-02 4.00e+02   7.09e-02 8.05e+00
        pdb=" N   PRO H 151 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO H 151 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO H 151 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1669 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 338
        2.68 -     3.24: 9285
        3.24 -     3.79: 14814
        3.79 -     4.35: 18704
        4.35 -     4.90: 29833
  Nonbonded interactions: 72974
  Sorted by model distance:
  nonbonded pdb=" O   TYR C 186 "
            pdb=" OH  TYR C 192 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OG  SER B 514 "
            pdb=" OE2 GLU B 516 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   SER H 192 "
            pdb=" OG  SER H 192 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OD2 ASP A 110 "
            pdb=" OH  TYR B 489 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OD1 ASP L 176 "
            pdb=" OG1 THR L 178 "
     model   vdw
     2.205 3.040
  ... (remaining 72969 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 
4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid  \ 
55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ 
d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213))
  selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 
3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through  \ 
58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ 
h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ 
hrough 219))
}

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=0.00 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:             1.050
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.380
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
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   0.112   9579  Z= 0.235
  Angle     :  0.812  13.087  13028  Z= 0.408
  Chirality :  0.047   0.273   1466
  Planarity :  0.006   0.095   1671
  Dihedral  : 17.647 108.673   3466
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.20 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 33.27 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.24), residues: 1209
  helix: -0.95 (0.39), residues: 146
  sheet:  0.33 (0.26), residues: 427
  loop : -1.22 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.003   TRP H 158 
 HIS   0.004   0.001   HIS D 214 
 PHE   0.020   0.002   PHE H 150 
 TYR   0.017   0.001   TYR B 423 
 ARG   0.006   0.001   ARG B 408 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 144
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.9002 (m90) cc_final: 0.8452 (m90)
REVERT: A   85 HIS cc_start: 0.8589 (m90) cc_final: 0.8090 (m90)
REVERT: B  495 TYR cc_start: 0.8539 (m-80) cc_final: 0.8092 (t80)
REVERT: C  179 LEU cc_start: 0.9171 (tp) cc_final: 0.8921 (tp)
REVERT: H   40 MET cc_start: 0.8982 (mmm) cc_final: 0.8588 (mmt)
REVERT: H   77 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7622 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 146
  average time/residue: 0.2011
  time to fit residues: 41.7764
Evaluate side-chains
  135 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 48 optimal weight:   20.0000
   chunk 93 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 56 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 108 optimal weight:    0.5980
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
B 474 GLN
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 137 ASN
C 138 ASN
C 155 GLN
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 GLN
** L  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 164 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.081900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.063821 restraints weight = 44335.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.065697 restraints weight = 24289.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.066929 restraints weight = 16143.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9579  Z= 0.317
  Angle     :  0.727   7.569  13028  Z= 0.375
  Chirality :  0.047   0.209   1466
  Planarity :  0.006   0.076   1671
  Dihedral  :  7.438  66.612   1374
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.44 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.45 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    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: -0.95 (0.24), residues: 1209
