Starting phenix.real_space_refine
on Sun Jul 27 15:41:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dw2_27749/07_2025/8dw2_27749.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dw2_27749/07_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_27749/07_2025/8dw2_27749.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2025/8dw2_27749.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2025/8dw2_27749.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.40, per 1000 atoms: 0.68
  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: 2.43
  Conformation dependent library (CDL) restraints added in 1.3 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: 1.19
  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: 2.79

  Time building geometry restraints manager: 2.86 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:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.090
  Find NCS groups from input model:        0.250
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.490
-------------------------------------------------------------------------------
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   9594  Z= 0.157
  Angle     :  0.815  13.087  13061  Z= 0.409
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00371 (    1)
  link_NAG-ASN         : angle       0.64739 (    3)
  link_BETA1-4         : bond        0.00465 (    2)
  link_BETA1-4         : angle       1.48649 (    6)
  hydrogen bonds       : bond        0.12757 (  329)
  hydrogen bonds       : angle       6.82853 (  948)
  SS BOND              : bond        0.00397 (   12)
  SS BOND              : angle       1.68646 (   24)
  covalent geometry    : bond        0.00350 ( 9579)
  covalent geometry    : angle       0.81197 (13028)

*********************** 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  : 1.208 
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: 0.2204
  time to fit residues: 46.2591
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  : 1.235 
-------------------------------------------------------------------------------
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:    5.9990
   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:    3.7188

-------------------------------------------------------------------------------
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 138 ASN
C 155 GLN
D  65 GLN
** L  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 164 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.082348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.064250 restraints weight = 44296.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.066147 restraints weight = 24174.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.067377 restraints weight = 16010.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    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 = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9594  Z= 0.200
  Angle     :  0.727   7.350  13061  Z= 0.374
  Chirality :  0.047   0.210   1466
  Planarity :  0.006   0.076   1671
  Dihedral  :  7.362  65.484   1374
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.35 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.35 %
    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: -0.92 (0.24), residues: 1209
  helix: -0.69 (0.41), residues: 141
  sheet:  0.34 (0.26), residues: 413
  loop : -1.23 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D  50 
 HIS   0.004   0.001   HIS D 214 
 PHE   0.028   0.003   PHE B 464 
 TYR   0.021   0.002   TYR L 102 
 ARG   0.006   0.001   ARG L 217 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00021 (    1)
  link_NAG-ASN         : angle       1.70291 (    3)
  link_BETA1-4         : bond        0.00341 (    2)
  link_BETA1-4         : angle       2.54272 (    6)
  hydrogen bonds       : bond        0.03675 (  329)
  hydrogen bonds       : angle       6.15588 (  948)
  SS BOND              : bond        0.00745 (   12)
  SS BOND              : angle       2.08219 (   24)
  covalent geometry    : bond        0.00437 ( 9579)
  covalent geometry    : angle       0.71966 (13028)

*********************** 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
  186 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 1.033 
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   52 HIS cc_start: 0.9289 (m90) cc_final: 0.8840 (m90)
REVERT: A   94 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7744 (mm-30)
REVERT: A  164 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8170 (pt)
REVERT: C   43 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: C  107 LYS cc_start: 0.9331 (mmmm) cc_final: 0.9095 (mmmm)
REVERT: C  138 ASN cc_start: 0.9179 (m-40) cc_final: 0.8934 (m110)
REVERT: D  178 HIS cc_start: 0.8880 (m90) cc_final: 0.8546 (m90)
REVERT: H    3 GLN cc_start: 0.9032 (mm110) cc_final: 0.8736 (mm-40)
REVERT: H   40 MET cc_start: 0.9121 (mmm) cc_final: 0.8909 (mmm)
REVERT: H   82 GLN cc_start: 0.8284 (mm110) cc_final: 0.7835 (mm-40)
REVERT: L  142 LEU cc_start: 0.9324 (tp) cc_final: 0.8923 (tt)
REVERT: L  167 GLU cc_start: 0.8709 (tt0) cc_final: 0.8331 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 185
  average time/residue: 0.2115
  time to fit residues: 54.0638
Evaluate side-chains
  132 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 45 optimal weight:   40.0000
   chunk 8 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 2 optimal weight:   30.0000
   chunk 88 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 103 optimal weight:    8.9990
   chunk 68 optimal weight:   20.0000
   chunk 108 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    4.5986

