Starting phenix.real_space_refine
on Wed May 14 13:37:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tcg_41154/05_2025/8tcg_41154_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tcg_41154/05_2025/8tcg_41154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tcg_41154/05_2025/8tcg_41154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tcg_41154/05_2025/8tcg_41154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tcg_41154/05_2025/8tcg_41154_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tcg_41154/05_2025/8tcg_41154_trim.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
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: 7
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     Mn      3      7.51       5
     S      28      5.16       5
     C    3763      2.51       5
     N     985      2.21       5
     O    1162      1.98       5
     H    5652      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11597
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 6564
          Classifications: {'peptide': 440}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 418}
    Chain: "B"
      Number of atoms: 3761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 3761
          Classifications: {'peptide': 242}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 229}
    Chain: "C"
      Number of atoms: 1187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1187
          Classifications: {'peptide': 72}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 32
          Unusual residues: {' CA': 4, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.44, per 1000 atoms: 0.56
  Number of scatterers: 11597
  At special positions: 0
  Unit cell: (75.174, 102.102, 84.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      3     24.99
     Ca      4     19.99
     S      28     16.00
     O    1162      8.00
     N     985      7.00
     C    3763      6.00
     H    5652      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 108 " - pdb=" SG  CYS A 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 155 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 401 " - pdb=" SG  CYS B 270 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 180 " - pdb=" SG  CYS B 187 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 235 " - pdb=" SG  CYS B 276 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C   3 " - pdb=" SG  CYS C  73 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-6
      " BMA D   3 " - " MAN D   4 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A2005 " - " ASN A  44 "
      " NAG A2006 " - " ASN A 260 "
      " NAG D   1 " - " ASN A 266 "
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 901.4 milliseconds
  

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1372

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 13 sheets defined
      22.1% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 188 through 194
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 428 through 430
      No H-bonds generated for 'chain 'A' and resid 428 through 430'
    Processing helix  chain 'B' and resid 125 through 129
    Processing helix  chain 'B' and resid 131 through 147
      removed outlier: 3.729A  pdb=" N   SER B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 178
    Processing helix  chain 'B' and resid 202 through 212
      removed outlier: 3.570A  pdb=" N   ASN B 212 " --> pdb=" O   GLU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 235
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 261 through 267
      removed outlier: 3.767A  pdb=" N   LEU B 265 " --> pdb=" O   ASP B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 305
    Processing helix  chain 'B' and resid 314 through 326
      removed outlier: 4.500A  pdb=" N   HIS B 319 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   LEU B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 350
      removed outlier: 3.590A  pdb=" N   LEU B 344 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU B 346 " --> pdb=" O   ASN B 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 29
    Processing helix  chain 'C' and resid 38 through 40
      No H-bonds generated for 'chain 'C' and resid 38 through 40'
    Processing helix  chain 'C' and resid 51 through 54
    Processing helix  chain 'C' and resid 55 through 64
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12
      removed outlier: 4.213A  pdb=" N   ARG A 437 " --> pdb=" O   ASP A   4 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   ASP A   6 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
      removed outlier: 10.919A  pdb=" N   LEU A 435 " --> pdb=" O   ASP A   6 " (cutoff:3.500A)
      removed outlier: 10.059A  pdb=" N   ALA A 433 " --> pdb=" O   PRO A   8 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   ASP A 422 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26
    Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81
      removed outlier: 7.014A  pdb=" N   ASP A  84 " --> pdb=" O   TYR A  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88
      removed outlier: 3.508A  pdb=" N   HIS A 113 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101