  helix: -0.68 (0.41), residues: 141
  sheet:  0.28 (0.26), residues: 415
  loop : -1.23 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP D  50 
 HIS   0.005   0.001   HIS C 198 
 PHE   0.028   0.003   PHE B 464 
 TYR   0.024   0.002   TYR L 102 
 ARG   0.009   0.001   ARG L 217 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.9275 (m90) cc_final: 0.8818 (m90)
REVERT: A   94 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7730 (mm-30)
REVERT: B  366 SER cc_start: 0.8903 (p) cc_final: 0.8631 (p)
REVERT: C   43 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7862 (tm-30)
REVERT: C  107 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9119 (mmmm)
REVERT: C  138 ASN cc_start: 0.9169 (m-40) cc_final: 0.8917 (m110)
REVERT: D  152 LEU cc_start: 0.8652 (mt) cc_final: 0.8348 (pp)
REVERT: D  178 HIS cc_start: 0.8844 (m90) cc_final: 0.8516 (m90)
REVERT: H    3 GLN cc_start: 0.9049 (mm110) cc_final: 0.8761 (mm-40)
REVERT: H   40 MET cc_start: 0.9108 (mmm) cc_final: 0.8896 (mmm)
REVERT: L  142 LEU cc_start: 0.9355 (tp) cc_final: 0.8945 (tt)
REVERT: L  167 GLU cc_start: 0.8688 (tt0) cc_final: 0.8361 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2540
  time to fit residues: 64.2153
Evaluate side-chains
  130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 45 optimal weight:   30.0000
   chunk 8 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 108 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN
** L  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.081025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.062168 restraints weight = 52975.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.064241 restraints weight = 27007.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.065617 restraints weight = 17252.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9579  Z= 0.258
  Angle     :  0.672   7.095  13028  Z= 0.346
  Chirality :  0.045   0.183   1466
  Planarity :  0.005   0.070   1671
  Dihedral  :  6.363  56.481   1374
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.53 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.83 (0.24), residues: 1209
  helix: -0.64 (0.40), residues: 142
  sheet:  0.35 (0.26), residues: 419
  loop : -1.14 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  50 
 HIS   0.004   0.001   HIS C 198 
 PHE   0.020   0.002   PHE L 122 
 TYR   0.023   0.002   TYR L 102 
 ARG   0.006   0.001   ARG L 217 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 HIS cc_start: 0.8875 (m90) cc_final: 0.8606 (m90)
REVERT: A   94 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: B  417 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8796 (ttpp)
REVERT: B  489 TYR cc_start: 0.6729 (m-80) cc_final: 0.6277 (m-80)
REVERT: C  138 ASN cc_start: 0.9159 (m-40) cc_final: 0.8912 (m110)
REVERT: D  178 HIS cc_start: 0.8822 (m90) cc_final: 0.8463 (m90)
REVERT: H    3 GLN cc_start: 0.9037 (mm110) cc_final: 0.8699 (mm-40)
REVERT: L   41 TRP cc_start: 0.8723 (m100) cc_final: 0.7891 (m100)
REVERT: L  142 LEU cc_start: 0.9372 (tp) cc_final: 0.8952 (tp)
REVERT: L  167 GLU cc_start: 0.8695 (tt0) cc_final: 0.8329 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1947
  time to fit residues: 46.2219
Evaluate side-chains
  127 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 95 optimal weight:    7.9990
   chunk 117 optimal weight:    7.9990
   chunk 94 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.080353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.061659 restraints weight = 53800.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.063700 restraints weight = 27491.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.065041 restraints weight = 17621.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9579  Z= 0.275
  Angle     :  0.681   7.594  13028  Z= 0.349
  Chirality :  0.045   0.165   1466
  Planarity :  0.005   0.063   1671
  Dihedral  :  5.965  56.319   1374
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.44 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.77 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.82 (0.24), residues: 1209
  helix: -0.65 (0.42), residues: 141
  sheet:  0.31 (0.26), residues: 418
  loop : -1.08 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H  47 
 HIS   0.004   0.001   HIS C 198 