-------------------------------------------------------------------------------
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 137 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.079575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.061592 restraints weight = 53467.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.063601 restraints weight = 29570.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.065162 restraints weight = 16792.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    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 = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9594  Z= 0.231
  Angle     :  0.718   8.260  13061  Z= 0.369
  Chirality :  0.045   0.186   1466
  Planarity :  0.006   0.071   1671
  Dihedral  :  6.603  56.969   1374
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.78 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.71 %
    Favored  : 94.20 %
  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: -0.93 (0.24), residues: 1209
  helix: -0.61 (0.41), residues: 141
  sheet:  0.24 (0.26), residues: 420
  loop : -1.21 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP D  50 
 HIS   0.005   0.001   HIS C 198 
 PHE   0.017   0.003   PHE H 150 
 TYR   0.023   0.002   TYR L 102 
 ARG   0.006   0.001   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.66479 (    3)
  link_BETA1-4         : bond        0.00376 (    2)
  link_BETA1-4         : angle       2.28048 (    6)
  hydrogen bonds       : bond        0.03638 (  329)
  hydrogen bonds       : angle       6.12948 (  948)
  SS BOND              : bond        0.00578 (   12)
  SS BOND              : angle       1.75511 (   24)
  covalent geometry    : bond        0.00509 ( 9579)
  covalent geometry    : angle       0.71299 (13028)

*********************** 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
  154 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.9272 (m90) cc_final: 0.8881 (m90)
REVERT: A   85 HIS cc_start: 0.8878 (m90) cc_final: 0.8592 (m90)
REVERT: B  417 LYS cc_start: 0.9121 (ttpp) cc_final: 0.8894 (ttpp)
REVERT: B  489 TYR cc_start: 0.6748 (m-80) cc_final: 0.6295 (m-80)
REVERT: B  498 GLN cc_start: 0.8260 (mm110) cc_final: 0.8034 (mm110)
REVERT: D  178 HIS cc_start: 0.8836 (m90) cc_final: 0.8482 (m90)
REVERT: H    3 GLN cc_start: 0.9057 (mm110) cc_final: 0.8723 (mm-40)
REVERT: H  144 CYS cc_start: 0.4509 (m) cc_final: 0.4113 (m)
REVERT: L  142 LEU cc_start: 0.9381 (tp) cc_final: 0.8950 (tp)
REVERT: L  167 GLU cc_start: 0.8673 (tt0) cc_final: 0.8328 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2249
  time to fit residues: 49.9631
Evaluate side-chains
  113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 52 optimal weight:   20.0000
   chunk 95 optimal weight:    0.3980
   chunk 117 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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
D 214 HIS
** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  96 GLN
L 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.082265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.064537 restraints weight = 52421.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.066527 restraints weight = 24596.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.067449 restraints weight = 15282.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    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 = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9594  Z= 0.127
  Angle     :  0.661   8.181  13061  Z= 0.337
  Chirality :  0.045   0.163   1466
  Planarity :  0.005   0.064   1671
  Dihedral  :  5.702  56.098   1374
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.87 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.51 %
    Favored  : 97.39 %
  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: -0.69 (0.24), residues: 1209
  helix: -0.67 (0.41), residues: 141
  sheet:  0.49 (0.26), residues: 415
  loop : -1.03 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 168 
 HIS   0.004   0.001   HIS A 118 
 PHE   0.021   0.002   PHE B 377 
 TYR   0.012   0.001   TYR L 102 
 ARG   0.004   0.000   ARG L 217 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00054 (    1)
  link_NAG-ASN         : angle       1.03105 (    3)
  link_BETA1-4         : bond        0.00303 (    2)
  link_BETA1-4         : angle       1.94797 (    6)
  hydrogen bonds       : bond        0.03177 (  329)
  hydrogen bonds       : angle       5.78007 (  948)
  SS BOND              : bond        0.00569 (   12)
  SS BOND              : angle       1.73506 (   24)
  covalent geometry    : bond        0.00286 ( 9579)
  covalent geometry    : angle       0.65614 (13028)