      removed outlier: 4.075A  pdb=" N   SER A  97 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163
      removed outlier: 3.705A  pdb=" N   SER A 160 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229
      removed outlier: 6.571A  pdb=" N   VAL A 253 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   ASN A 266 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ILE A 255 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283
    Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303
    Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348
      removed outlier: 6.306A  pdb=" N   ILE A 344 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   ALA A 361 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   ALA A 359 " --> pdb=" O   PRO A 346 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLY A 348 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379
    Processing sheet with id=AB3, first strand: chain 'B' and resid 193 through 200
      removed outlier: 5.380A  pdb=" N   HIS B 195 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   SER B 159 " --> pdb=" O   HIS B 195 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   LEU B 199 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   LEU B 155 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 37
      removed outlier: 3.536A  pdb=" N   ASN C  33 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    573 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: 4.20

  Time building geometry restraints manager: 3.93 seconds

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

  Histogram of bond lengths:
        0.95 -     1.13: 5652
        1.13 -     1.31: 1052
        1.31 -     1.49: 2547
        1.49 -     1.67: 2431
        1.67 -     1.84: 42
  Bond restraints: 11724
  Sorted by residual:
  bond pdb=" NE1 TRP B 241 "
       pdb=" HE1 TRP B 241 "
    ideal  model  delta    sigma   weight residual
    0.860  1.034 -0.174 2.00e-02 2.50e+03 7.54e+01
  bond pdb=" NE1 TRP A 395 "
       pdb=" HE1 TRP A 395 "
    ideal  model  delta    sigma   weight residual
    0.860  1.030 -0.170 2.00e-02 2.50e+03 7.26e+01
  bond pdb=" CE2 PHE A   1 "
       pdb=" HE2 PHE A   1 "
    ideal  model  delta    sigma   weight residual
    0.930  1.096 -0.166 2.00e-02 2.50e+03 6.90e+01
  bond pdb=" NH2 ARG C  10 "
       pdb="HH22 ARG C  10 "
    ideal  model  delta    sigma   weight residual
    0.860  1.026 -0.166 2.00e-02 2.50e+03 6.88e+01
  bond pdb=" CD2 PHE A 177 "
       pdb=" HD2 PHE A 177 "
    ideal  model  delta    sigma   weight residual
    0.930  1.096 -0.166 2.00e-02 2.50e+03 6.87e+01
  ... (remaining 11719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    15.36: 21097
       15.36 -    30.71: 2
       30.71 -    46.07: 0
       46.07 -    61.42: 0
       61.42 -    76.78: 1
  Bond angle restraints: 21100
  Sorted by residual:
  angle pdb=" CB  ASN C  39 "
        pdb=" CG  ASN C  39 "
        pdb=" OD1 ASN C  39 "
      ideal   model   delta    sigma   weight residual
     120.80   44.02   76.78 2.00e+00 2.50e-01 1.47e+03
  angle pdb=" OD1 ASN C  39 "
        pdb=" CG  ASN C  39 "
        pdb=" ND2 ASN C  39 "
      ideal   model   delta    sigma   weight residual
     122.60  138.21  -15.61 1.00e+00 1.00e+00 2.44e+02
  angle pdb=" CB  ASN C  39 "
        pdb=" CG  ASN C  39 "
        pdb=" ND2 ASN C  39 "
      ideal   model   delta    sigma   weight residual
     116.40   94.20   22.20 1.50e+00 4.44e-01 2.19e+02
  angle pdb=" C   GLY A 173 "
        pdb=" N   PRO A 174 "
        pdb=" CA  PRO A 174 "
      ideal   model   delta    sigma   weight residual
     119.56  127.93   -8.37 1.02e+00 9.61e-01 6.74e+01
  angle pdb=" C   ALA A 297 "
        pdb=" N   PRO A 298 "
        pdb=" CA  PRO A 298 "
      ideal   model   delta    sigma   weight residual
     119.56  127.79   -8.23 1.02e+00 9.61e-01 6.50e+01
  ... (remaining 21095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.69: 5408
       21.69 -    43.38: 185
       43.38 -    65.07: 55
       65.07 -    86.76: 13
       86.76 -   108.45: 5
  Dihedral angle restraints: 5666
    sinusoidal: 3087
      harmonic: 2579
  Sorted by residual:
  dihedral pdb=" CB  CYS A 142 "
           pdb=" SG  CYS A 142 "
           pdb=" SG  CYS A 155 "
           pdb=" CB  CYS A 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.64   54.36     1      1.00e+01 1.00e-02 4.01e+01
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -179.74  108.45     1      3.00e+01 1.11e-03 1.40e+01
  dihedral pdb=" CA  VAL A 243 "
           pdb=" C   VAL A 243 "
           pdb=" N   PRO A 244 "
           pdb=" CA  PRO A 244 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.33  -18.67     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 616
       0.072 -    0.144: 215
       0.144 -    0.217: 55
       0.217 -    0.289: 8
       0.289 -    0.361: 7
  Chirality restraints: 901
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.51    0.11 2.00e-02 2.50e+03 2.80e+01
  chirality pdb=" C1  BMA D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.45    0.05 2.00e-02 2.50e+03 6.71e+00
  chirality pdb=" C1  MAN D   4 "
            pdb=" O6  BMA D   3 "
            pdb=" C2  MAN D   4 "