 PHE   0.024   0.002   PHE B 377 
 TYR   0.033   0.002   TYR L 102 
 ARG   0.012   0.001   ARG A  81 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLU cc_start: 0.9301 (mp0) cc_final: 0.8989 (pm20)
REVERT: A   62 ILE cc_start: 0.8845 (pt) cc_final: 0.8353 (pt)
REVERT: A   82 THR cc_start: 0.9218 (p) cc_final: 0.8312 (p)
REVERT: A   85 HIS cc_start: 0.8874 (m90) cc_final: 0.8661 (m90)
REVERT: A   90 THR cc_start: 0.7866 (t) cc_final: 0.7573 (p)
REVERT: A   94 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7724 (mm-30)
REVERT: B  421 TYR cc_start: 0.8725 (m-80) cc_final: 0.8289 (m-80)
REVERT: B  489 TYR cc_start: 0.6827 (m-80) cc_final: 0.6304 (m-80)
REVERT: C  138 ASN cc_start: 0.9137 (m-40) cc_final: 0.8886 (m110)
REVERT: D  178 HIS cc_start: 0.8818 (m90) cc_final: 0.8459 (m90)
REVERT: H    3 GLN cc_start: 0.9048 (mm110) cc_final: 0.8684 (mm-40)
REVERT: H  144 CYS cc_start: 0.4524 (m) cc_final: 0.4209 (m)
REVERT: L   41 TRP cc_start: 0.8733 (m100) cc_final: 0.8045 (m100)
REVERT: L  167 GLU cc_start: 0.8736 (tt0) cc_final: 0.8327 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 160
  average time/residue: 0.2145
  time to fit residues: 47.7011
Evaluate side-chains
  124 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 33 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 115 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    3.6988

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** C  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 HIS
L 164 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.079741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.061039 restraints weight = 53851.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.063069 restraints weight = 27381.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.064405 restraints weight = 17538.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9579  Z= 0.277
  Angle     :  0.682   8.358  13028  Z= 0.351
  Chirality :  0.045   0.162   1466
  Planarity :  0.005   0.063   1671
  Dihedral  :  5.808  56.067   1374
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.11 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    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: -0.89 (0.24), residues: 1209
  helix: -0.72 (0.41), residues: 148
  sheet:  0.28 (0.26), residues: 418
  loop : -1.15 (0.25), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H  47 
 HIS   0.004   0.001   HIS C 198 
 PHE   0.020   0.002   PHE D 106 
 TYR   0.034   0.002   TYR L 102 
 ARG   0.005   0.001   ARG L  67 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.9306 (m90) cc_final: 0.8927 (m90)
REVERT: A   61 GLU cc_start: 0.9287 (mp0) cc_final: 0.8970 (pm20)
REVERT: A   62 ILE cc_start: 0.8858 (pt) cc_final: 0.8334 (pt)
REVERT: A   90 THR cc_start: 0.7782 (t) cc_final: 0.7482 (p)
REVERT: B  421 TYR cc_start: 0.8849 (m-80) cc_final: 0.8309 (m-80)
REVERT: B  498 GLN cc_start: 0.8266 (mm110) cc_final: 0.8041 (mm110)
REVERT: D    3 GLN cc_start: 0.8807 (mm110) cc_final: 0.8461 (mp10)
REVERT: D  154 CYS cc_start: 0.5839 (m) cc_final: 0.4956 (m)
REVERT: D  178 HIS cc_start: 0.8827 (m90) cc_final: 0.8446 (m90)
REVERT: H    3 GLN cc_start: 0.9085 (mm110) cc_final: 0.8721 (mm-40)
REVERT: H  144 CYS cc_start: 0.4706 (m) cc_final: 0.4322 (m)
REVERT: H  150 PHE cc_start: 0.8252 (t80) cc_final: 0.8002 (t80)
REVERT: L   41 TRP cc_start: 0.8731 (m100) cc_final: 0.8036 (m100)
REVERT: L  142 LEU cc_start: 0.9424 (tt) cc_final: 0.9055 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1871
  time to fit residues: 40.2429
Evaluate side-chains
  112 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 46 optimal weight:   30.0000
   chunk 106 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 116 optimal weight:    6.9990
   chunk 98 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** 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 = 0.3574 r_free = 0.3574 target = 0.078298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.059965 restraints weight = 52562.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.061868 restraints weight = 27572.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.063101 restraints weight = 17925.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9579  Z= 0.344
  Angle     :  0.706   9.108  13028  Z= 0.362
  Chirality :  0.046   0.246   1466