*********************** 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
  181 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 1.003 
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   34 MET cc_start: 0.6870 (ppp) cc_final: 0.6508 (ppp)
REVERT: A   61 GLU cc_start: 0.9293 (mp0) cc_final: 0.8995 (mm-30)
REVERT: A   82 THR cc_start: 0.9176 (p) cc_final: 0.8296 (p)
REVERT: A   85 HIS cc_start: 0.8808 (m90) cc_final: 0.8604 (m90)
REVERT: A   90 THR cc_start: 0.7801 (t) cc_final: 0.7493 (p)
REVERT: B  498 GLN cc_start: 0.8221 (mm110) cc_final: 0.8014 (mm110)
REVERT: C  138 ASN cc_start: 0.9122 (m-40) cc_final: 0.8883 (m110)
REVERT: D    3 GLN cc_start: 0.8888 (mm110) cc_final: 0.8525 (mp10)
REVERT: D  154 CYS cc_start: 0.5395 (m) cc_final: 0.4407 (m)
REVERT: D  178 HIS cc_start: 0.8772 (m90) cc_final: 0.8417 (m90)
REVERT: H    3 GLN cc_start: 0.8998 (mm110) cc_final: 0.8616 (mm-40)
REVERT: H   48 MET cc_start: 0.7305 (pmm) cc_final: 0.7102 (pmm)
REVERT: H  144 CYS cc_start: 0.4397 (m) cc_final: 0.4065 (m)
REVERT: L   41 TRP cc_start: 0.8705 (m100) cc_final: 0.7960 (m100)
REVERT: L  142 LEU cc_start: 0.9334 (tp) cc_final: 0.9133 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1959
  time to fit residues: 49.8990
Evaluate side-chains
  126 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 24 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 2 optimal weight:   30.0000
   chunk 33 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 115 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 34 optimal weight:    8.9990
   overall best weight:    4.3386

-------------------------------------------------------------------------------
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  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 164 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.079297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.060603 restraints weight = 53475.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.062623 restraints weight = 27298.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.063949 restraints weight = 17486.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    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 = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9594  Z= 0.218
  Angle     :  0.701   8.563  13061  Z= 0.359
  Chirality :  0.045   0.161   1466
  Planarity :  0.005   0.061   1671
  Dihedral  :  5.816  55.925   1374
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.52 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  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: -0.84 (0.24), residues: 1209
  helix: -0.76 (0.41), residues: 148
  sheet:  0.36 (0.26), residues: 417
  loop : -1.13 (0.25), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP H  47 
 HIS   0.008   0.001   HIS C 198 
 PHE   0.018   0.002   PHE B 377 
 TYR   0.039   0.002   TYR L 102 
 ARG   0.003   0.000   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00205 (    1)
  link_NAG-ASN         : angle       1.45186 (    3)
  link_BETA1-4         : bond        0.00502 (    2)
  link_BETA1-4         : angle       1.83889 (    6)
  hydrogen bonds       : bond        0.03391 (  329)
  hydrogen bonds       : angle       5.91884 (  948)
  SS BOND              : bond        0.00448 (   12)
  SS BOND              : angle       1.58175 (   24)
  covalent geometry    : bond        0.00482 ( 9579)
  covalent geometry    : angle       0.69739 (13028)

*********************** 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
  142 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.7007 (ppp) cc_final: 0.6699 (ppp)
REVERT: A   52 HIS cc_start: 0.9264 (m90) cc_final: 0.8845 (m90)
REVERT: A   61 GLU cc_start: 0.9302 (mp0) cc_final: 0.8979 (pm20)
REVERT: A   62 ILE cc_start: 0.8850 (pt) cc_final: 0.8331 (pt)
REVERT: A   85 HIS cc_start: 0.8883 (m90) cc_final: 0.8638 (m90)
REVERT: A   90 THR cc_start: 0.7855 (t) cc_final: 0.7563 (p)
REVERT: B  498 GLN cc_start: 0.8201 (mm110) cc_final: 0.7973 (mm110)
REVERT: D  154 CYS cc_start: 0.5454 (m) cc_final: 0.4335 (m)
REVERT: D  178 HIS cc_start: 0.8825 (m90) cc_final: 0.8440 (m90)
REVERT: H    3 GLN cc_start: 0.9107 (mm110) cc_final: 0.8713 (mm-40)
REVERT: H  144 CYS cc_start: 0.4374 (m) cc_final: 0.3812 (m)
REVERT: L   41 TRP cc_start: 0.8696 (m100) cc_final: 0.8047 (m100)
REVERT: L  142 LEU cc_start: 0.9353 (tp) cc_final: 0.8880 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2086
  time to fit residues: 43.3839
Evaluate side-chains
  110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 106 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 52 optimal weight:    8.9990
   chunk 95 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 116 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.079141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.060595 restraints weight = 52420.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.062570 restraints weight = 27079.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.063876 restraints weight = 17478.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    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 = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9594  Z= 0.193
  Angle     :  0.689   9.024  13061  Z= 0.353
  Chirality :  0.045   0.249   1466
  Planarity :  0.005   0.061   1671
  Dihedral  :  5.766  55.811   1374
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.52 %
    Favored  : 91.40 %
  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: -0.88 (0.24), residues: 1209
  helix: -0.79 (0.40), residues: 148
  sheet:  0.29 (0.26), residues: 418
  loop : -1.13 (0.25), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 168 
 HIS   0.007   0.001   HIS C 198 
 PHE   0.018   0.002   PHE C  72 
 TYR   0.032   0.002   TYR L 102 
 ARG   0.004   0.000   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00081 (    1)
  link_NAG-ASN         : angle       1.25069 (    3)
  link_BETA1-4         : bond        0.00517 (    2)
  link_BETA1-4         : angle       1.83440 (    6)
  hydrogen bonds       : bond        0.03332 (  329)
  hydrogen bonds       : angle       5.87847 (  948)
  SS BOND              : bond        0.00470 (   12)
  SS BOND              : angle       2.05101 (   24)
  covalent geometry    : bond        0.00432 ( 9579)
  covalent geometry    : angle       0.68257 (13028)