            pdb=" O5  MAN D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.45   -0.05 2.00e-02 2.50e+03 6.66e+00
  ... (remaining 898 not shown)

  Planarity restraints: 1797
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 395 "   -0.068 2.00e-02 2.50e+03   2.51e-02 2.53e+01
        pdb=" CG  TRP A 395 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 395 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 395 "    0.019 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 395 "    0.019 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 395 "    0.014 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 395 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 395 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 395 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 395 "   -0.016 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 395 "   -0.007 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 395 "    0.018 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 395 "    0.035 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 395 "   -0.015 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 395 "    0.004 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 395 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 114 "   -0.062 2.00e-02 2.50e+03   2.35e-02 2.20e+01
        pdb=" CG  TRP A 114 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 114 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 114 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 114 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 114 "    0.021 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 114 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 114 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 114 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 114 "   -0.013 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 114 "   -0.019 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 114 "    0.001 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 114 "    0.030 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 114 "   -0.007 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 114 "   -0.008 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 114 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 266 "    0.031 2.00e-02 2.50e+03   3.82e-02 2.19e+01
        pdb=" CG  ASN A 266 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 266 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 266 "   -0.036 2.00e-02 2.50e+03
        pdb="HD21 ASN A 266 "   -0.042 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "    0.067 2.00e-02 2.50e+03
  ... (remaining 1794 not shown)

  Histogram of nonbonded interaction distances:
        1.04 -     1.75: 29
        1.75 -     2.46: 5801
        2.46 -     3.17: 37052
        3.17 -     3.89: 48022
        3.89 -     4.60: 76469
  Nonbonded interactions: 167373
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C  39 "
            pdb=" HB2 ASN C  39 "
     model   vdw
     1.037 2.096
  nonbonded pdb=" O   SER B 182 "
            pdb="HH22 ARG C  63 "
     model   vdw
     1.655 2.450
  nonbonded pdb=" OD2 ASP A  73 "
            pdb=" HZ3 LYS A  89 "
     model   vdw
     1.658 2.450
  nonbonded pdb="HD21 ASN A 266 "
            pdb=" O5  NAG D   1 "
     model   vdw
     1.663 1.960
  nonbonded pdb="HD21 ASN A 260 "
            pdb=" O5  NAG A2006 "
     model   vdw
     1.663 1.960
  ... (remaining 167368 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.840
  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:             0.190
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     29.110
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.074   6085  Z= 0.739
  Angle     :  1.690  76.776   8257  Z= 1.081
  Chirality :  0.083   0.361    901
  Planarity :  0.006   0.034   1078
  Dihedral  : 12.479 108.448   2300
  Min Nonbonded Distance : 1.790

Molprobity Statistics.
  All-atom Clashscore : 0.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.27 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.10 (0.29), residues: 748
  helix: -0.81 (0.41), residues: 117
  sheet:  0.41 (0.34), residues: 206
  loop :  0.29 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.009   TRP A 114 
 HIS   0.005   0.001   HIS B 195 
 PHE   0.021   0.004   PHE B 311 
 TYR   0.031   0.005   TYR B 120 
 ARG   0.004   0.001   ARG A 245 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.06769 (    3)
  link_NAG-ASN         : angle       2.23795 (    9)
  link_ALPHA1-6        : bond        0.06312 (    1)
  link_ALPHA1-6        : angle       2.50149 (    3)
  link_BETA1-4         : bond        0.06388 (    2)
  link_BETA1-4         : angle       4.31029 (    6)
  hydrogen bonds       : bond        0.17491 (  221)
  hydrogen bonds       : angle       8.77155 (  573)
  SS BOND              : bond        0.01551 (    7)
  SS BOND              : angle       3.59193 (   14)
  covalent geometry    : bond        0.01353 ( 6072)
  covalent geometry    : angle       1.68087 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.953 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8953 (mp) cc_final: 0.8750 (mt)
REVERT: A   75 THR cc_start: 0.6994 (p) cc_final: 0.6789 (t)
