Starting phenix.real_space_refine
on Thu Mar  6 05:52:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ez7_28729/03_2025/8ez7_28729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ez7_28729/03_2025/8ez7_28729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ez7_28729/03_2025/8ez7_28729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ez7_28729/03_2025/8ez7_28729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ez7_28729/03_2025/8ez7_28729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ez7_28729/03_2025/8ez7_28729.cif"
  }
  resolution = 2.6
  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=   0.202
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      28      5.16       5
     C    3065      2.51       5
     N     845      2.21       5
     O     989      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4927
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 984
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
    Chain: "L"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 833
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 9, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 2996
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 372}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {'MAN': 1, 'NAG': 3}
          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
  Time building chain proxies: 4.25, per 1000 atoms: 0.86
  Number of scatterers: 4927
  At special positions: 0
  Unit cell: (95.4, 83.74, 89.04, 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      28     16.00
     O     989      8.00
     N     845      7.00
     C    3065      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS A 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 124 " - pdb=" SG  CYS A 129 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 175 " - pdb=" SG  CYS A 193 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 183 " - pdb=" SG  CYS A 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 289 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 318 " - pdb=" SG  CYS A 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 421 " - pdb=" SG  CYS A 447 " 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
    ALPHA1-2
      " MAN B   4 " - " MAN B   5 "
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A 502 " - " ASN A 146 "
      " NAG A 503 " - " ASN A 329 "
      " NAG A 504 " - " ASN A 234 "
      " NAG B   1 " - " ASN A 200 "
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 612.6 milliseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1120

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 12 sheets defined
      4.8% alpha, 45.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'L' and resid 29 through 31
      No H-bonds generated for 'chain 'L' and resid 29 through 31'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.744A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 110
      removed outlier: 3.585A  pdb=" N   ALA A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.547A  pdb=" N   ASN A 146 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.784A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.788A  pdb=" N   CYS H  92 " --> pdb=" O   TRP H 103 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TRP H 103 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ARG H  94 " --> pdb=" O   ASP H 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6
      removed outlier: 5.412A  pdb=" N   THR L  69 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 9.976A  pdb=" N   GLN L  27 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 9.627A  pdb=" N   SER L  67 " --> pdb=" O   GLN L  27 " (cutoff:3.500A)
      removed outlier: 11.239A  pdb=" N   LEU L  28 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 11.310A  pdb=" N   SER L  65 " --> pdb=" O   LEU L  28 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.090A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102
      removed outlier: 3.648A  pdb=" N   GLY A  96 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL A 445 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LYS A 102 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ILE A 443 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   ARG A 420 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 124
      removed outlier: 5.343A  pdb=" N   THR A 138 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 8.982A  pdb=" N   ARG A 118 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   GLN A 136 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   LEU A 134 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   VAL A 122 " --> pdb=" O   PHE A 132 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   PHE A 132 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   CYS A 124 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   TYR A 130 " --> pdb=" O   CYS A 124 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   CYS A 175 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   MET A 160 " --> pdb=" O   GLN A 173 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   GLN A 173 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 184
      removed outlier: 6.276A  pdb=" N   TYR A 207 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   LEU A 211 " --> pdb=" O   TYR A 207 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 223 through 224
      removed outlier: 3.733A  pdb=" N   VAL A 231 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224
      removed outlier: 6.637A  pdb=" N   GLU A 258 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 5.460A  pdb=" N   ILE A 262 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 276 through 283
      removed outlier: 5.321A  pdb=" N   GLU A 277 " --> pdb=" O   ARG A 292 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ARG A 292 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 352 through 356
      removed outlier: 4.561A  pdb=" N   TRP A 352 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY A 363 " --> pdb=" O   TRP A 352 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   SER A 372 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ASP A 399 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   TYR A 374 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   LYS A 378 " --> pdb=" O   ASN A 393 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   ASN A 393 " --> pdb=" O   LYS A 378 " (cutoff:3.500A)