*********************** 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
  147 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9008 (p) cc_final: 0.8133 (p)
REVERT: A   52 HIS cc_start: 0.9291 (m90) cc_final: 0.9016 (m90)
REVERT: A   61 GLU cc_start: 0.9266 (mp0) cc_final: 0.8958 (pm20)
REVERT: A   62 ILE cc_start: 0.8889 (pt) cc_final: 0.8360 (pt)
REVERT: A   82 THR cc_start: 0.9235 (p) cc_final: 0.8104 (p)
REVERT: A   90 THR cc_start: 0.7814 (t) cc_final: 0.7499 (p)
REVERT: D    3 GLN cc_start: 0.8766 (mm110) cc_final: 0.8445 (mp10)
REVERT: D  143 LYS cc_start: 0.6562 (pttt) cc_final: 0.6067 (tppt)
REVERT: D  154 CYS cc_start: 0.5690 (m) cc_final: 0.4588 (m)
REVERT: D  178 HIS cc_start: 0.8791 (m90) cc_final: 0.8376 (m90)
REVERT: H    3 GLN cc_start: 0.9074 (mm110) cc_final: 0.8711 (mm-40)
REVERT: H  144 CYS cc_start: 0.4574 (m) cc_final: 0.4016 (m)
REVERT: H  150 PHE cc_start: 0.8310 (t80) cc_final: 0.8030 (t80)
REVERT: L   31 TYR cc_start: 0.6547 (t80) cc_final: 0.6331 (t80)
REVERT: L   41 TRP cc_start: 0.8719 (m100) cc_final: 0.8080 (m100)
REVERT: L  142 LEU cc_start: 0.9336 (tp) cc_final: 0.8869 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2149
  time to fit residues: 44.7615
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  : 1.167 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 90 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9990
   chunk 104 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 115 optimal weight:    9.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.080455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.062968 restraints weight = 53434.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.065095 restraints weight = 24199.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.065987 restraints weight = 14965.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    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 = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9594  Z= 0.145
  Angle     :  0.668   8.379  13061  Z= 0.342
  Chirality :  0.045   0.238   1466
  Planarity :  0.005   0.059   1671
  Dihedral  :  5.582  55.350   1374
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.94 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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: -0.78 (0.41), residues: 147
  sheet:  0.28 (0.25), residues: 423
  loop : -1.05 (0.25), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 168 
 HIS   0.005   0.001   HIS C 198 
 PHE   0.021   0.002   PHE D 106 
 TYR   0.022   0.001   TYR L 102 
 ARG   0.004   0.000   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       1.07729 (    3)
  link_BETA1-4         : bond        0.00294 (    2)
  link_BETA1-4         : angle       1.70082 (    6)
  hydrogen bonds       : bond        0.03187 (  329)
  hydrogen bonds       : angle       5.74390 (  948)
  SS BOND              : bond        0.00418 (   12)
  SS BOND              : angle       1.91066 (   24)
  covalent geometry    : bond        0.00331 ( 9579)
  covalent geometry    : angle       0.66300 (13028)