REVERT: A  114 TRP cc_start: 0.7678 (t60) cc_final: 0.7292 (t60)
REVERT: B  128 MET cc_start: 0.7740 (mmm) cc_final: 0.7186 (mmm)
REVERT: C   39 ASN cc_start: 0.5563 (m110) cc_final: 0.4991 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 0.5144
  time to fit residues: 110.4165
Evaluate side-chains
  91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 317 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.116931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.103712 restraints weight = 33478.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.99
r_work: 0.3477 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   6085  Z= 0.195
  Angle     :  0.900  35.315   8257  Z= 0.427
  Chirality :  0.049   0.303    901
  Planarity :  0.005   0.056   1078
  Dihedral  :  8.325  68.657    936
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.48 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.33 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  0.22 (0.30), residues: 748
  helix:  0.35 (0.46), residues: 122
  sheet:  0.20 (0.32), residues: 238
  loop :  0.20 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 395 
 HIS   0.003   0.001   HIS C  49 
 PHE   0.017   0.002   PHE C  64 
 TYR   0.013   0.002   TYR B 351 
 ARG   0.006   0.001   ARG C  63 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01283 (    3)
  link_NAG-ASN         : angle      16.67573 (    9)
  link_ALPHA1-6        : bond        0.00440 (    1)
  link_ALPHA1-6        : angle       1.93135 (    3)
  link_BETA1-4         : bond        0.00350 (    2)
  link_BETA1-4         : angle       3.87463 (    6)
  hydrogen bonds       : bond        0.05670 (  221)
  hydrogen bonds       : angle       7.48892 (  573)
  SS BOND              : bond        0.00551 (    7)
  SS BOND              : angle       2.63263 (   14)
  covalent geometry    : bond        0.00426 ( 6072)
  covalent geometry    : angle       0.69565 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.902 
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: symmetry clash
   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   75 THR cc_start: 0.7600 (p) cc_final: 0.7333 (t)
REVERT: A  114 TRP cc_start: 0.7937 (t60) cc_final: 0.7377 (t60)
REVERT: A  301 MET cc_start: 0.7887 (mtm) cc_final: 0.7642 (mtm)
REVERT: B  323 ASN cc_start: 0.9021 (m-40) cc_final: 0.8661 (m110)
  outliers start: 8
  outliers final: 4
  residues processed: 111
  average time/residue: 0.4285
  time to fit residues: 61.4241
Evaluate side-chains
  90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 ASP
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain C residue    4 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.113219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.099919 restraints weight = 34626.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 3.04
r_work: 0.3401 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6085  Z= 0.168
  Angle     :  0.831  37.278   8257  Z= 0.375
  Chirality :  0.046   0.218    901
  Planarity :  0.004   0.048   1078
  Dihedral  :  6.534  47.114    936
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  9.86 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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: -0.11 (0.30), residues: 748
  helix:  0.89 (0.47), residues: 120
  sheet: -0.27 (0.32), residues: 244
  loop : -0.11 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 395 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.015   0.001   PHE A 376 
 TYR   0.022   0.001   TYR B 321 
 ARG   0.006   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00399 (    3)
  link_NAG-ASN         : angle      17.44710 (    9)
  link_ALPHA1-6        : bond        0.00553 (    1)
  link_ALPHA1-6        : angle       1.62051 (    3)
  link_BETA1-4         : bond        0.00164 (    2)
  link_BETA1-4         : angle       2.44454 (    6)
  hydrogen bonds       : bond        0.04324 (  221)
  hydrogen bonds       : angle       6.76005 (  573)
  SS BOND              : bond        0.00948 (    7)
  SS BOND              : angle       2.57784 (   14)
  covalent geometry    : bond        0.00390 ( 6072)
  covalent geometry    : angle       0.58546 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.984 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 THR cc_start: 0.7829 (p) cc_final: 0.7603 (t)
REVERT: A  132 ASP cc_start: 0.8047 (t0) cc_final: 0.7586 (p0)
REVERT: B  323 ASN cc_start: 0.9088 (m-40) cc_final: 0.8825 (m110)
REVERT: C   49 HIS cc_start: 0.6174 (t70) cc_final: 0.5960 (t70)
  outliers start: 2
  outliers final: 2
  residues processed: 81
  average time/residue: 0.4213
  time to fit residues: 44.7831
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 ASP
Chi-restraints excluded: chain C residue    4 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.111245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.097913 restraints weight = 34774.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 3.05
r_work: 0.3375 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6085  Z= 0.160
  Angle     :  0.805  37.228   8257  Z= 0.358
  Chirality :  0.046   0.222    901
  Planarity :  0.004   0.048   1078
  Dihedral  :  5.576  47.561    936