  Planarity :  0.005   0.061   1671
  Dihedral  :  5.961  56.020   1374
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.93 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.24), residues: 1209
  helix: -0.79 (0.41), residues: 148
  sheet:  0.10 (0.25), residues: 423
  loop : -1.19 (0.25), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP H  47 
 HIS   0.005   0.001   HIS C 198 
 PHE   0.018   0.002   PHE C  72 
 TYR   0.046   0.002   TYR L 102 
 ARG   0.005   0.001   ARG B 408 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 2.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.8984 (p) cc_final: 0.7999 (p)
REVERT: A   52 HIS cc_start: 0.9322 (m90) cc_final: 0.9015 (m90)
REVERT: A   61 GLU cc_start: 0.9252 (mp0) cc_final: 0.8944 (pm20)
REVERT: A   62 ILE cc_start: 0.8881 (pt) cc_final: 0.8353 (pt)
REVERT: A   82 THR cc_start: 0.9158 (p) cc_final: 0.8215 (p)
REVERT: A   90 THR cc_start: 0.7843 (t) cc_final: 0.7545 (p)
REVERT: B  421 TYR cc_start: 0.8865 (m-80) cc_final: 0.8408 (m-80)
REVERT: B  498 GLN cc_start: 0.8248 (mm110) cc_final: 0.8003 (mm110)
REVERT: B  518 LEU cc_start: 0.7950 (tp) cc_final: 0.7735 (tp)
REVERT: D    3 GLN cc_start: 0.8736 (mm110) cc_final: 0.8420 (mp10)
REVERT: D  154 CYS cc_start: 0.5708 (m) cc_final: 0.4914 (m)
REVERT: D  168 TRP cc_start: 0.8089 (m-10) cc_final: 0.7825 (m-10)
REVERT: D  178 HIS cc_start: 0.8808 (m90) cc_final: 0.8378 (m90)
REVERT: H    3 GLN cc_start: 0.9103 (mm110) cc_final: 0.8750 (mm-40)
REVERT: H  144 CYS cc_start: 0.4574 (m) cc_final: 0.4326 (m)
REVERT: H  149 TYR cc_start: 0.7427 (p90) cc_final: 0.7151 (p90)
REVERT: H  150 PHE cc_start: 0.8307 (t80) cc_final: 0.8040 (t80)
REVERT: H  213 LYS cc_start: 0.6439 (tptm) cc_final: 0.6033 (tptp)
REVERT: L   41 TRP cc_start: 0.8765 (m100) cc_final: 0.8060 (m100)
REVERT: L  142 LEU cc_start: 0.9450 (tt) cc_final: 0.9111 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2510
  time to fit residues: 52.5721
Evaluate side-chains
  118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 108 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** 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 = 0.3600 r_free = 0.3600 target = 0.079679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.061191 restraints weight = 53247.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.063205 restraints weight = 26763.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.064555 restraints weight = 17032.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9579  Z= 0.232
  Angle     :  0.673   8.616  13028  Z= 0.346
  Chirality :  0.045   0.247   1466
  Planarity :  0.005   0.060   1671
  Dihedral  :  5.708  55.604   1374
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.86 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.89 (0.24), residues: 1209
  helix: -0.76 (0.41), residues: 147
  sheet:  0.17 (0.25), residues: 423
  loop : -1.05 (0.25), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP H 158 
 HIS   0.004   0.001   HIS C 198 
 PHE   0.016   0.002   PHE C  72 
 TYR   0.028   0.001   TYR L 102 
 ARG   0.003   0.000   ARG C  18 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.9300 (m90) cc_final: 0.8997 (m90)
REVERT: A   61 GLU cc_start: 0.9231 (mp0) cc_final: 0.8954 (pm20)
REVERT: A   62 ILE cc_start: 0.8875 (pt) cc_final: 0.8335 (pt)
REVERT: A   90 THR cc_start: 0.7687 (t) cc_final: 0.7379 (p)
REVERT: B  421 TYR cc_start: 0.8852 (m-80) cc_final: 0.8332 (m-80)
REVERT: B  498 GLN cc_start: 0.8192 (mm110) cc_final: 0.7973 (mm110)
REVERT: D  143 LYS cc_start: 0.6544 (pttt) cc_final: 0.6063 (tppt)
REVERT: D  178 HIS cc_start: 0.8789 (m90) cc_final: 0.8344 (m90)
REVERT: H    3 GLN cc_start: 0.9039 (mm110) cc_final: 0.8682 (mm-40)
REVERT: H  149 TYR cc_start: 0.7533 (p90) cc_final: 0.7330 (p90)
REVERT: H  150 PHE cc_start: 0.8302 (t80) cc_final: 0.7920 (t80)
REVERT: L   41 TRP cc_start: 0.8719 (m100) cc_final: 0.7845 (m100)
REVERT: L  142 LEU cc_start: 0.9444 (tt) cc_final: 0.9119 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2054
  time to fit residues: 43.5724
Evaluate side-chains
  115 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 117 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 116 optimal weight:    5.9990
   chunk 114 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 70 optimal weight:   20.0000