*********************** 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
  156 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.9273 (m90) cc_final: 0.8958 (m90)
REVERT: A   61 GLU cc_start: 0.9211 (mp0) cc_final: 0.8986 (mm-30)
REVERT: A   82 THR cc_start: 0.9109 (p) cc_final: 0.8252 (p)
REVERT: A   90 THR cc_start: 0.7782 (t) cc_final: 0.7466 (p)
REVERT: B  421 TYR cc_start: 0.8648 (m-80) cc_final: 0.8183 (m-80)
REVERT: D    3 GLN cc_start: 0.8745 (mm110) cc_final: 0.8427 (mp10)
REVERT: D  143 LYS cc_start: 0.6510 (pttt) cc_final: 0.6025 (tppt)
REVERT: D  154 CYS cc_start: 0.5372 (m) cc_final: 0.4350 (m)
REVERT: D  178 HIS cc_start: 0.8728 (m90) cc_final: 0.8326 (m90)
REVERT: H    3 GLN cc_start: 0.9061 (mm110) cc_final: 0.8698 (mm-40)
REVERT: H  144 CYS cc_start: 0.3910 (m) cc_final: 0.3455 (m)
REVERT: H  150 PHE cc_start: 0.8253 (t80) cc_final: 0.7908 (t80)
REVERT: H  213 LYS cc_start: 0.6326 (tptm) cc_final: 0.5956 (tptp)
REVERT: L   31 TYR cc_start: 0.6560 (t80) cc_final: 0.6314 (t80)
REVERT: L   41 TRP cc_start: 0.8719 (m100) cc_final: 0.8064 (m100)
REVERT: L  142 LEU cc_start: 0.9344 (tp) cc_final: 0.8870 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1941
  time to fit residues: 43.8669
Evaluate side-chains
  123 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 116 optimal weight:    5.9990
   chunk 114 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:   30.0000
   chunk 70 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 111 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    5.1788

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.077135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.058840 restraints weight = 53890.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.060696 restraints weight = 27865.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.061973 restraints weight = 18103.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    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 = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   9594  Z= 0.256
  Angle     :  0.752   9.083  13061  Z= 0.386
  Chirality :  0.047   0.220   1466
  Planarity :  0.006   0.112   1671
  Dihedral  :  6.090  55.747   1374
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.18 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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: -1.12 (0.24), residues: 1209
  helix: -0.87 (0.40), residues: 148
  sheet: -0.02 (0.25), residues: 426
  loop : -1.20 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP D 168 
 HIS   0.010   0.002   HIS C 198 
 PHE   0.020   0.003   PHE B 377 
 TYR   0.030   0.002   TYR L 102 
 ARG   0.004   0.001   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00307 (    1)
  link_NAG-ASN         : angle       1.71433 (    3)
  link_BETA1-4         : bond        0.00491 (    2)
  link_BETA1-4         : angle       1.94917 (    6)
  hydrogen bonds       : bond        0.03634 (  329)
  hydrogen bonds       : angle       6.16439 (  948)
  SS BOND              : bond        0.00587 (   12)
  SS BOND              : angle       2.16449 (   24)
  covalent geometry    : bond        0.00565 ( 9579)
  covalent geometry    : angle       0.74567 (13028)