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 10.17 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.30), residues: 748
  helix:  1.00 (0.49), residues: 120
  sheet: -0.35 (0.33), residues: 237
  loop : -0.33 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 114 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.014   0.001   PHE A 376 
 TYR   0.015   0.001   TYR B 120 
 ARG   0.006   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00021 (    3)
  link_NAG-ASN         : angle      17.39076 (    9)
  link_ALPHA1-6        : bond        0.00070 (    1)
  link_ALPHA1-6        : angle       1.54352 (    3)
  link_BETA1-4         : bond        0.00044 (    2)
  link_BETA1-4         : angle       2.34500 (    6)
  hydrogen bonds       : bond        0.03911 (  221)
  hydrogen bonds       : angle       6.40845 (  573)
  SS BOND              : bond        0.00652 (    7)
  SS BOND              : angle       2.14191 (   14)
  covalent geometry    : bond        0.00370 ( 6072)
  covalent geometry    : angle       0.55416 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.945 
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  132 ASP cc_start: 0.7996 (t0) cc_final: 0.7720 (p0)
REVERT: B  323 ASN cc_start: 0.9164 (m-40) cc_final: 0.8931 (m110)
REVERT: C   49 HIS cc_start: 0.6272 (t70) cc_final: 0.6049 (t70)
  outliers start: 4
  outliers final: 3
  residues processed: 79
  average time/residue: 0.3739
  time to fit residues: 39.7465
Evaluate side-chains
  72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  325 ASP
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
A 182 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.110956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.097506 restraints weight = 35022.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 3.08
r_work: 0.3370 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.5166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6085  Z= 0.134
  Angle     :  0.785  37.495   8257  Z= 0.343
  Chirality :  0.045   0.205    901
  Planarity :  0.004   0.044   1078
  Dihedral  :  5.232  46.968    936
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.81 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.31), residues: 748
  helix:  0.93 (0.48), residues: 123
  sheet: -0.33 (0.33), residues: 244
  loop : -0.40 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 114 
 HIS   0.002   0.001   HIS C  31 
 PHE   0.014   0.001   PHE B 311 
 TYR   0.011   0.001   TYR B 321 
 ARG   0.006   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00151 (    3)
  link_NAG-ASN         : angle      17.56099 (    9)
  link_ALPHA1-6        : bond        0.00332 (    1)
  link_ALPHA1-6        : angle       1.40974 (    3)
  link_BETA1-4         : bond        0.00207 (    2)
  link_BETA1-4         : angle       1.85263 (    6)
  hydrogen bonds       : bond        0.03697 (  221)
  hydrogen bonds       : angle       6.25776 (  573)
  SS BOND              : bond        0.00533 (    7)
  SS BOND              : angle       1.90528 (   14)
  covalent geometry    : bond        0.00309 ( 6072)
  covalent geometry    : angle       0.52087 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.926 
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: B  323 ASN cc_start: 0.9241 (m-40) cc_final: 0.8940 (m110)
  outliers start: 8
  outliers final: 5
  residues processed: 77
  average time/residue: 0.3851
  time to fit residues: 39.4800
Evaluate side-chains
  72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 73 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 394 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.106414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.093360 restraints weight = 35649.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 3.02
r_work: 0.3301 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.5565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6085  Z= 0.236
  Angle     :  0.827  36.717   8257  Z= 0.378
  Chirality :  0.046   0.253    901
  Planarity :  0.005   0.050   1078
  Dihedral  :  5.700  48.559    936
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.40 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.30), residues: 748
  helix:  0.64 (0.46), residues: 124
  sheet: -0.42 (0.33), residues: 238
  loop : -0.79 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 114 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.026   0.002   PHE A 376 
 TYR   0.013   0.002   TYR A 420 
 ARG   0.007   0.001   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    3)
  link_NAG-ASN         : angle      17.10906 (    9)
  link_ALPHA1-6        : bond        0.00226 (    1)
  link_ALPHA1-6        : angle       1.61891 (    3)
  link_BETA1-4         : bond        0.00263 (    2)
  link_BETA1-4         : angle       2.55985 (    6)
  hydrogen bonds       : bond        0.04202 (  221)
  hydrogen bonds       : angle       6.34673 (  573)
  SS BOND              : bond        0.00549 (    7)
  SS BOND              : angle       1.92173 (   14)
  covalent geometry    : bond        0.00536 ( 6072)
  covalent geometry    : angle       0.59489 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.911 