   chunk 96 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** 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 = 0.3550 r_free = 0.3550 target = 0.077156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.058811 restraints weight = 53308.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.060716 restraints weight = 27453.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.061987 restraints weight = 17781.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   9579  Z= 0.369
  Angle     :  0.750   9.429  13028  Z= 0.386
  Chirality :  0.047   0.223   1466
  Planarity :  0.006   0.065   1671
  Dihedral  :  6.163  55.677   1374
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.26 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.24), residues: 1209
  helix: -0.90 (0.41), residues: 148
  sheet: -0.12 (0.25), residues: 430
  loop : -1.23 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP H  47 
 HIS   0.005   0.001   HIS H 168 
 PHE   0.021   0.003   PHE C  72 
 TYR   0.047   0.002   TYR L 102 
 ARG   0.005   0.001   ARG A  31 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 THR cc_start: 0.9236 (p) cc_final: 0.8625 (p)
REVERT: B  421 TYR cc_start: 0.8890 (m-80) cc_final: 0.8472 (m-80)
REVERT: D    3 GLN cc_start: 0.8656 (mm110) cc_final: 0.8370 (mp10)
REVERT: D   57 ASN cc_start: 0.9212 (m110) cc_final: 0.9011 (m110)
REVERT: D  143 LYS cc_start: 0.6613 (pttt) cc_final: 0.6091 (tppt)
REVERT: D  154 CYS cc_start: 0.5851 (m) cc_final: 0.5169 (m)
REVERT: D  168 TRP cc_start: 0.8430 (m-10) cc_final: 0.7921 (m-10)
REVERT: D  178 HIS cc_start: 0.8756 (m90) cc_final: 0.8266 (m90)
REVERT: H    3 GLN cc_start: 0.9130 (mm110) cc_final: 0.8747 (mm-40)
REVERT: H  144 CYS cc_start: 0.4723 (m) cc_final: 0.4348 (m)
REVERT: H  150 PHE cc_start: 0.8422 (t80) cc_final: 0.8117 (t80)
REVERT: L   41 TRP cc_start: 0.8779 (m100) cc_final: 0.7849 (m100)
REVERT: L  142 LEU cc_start: 0.9469 (tt) cc_final: 0.9083 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2122
  time to fit residues: 42.1617
Evaluate side-chains
  114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 69 optimal weight:   20.0000
   chunk 42 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 113 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0670
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 198 HIS
L 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.080916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.063096 restraints weight = 52306.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.065119 restraints weight = 23405.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.066691 restraints weight = 14429.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9579  Z= 0.186
  Angle     :  0.693   8.620  13028  Z= 0.351
  Chirality :  0.046   0.219   1466
  Planarity :  0.005   0.060   1671
  Dihedral  :  5.474  55.571   1374
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.11 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    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: -0.84 (0.24), residues: 1209
  helix: -0.83 (0.40), residues: 148
  sheet:  0.26 (0.26), residues: 409
  loop : -1.01 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP D 168 
 HIS   0.005   0.001   HIS C 198 
 PHE   0.022   0.002   PHE C 118 
 TYR   0.024   0.001   TYR B 369 
 ARG   0.002   0.000   ARG C  18 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9006 (p) cc_final: 0.8140 (p)
REVERT: A   82 THR cc_start: 0.9202 (p) cc_final: 0.8482 (p)
REVERT: B  406 GLU cc_start: 0.8722 (mp0) cc_final: 0.8246 (mp0)
REVERT: B  421 TYR cc_start: 0.8876 (m-80) cc_final: 0.8321 (m-80)
REVERT: D  143 LYS cc_start: 0.6524 (pttt) cc_final: 0.6092 (tppt)
REVERT: D  154 CYS cc_start: 0.5745 (m) cc_final: 0.4928 (m)
REVERT: D  168 TRP cc_start: 0.8479 (m-10) cc_final: 0.8087 (m-10)
REVERT: D  178 HIS cc_start: 0.8734 (m90) cc_final: 0.8221 (m90)
REVERT: D  203 LEU cc_start: 0.8589 (mm) cc_final: 0.8326 (tt)
REVERT: D  210 CYS cc_start: 0.6722 (p) cc_final: 0.5548 (p)
REVERT: H    3 GLN cc_start: 0.9003 (mm110) cc_final: 0.8676 (mm-40)
REVERT: H   83 TRP cc_start: 0.8589 (m100) cc_final: 0.8349 (m100)
REVERT: H  144 CYS cc_start: 0.4338 (m) cc_final: 0.3557 (m)
REVERT: H  150 PHE cc_start: 0.8225 (t80) cc_final: 0.7888 (t80)
REVERT: H  213 LYS cc_start: 0.6212 (tptm) cc_final: 0.5746 (tptp)