*********************** 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
  138 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.8977 (p) cc_final: 0.8044 (p)
REVERT: A   52 HIS cc_start: 0.9264 (m90) cc_final: 0.9023 (m90)
REVERT: A   61 GLU cc_start: 0.9283 (mp0) cc_final: 0.8959 (pm20)
REVERT: A   85 HIS cc_start: 0.8944 (m90) cc_final: 0.8734 (m90)
REVERT: A   90 THR cc_start: 0.7827 (t) cc_final: 0.7505 (p)
REVERT: B  421 TYR cc_start: 0.8884 (m-80) cc_final: 0.8350 (m-80)
REVERT: D  143 LYS cc_start: 0.6573 (pttt) cc_final: 0.6078 (tppt)
REVERT: D  154 CYS cc_start: 0.5899 (m) cc_final: 0.5141 (m)
REVERT: D  168 TRP cc_start: 0.8464 (m-10) cc_final: 0.8118 (m-10)
REVERT: D  178 HIS cc_start: 0.8755 (m90) cc_final: 0.8192 (m90)
REVERT: D  203 LEU cc_start: 0.8600 (mm) cc_final: 0.8331 (tt)
REVERT: H    3 GLN cc_start: 0.9127 (mm110) cc_final: 0.8752 (mm-40)
REVERT: H  144 CYS cc_start: 0.4380 (m) cc_final: 0.3763 (m)
REVERT: H  150 PHE cc_start: 0.8415 (t80) cc_final: 0.8072 (t80)
REVERT: L   31 TYR cc_start: 0.6726 (t80) cc_final: 0.6427 (t80)
REVERT: L   41 TRP cc_start: 0.8803 (m100) cc_final: 0.8169 (m100)
REVERT: L  142 LEU cc_start: 0.9388 (tp) cc_final: 0.8861 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2007
  time to fit residues: 39.9909
Evaluate side-chains
  109 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 69 optimal weight:   30.0000
   chunk 42 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 56 optimal weight:    0.2980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3603 r_free = 0.3603 target = 0.079974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.062305 restraints weight = 52671.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.064452 restraints weight = 23722.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.065444 restraints weight = 14344.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    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 = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9594  Z= 0.128
  Angle     :  0.694   8.398  13061  Z= 0.353
  Chirality :  0.046   0.221   1466
  Planarity :  0.006   0.084   1671
  Dihedral  :  5.569  55.660   1374
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.28 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  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: -0.83 (0.24), residues: 1209
  helix: -0.73 (0.41), residues: 148
  sheet:  0.30 (0.25), residues: 408
  loop : -1.06 (0.26), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP H 158 
 HIS   0.004   0.001   HIS C 198 
 PHE   0.023   0.002   PHE C 118 
 TYR   0.018   0.001   TYR L 102 
 ARG   0.005   0.000   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       1.02601 (    3)
  link_BETA1-4         : bond        0.00385 (    2)
  link_BETA1-4         : angle       1.64558 (    6)
  hydrogen bonds       : bond        0.03223 (  329)
  hydrogen bonds       : angle       5.81220 (  948)
  SS BOND              : bond        0.00428 (   12)
  SS BOND              : angle       2.39499 (   24)
  covalent geometry    : bond        0.00293 ( 9579)
  covalent geometry    : angle       0.68662 (13028)

*********************** 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
  158 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.8937 (p) cc_final: 0.7955 (p)
REVERT: A   61 GLU cc_start: 0.9260 (mp0) cc_final: 0.8971 (pm20)
REVERT: A   82 THR cc_start: 0.9133 (p) cc_final: 0.8894 (t)
REVERT: B  406 GLU cc_start: 0.8743 (mp0) cc_final: 0.8332 (mp0)
REVERT: B  421 TYR cc_start: 0.8910 (m-80) cc_final: 0.8228 (m-80)
REVERT: C   24 ARG cc_start: 0.8809 (mtp180) cc_final: 0.8471 (tpp80)
REVERT: D  143 LYS cc_start: 0.6617 (pttt) cc_final: 0.6188 (tppt)
REVERT: D  154 CYS cc_start: 0.5433 (m) cc_final: 0.4663 (m)
REVERT: D  168 TRP cc_start: 0.8440 (m-10) cc_final: 0.8146 (m-10)
REVERT: D  178 HIS cc_start: 0.8742 (m90) cc_final: 0.8153 (m90)
REVERT: H    3 GLN cc_start: 0.9024 (mm110) cc_final: 0.8664 (mm-40)
REVERT: H  150 PHE cc_start: 0.8264 (t80) cc_final: 0.7919 (t80)
REVERT: L   31 TYR cc_start: 0.6637 (t80) cc_final: 0.6307 (t80)
REVERT: L   41 TRP cc_start: 0.8670 (m100) cc_final: 0.7707 (m100)
REVERT: L  142 LEU cc_start: 0.9366 (tp) cc_final: 0.8821 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2339
  time to fit residues: 52.6947
Evaluate side-chains
  129 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
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:    0.0010
   chunk 86 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 104 optimal weight:    8.9990
   chunk 109 optimal weight:    9.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    2.0988