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: symmetry clash
   revert: symmetry clash
REVERT: B  323 ASN cc_start: 0.9290 (m-40) cc_final: 0.9040 (m110)
  outliers start: 9
  outliers final: 7
  residues processed: 75
  average time/residue: 0.3713
  time to fit residues: 37.2436
Evaluate side-chains
  71 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  325 ASP
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 74 optimal weight:    0.3980
   chunk 41 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.108709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.095616 restraints weight = 35580.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 3.04
r_work: 0.3331 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.5710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6085  Z= 0.134
  Angle     :  0.789  37.287   8257  Z= 0.347
  Chirality :  0.045   0.212    901
  Planarity :  0.004   0.044   1078
  Dihedral  :  5.341  48.394    936
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.40 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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: -0.60 (0.30), residues: 748
  helix:  0.78 (0.48), residues: 123
  sheet: -0.37 (0.33), residues: 238
  loop : -0.74 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 114 
 HIS   0.001   0.000   HIS B 195 
 PHE   0.011   0.001   PHE A 376 
 TYR   0.010   0.001   TYR B 321 
 ARG   0.007   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00109 (    3)
  link_NAG-ASN         : angle      17.43888 (    9)
  link_ALPHA1-6        : bond        0.00543 (    1)
  link_ALPHA1-6        : angle       1.57533 (    3)
  link_BETA1-4         : bond        0.00152 (    2)
  link_BETA1-4         : angle       1.77510 (    6)
  hydrogen bonds       : bond        0.03678 (  221)
  hydrogen bonds       : angle       6.20274 (  573)
  SS BOND              : bond        0.00464 (    7)
  SS BOND              : angle       1.70921 (   14)
  covalent geometry    : bond        0.00310 ( 6072)
  covalent geometry    : angle       0.53284 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.870 
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: symmetry clash
REVERT: A  186 ASP cc_start: 0.8498 (t0) cc_final: 0.8230 (t0)
REVERT: B  323 ASN cc_start: 0.9322 (m-40) cc_final: 0.9111 (m110)
  outliers start: 9
  outliers final: 7
  residues processed: 73
  average time/residue: 0.3780
  time to fit residues: 36.8223
Evaluate side-chains
  72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 72 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.108759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.095602 restraints weight = 35134.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 3.03
r_work: 0.3335 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.5853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6085  Z= 0.141
  Angle     :  0.788  37.444   8257  Z= 0.346
  Chirality :  0.045   0.208    901
  Planarity :  0.004   0.039   1078
  Dihedral  :  5.205  46.084    936
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.04 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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: -0.65 (0.30), residues: 748
  helix:  0.72 (0.48), residues: 124
  sheet: -0.40 (0.33), residues: 238
  loop : -0.76 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 114 
 HIS   0.002   0.001   HIS A 113 
 PHE   0.013   0.001   PHE A 376 
 TYR   0.015   0.001   TYR A 139 
 ARG   0.007   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00074 (    3)
  link_NAG-ASN         : angle      17.51561 (    9)
  link_ALPHA1-6        : bond        0.00371 (    1)
  link_ALPHA1-6        : angle       1.51458 (    3)
  link_BETA1-4         : bond        0.00130 (    2)
  link_BETA1-4         : angle       1.87541 (    6)
  hydrogen bonds       : bond        0.03602 (  221)
  hydrogen bonds       : angle       6.06483 (  573)
  SS BOND              : bond        0.00488 (    7)
  SS BOND              : angle       1.65566 (   14)
  covalent geometry    : bond        0.00330 ( 6072)
  covalent geometry    : angle       0.52945 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.897 
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: symmetry clash
REVERT: B  323 ASN cc_start: 0.9340 (m-40) cc_final: 0.9139 (m110)
  outliers start: 6
  outliers final: 6
  residues processed: 74
  average time/residue: 0.3710
  time to fit residues: 36.7989
Evaluate side-chains
  75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0970
   overall best weight:    0.7978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.107863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.094632 restraints weight = 35233.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.05
r_work: 0.3322 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.6024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6085  Z= 0.162
  Angle     :  0.794  37.259   8257  Z= 0.351
  Chirality :  0.045   0.219    901
  Planarity :  0.004   0.043   1078
  Dihedral  :  5.245  44.453    936
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.40 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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: -0.72 (0.30), residues: 748