REVERT: L   41 TRP cc_start: 0.8687 (m100) cc_final: 0.7852 (m100)
REVERT: L  142 LEU cc_start: 0.9386 (tt) cc_final: 0.8949 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1942
  time to fit residues: 45.6708
Evaluate side-chains
  124 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 86 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 104 optimal weight:    8.9990
   chunk 109 optimal weight:    7.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    3.6586

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 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 = 0.3582 r_free = 0.3582 target = 0.078738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.060096 restraints weight = 54076.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.062083 restraints weight = 27526.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.063405 restraints weight = 17638.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9579  Z= 0.288
  Angle     :  0.709   9.271  13028  Z= 0.360
  Chirality :  0.046   0.210   1466
  Planarity :  0.005   0.059   1671
  Dihedral  :  5.670  55.002   1374
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.19 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    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: -0.94 (0.25), residues: 1209
  helix: -0.80 (0.41), residues: 148
  sheet:  0.06 (0.25), residues: 435
  loop : -1.04 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP H  47 
 HIS   0.007   0.001   HIS C 198 
 PHE   0.019   0.002   PHE C 118 
 TYR   0.031   0.001   TYR L 102 
 ARG   0.004   0.000   ARG L  18 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9071 (p) cc_final: 0.8434 (p)
REVERT: A   82 THR cc_start: 0.9216 (p) cc_final: 0.8507 (p)
REVERT: B  402 ILE cc_start: 0.9224 (tp) cc_final: 0.8833 (pt)
REVERT: B  406 GLU cc_start: 0.8774 (mp0) cc_final: 0.8318 (mp0)
REVERT: B  421 TYR cc_start: 0.8895 (m-80) cc_final: 0.8434 (m-80)
REVERT: D   57 ASN cc_start: 0.9241 (m110) cc_final: 0.9036 (m110)
REVERT: D  143 LYS cc_start: 0.6618 (pttt) cc_final: 0.6144 (tppt)
REVERT: D  154 CYS cc_start: 0.6105 (m) cc_final: 0.5143 (m)
REVERT: D  168 TRP cc_start: 0.8562 (m-10) cc_final: 0.8134 (m-10)
REVERT: D  178 HIS cc_start: 0.8782 (m90) cc_final: 0.8197 (m90)
REVERT: D  210 CYS cc_start: 0.6855 (p) cc_final: 0.5766 (p)
REVERT: H    3 GLN cc_start: 0.9073 (mm110) cc_final: 0.8714 (mm-40)
REVERT: H  144 CYS cc_start: 0.4557 (m) cc_final: 0.4211 (m)
REVERT: H  149 TYR cc_start: 0.7614 (p90) cc_final: 0.7231 (p90)
REVERT: H  150 PHE cc_start: 0.8439 (t80) cc_final: 0.8003 (t80)
REVERT: L   41 TRP cc_start: 0.8763 (m100) cc_final: 0.7898 (m100)
REVERT: L  142 LEU cc_start: 0.9439 (tt) cc_final: 0.9064 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1759
  time to fit residues: 38.0903
Evaluate side-chains
  118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 81 optimal weight:    0.3980
   chunk 36 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 13 optimal weight:    0.4980
   chunk 66 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 106 optimal weight:    0.4980
   chunk 17 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** C  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.082470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.062960 restraints weight = 71451.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.065365 restraints weight = 32142.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.066947 restraints weight = 19301.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9579  Z= 0.180
  Angle     :  0.696   8.799  13028  Z= 0.350
  Chirality :  0.046   0.205   1466
  Planarity :  0.005   0.060   1671
  Dihedral  :  5.284  55.266   1374
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.37 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    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: -0.70 (0.25), residues: 1209
  helix: -0.73 (0.41), residues: 149
  sheet:  0.37 (0.26), residues: 425
  loop : -0.96 (0.26), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP H  83 
 HIS   0.006   0.001   HIS A  52 
 PHE   0.019   0.002   PHE C 118 
 TYR   0.018   0.001   TYR L 102 
 ARG   0.005   0.000   ARG L  18 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 4172.55 seconds
wall clock time: 74 minutes 35.03 seconds (4475.03 seconds total)