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.079887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.061257 restraints weight = 53996.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.063266 restraints weight = 27325.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.064615 restraints weight = 17492.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    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 = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9594  Z= 0.137
  Angle     :  0.682   8.111  13061  Z= 0.345
  Chirality :  0.046   0.204   1466
  Planarity :  0.005   0.075   1671
  Dihedral  :  5.434  54.954   1374
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.28 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.77 (0.25), residues: 1209
  helix: -0.74 (0.41), residues: 149
  sheet:  0.34 (0.26), residues: 410
  loop : -1.00 (0.26), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D 168 
 HIS   0.006   0.001   HIS A  52 
 PHE   0.020   0.002   PHE C 118 
 TYR   0.019   0.001   TYR L 102 
 ARG   0.004   0.000   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00052 (    1)
  link_NAG-ASN         : angle       0.96888 (    3)
  link_BETA1-4         : bond        0.00357 (    2)
  link_BETA1-4         : angle       1.63199 (    6)
  hydrogen bonds       : bond        0.03200 (  329)
  hydrogen bonds       : angle       5.67226 (  948)
  SS BOND              : bond        0.00518 (   12)
  SS BOND              : angle       1.91355 (   24)
  covalent geometry    : bond        0.00317 ( 9579)
  covalent geometry    : angle       0.67639 (13028)

********************** 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
  161 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9031 (p) cc_final: 0.8357 (p)
REVERT: A   61 GLU cc_start: 0.9307 (mp0) cc_final: 0.9017 (pm20)
REVERT: A   82 THR cc_start: 0.9192 (p) cc_final: 0.8541 (p)
REVERT: B  402 ILE cc_start: 0.9210 (tp) cc_final: 0.8745 (pt)
REVERT: B  406 GLU cc_start: 0.8793 (mp0) cc_final: 0.8414 (mp0)
REVERT: B  421 TYR cc_start: 0.8826 (m-80) cc_final: 0.8167 (m-80)
REVERT: D  143 LYS cc_start: 0.6614 (pttt) cc_final: 0.6175 (tppt)
REVERT: D  154 CYS cc_start: 0.5396 (m) cc_final: 0.4714 (m)
REVERT: D  168 TRP cc_start: 0.8412 (m-10) cc_final: 0.8077 (m-10)
REVERT: D  178 HIS cc_start: 0.8669 (m90) cc_final: 0.8097 (m90)
REVERT: D  203 LEU cc_start: 0.8605 (mm) cc_final: 0.8387 (tt)
REVERT: H    3 GLN cc_start: 0.9047 (mm110) cc_final: 0.8682 (mm-40)
REVERT: H  144 CYS cc_start: 0.4043 (m) cc_final: 0.3646 (m)
REVERT: H  149 TYR cc_start: 0.7405 (p90) cc_final: 0.7166 (p90)
REVERT: H  150 PHE cc_start: 0.8315 (t80) cc_final: 0.7900 (t80)
REVERT: L   31 TYR cc_start: 0.6666 (t80) cc_final: 0.6385 (t80)
REVERT: L   41 TRP cc_start: 0.8670 (m100) cc_final: 0.7854 (m100)
REVERT: L  142 LEU cc_start: 0.9377 (tp) cc_final: 0.8865 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2061
  time to fit residues: 49.1265
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  : 1.164 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 10 optimal weight:   50.0000
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 106 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.081931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.062358 restraints weight = 71948.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.064734 restraints weight = 32371.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.066308 restraints weight = 19438.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    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 = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9594  Z= 0.114
  Angle     :  0.674   8.201  13061  Z= 0.341
  Chirality :  0.045   0.204   1466
  Planarity :  0.005   0.060   1671
  Dihedral  :  5.200  55.120   1374
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.78 %
    Favored  : 93.13 %
  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: -0.66 (0.25), residues: 1209
  helix: -0.73 (0.41), residues: 149
  sheet:  0.49 (0.26), residues: 422
  loop : -1.00 (0.25), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP H  83 
 HIS   0.006   0.001   HIS A  52 
 PHE   0.021   0.001   PHE C 118 
 TYR   0.015   0.001   TYR L 102 
 ARG   0.003   0.000   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    1)
  link_NAG-ASN         : angle       0.69826 (    3)
  link_BETA1-4         : bond        0.00375 (    2)
  link_BETA1-4         : angle       1.52163 (    6)
  hydrogen bonds       : bond        0.03110 (  329)
  hydrogen bonds       : angle       5.43091 (  948)
  SS BOND              : bond        0.00414 (   12)
  SS BOND              : angle       1.63281 (   24)
  covalent geometry    : bond        0.00260 ( 9579)
  covalent geometry    : angle       0.67034 (13028)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3919.15 seconds
wall clock time: 70 minutes 21.73 seconds (4221.73 seconds total)