  helix:  0.61 (0.47), residues: 125
  sheet: -0.42 (0.32), residues: 246
  loop : -0.82 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 114 
 HIS   0.002   0.001   HIS A 113 
 PHE   0.016   0.001   PHE A 376 
 TYR   0.014   0.001   TYR A 139 
 ARG   0.009   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00098 (    3)
  link_NAG-ASN         : angle      17.42458 (    9)
  link_ALPHA1-6        : bond        0.00398 (    1)
  link_ALPHA1-6        : angle       1.56162 (    3)
  link_BETA1-4         : bond        0.00080 (    2)
  link_BETA1-4         : angle       1.95175 (    6)
  hydrogen bonds       : bond        0.03666 (  221)
  hydrogen bonds       : angle       6.01742 (  573)
  SS BOND              : bond        0.00533 (    7)
  SS BOND              : angle       1.58582 (   14)
  covalent geometry    : bond        0.00374 ( 6072)
  covalent geometry    : angle       0.54043 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  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: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.3754
  time to fit residues: 38.8591
Evaluate side-chains
  72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 30 optimal weight:    0.0370
   chunk 51 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0870
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
B 319 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.109005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.095688 restraints weight = 34875.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 3.05
r_work: 0.3338 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.6115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6085  Z= 0.117
  Angle     :  0.785  37.705   8257  Z= 0.340
  Chirality :  0.044   0.203    901
  Planarity :  0.004   0.043   1078
  Dihedral  :  5.009  42.431    936
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.35 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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: -0.57 (0.31), residues: 748
  helix:  0.83 (0.48), residues: 122
  sheet: -0.34 (0.32), residues: 246
  loop : -0.74 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 114 
 HIS   0.001   0.000   HIS B 195 
 PHE   0.012   0.001   PHE A 376 
 TYR   0.015   0.001   TYR A 139 
 ARG   0.010   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00118 (    3)
  link_NAG-ASN         : angle      17.63720 (    9)
  link_ALPHA1-6        : bond        0.00454 (    1)
  link_ALPHA1-6        : angle       1.50849 (    3)
  link_BETA1-4         : bond        0.00204 (    2)
  link_BETA1-4         : angle       1.64728 (    6)
  hydrogen bonds       : bond        0.03429 (  221)
  hydrogen bonds       : angle       5.91664 (  573)
  SS BOND              : bond        0.00475 (    7)
  SS BOND              : angle       1.45004 (   14)
  covalent geometry    : bond        0.00271 ( 6072)
  covalent geometry    : angle       0.52158 ( 8225)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.962 
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: symmetry clash
   revert: symmetry clash
REVERT: A  349 ASP cc_start: 0.7560 (t0) cc_final: 0.7043 (p0)
  outliers start: 6
  outliers final: 6
  residues processed: 74
  average time/residue: 0.3742
  time to fit residues: 37.0662
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0060
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0970
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.3794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.109328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.096340 restraints weight = 35177.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 3.03
r_work: 0.3345 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.6193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6085  Z= 0.106
  Angle     :  0.780  37.912   8257  Z= 0.336
  Chirality :  0.044   0.197    901
  Planarity :  0.004   0.043   1078
  Dihedral  :  4.789  39.779    936
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.04 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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: -0.49 (0.31), residues: 748
  helix:  0.91 (0.48), residues: 122
  sheet: -0.25 (0.33), residues: 246
  loop : -0.71 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 114 
 HIS   0.001   0.000   HIS B 258 
 PHE   0.010   0.001   PHE A 376 
 TYR   0.012   0.001   TYR A 139 
 ARG   0.009   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00118 (    3)
  link_NAG-ASN         : angle      17.76379 (    9)
  link_ALPHA1-6        : bond        0.00443 (    1)
  link_ALPHA1-6        : angle       1.47981 (    3)
  link_BETA1-4         : bond        0.00261 (    2)
  link_BETA1-4         : angle       1.62605 (    6)
  hydrogen bonds       : bond        0.03260 (  221)
  hydrogen bonds       : angle       5.81747 (  573)
  SS BOND              : bond        0.00403 (    7)
  SS BOND              : angle       1.36697 (   14)
  covalent geometry    : bond        0.00244 ( 6072)
  covalent geometry    : angle       0.50974 ( 8225)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5092.81 seconds
wall clock time: 88 minutes 13.85 seconds (5293.85 seconds total)