    169 hydrogen bonds defined for protein.
    429 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 1.71 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: 1609
        1.34 -     1.46: 1256
        1.46 -     1.58: 2139
        1.58 -     1.70: 0
        1.70 -     1.81: 34
  Bond restraints: 5038
  Sorted by residual:
  bond pdb=" C1  NAG A 503 "
       pdb=" O5  NAG A 503 "
    ideal  model  delta    sigma   weight residual
    1.406  1.491 -0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C5  MAN B   5 "
       pdb=" O5  MAN B   5 "
    ideal  model  delta    sigma   weight residual
    1.418  1.450 -0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" C1  MAN B   5 "
       pdb=" O5  MAN B   5 "
    ideal  model  delta    sigma   weight residual
    1.399  1.431 -0.032 2.00e-02 2.50e+03 2.55e+00
  bond pdb=" C1  MAN B   5 "
       pdb=" C2  MAN B   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.556 -0.030 2.00e-02 2.50e+03 2.29e+00
  bond pdb=" N   PRO L  95A"
       pdb=" CA  PRO L  95A"
    ideal  model  delta    sigma   weight residual
    1.469  1.487 -0.018 1.28e-02 6.10e+03 2.03e+00
  ... (remaining 5033 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 6605
        1.43 -     2.87: 191
        2.87 -     4.30: 25
        4.30 -     5.74: 7
        5.74 -     7.17: 8
  Bond angle restraints: 6836
  Sorted by residual:
  angle pdb=" C   PRO L  95 "
        pdb=" N   PRO L  95A"
        pdb=" CA  PRO L  95A"
      ideal   model   delta    sigma   weight residual
     119.84  115.33    4.51 1.25e+00 6.40e-01 1.30e+01
  angle pdb=" C   ARG A 430 "
        pdb=" N   LYS A 431 "
        pdb=" CA  LYS A 431 "
      ideal   model   delta    sigma   weight residual
     121.54  127.75   -6.21 1.91e+00 2.74e-01 1.06e+01
  angle pdb=" N   PRO L  95 "
        pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
      ideal   model   delta    sigma   weight residual
     110.70  113.47   -2.77 1.22e+00 6.72e-01 5.14e+00
  angle pdb=" C3  BMA B   3 "
        pdb=" C2  BMA B   3 "
        pdb=" O2  BMA B   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.51    6.44 3.00e+00 1.11e-01 4.61e+00
  angle pdb=" N   CYS A 337 "
        pdb=" CA  CYS A 337 "
        pdb=" CB  CYS A 337 "
      ideal   model   delta    sigma   weight residual
     113.65  110.51    3.14 1.47e+00 4.63e-01 4.56e+00
  ... (remaining 6831 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.46: 2853
       23.46 -    46.93: 196
       46.93 -    70.39: 28
       70.39 -    93.85: 15
       93.85 -   117.31: 11
  Dihedral angle restraints: 3103
    sinusoidal: 1336
      harmonic: 1767
  Sorted by residual:
  dihedral pdb=" CB  CYS A 318 "
           pdb=" SG  CYS A 318 "
           pdb=" SG  CYS A 337 "
           pdb=" CB  CYS A 337 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.03  -41.03     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CA  ALA A 177 "
           pdb=" C   ALA A 177 "
           pdb=" N   TRP A 178 "
           pdb=" CA  TRP A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.98   21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" C2  NAG A 503 "
           pdb=" C1  NAG A 503 "
           pdb=" O5  NAG A 503 "
           pdb=" C5  NAG A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   54.35 -117.31     1      3.00e+01 1.11e-03 1.56e+01
  ... (remaining 3100 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.126: 754
       0.126 -    0.252: 5
       0.252 -    0.378: 1
       0.378 -    0.504: 0
       0.504 -    0.630: 1
  Chirality restraints: 761
  Sorted by residual:
  chirality pdb=" C1  NAG A 503 "
            pdb=" ND2 ASN A 329 "
            pdb=" C2  NAG A 503 "
            pdb=" O5  NAG A 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.77   -0.63 2.00e-01 2.50e+01 9.93e+00
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.53    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ILE A 392 "
            pdb=" N   ILE A 392 "
            pdb=" C   ILE A 392 "
            pdb=" CB  ILE A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.99e-01
  ... (remaining 758 not shown)

  Planarity restraints: 880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 329 "   -0.121 2.00e-02 2.50e+03   1.70e-01 3.63e+02
        pdb=" CG  ASN A 329 "    0.051 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 329 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 329 "    0.299 2.00e-02 2.50e+03
        pdb=" C1  NAG A 503 "   -0.194 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 125 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.06e+00
        pdb=" N   PRO A 126 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 126 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 126 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  94 "   -0.021 5.00e-02 4.00e+02   3.18e-02 1.61e+00
        pdb=" N   PRO L  95 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO L  95 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO L  95 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 877 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 325
        2.73 -     3.27: 4643
        3.27 -     3.81: 8984
        3.81 -     4.36: 11401
        4.36 -     4.90: 19097
  Nonbonded interactions: 44450
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 179 "
            pdb=" OE2 GLU A 227 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER L  27A"
            pdb=" O   ASP A 309 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OD1 ASP A 309 "
            pdb=" OG  SER A 311 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP A 399 "
            pdb=" OG  SER A 457 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ASP L  82 "
            pdb=" OH  TYR L  86 "
     model   vdw
     2.290 3.040
  ... (remaining 44445 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=0.34 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:             5.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.120
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:16.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
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      :  0.004   0.085   5038  Z= 0.270
  Angle     :  0.611   7.172   6836  Z= 0.311
  Chirality :  0.051   0.630    761
  Planarity :  0.004   0.044    876
  Dihedral  : 18.250 117.313   1950
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.76 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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 (0.34), residues: 618
  helix:  0.60 (2.68), residues: 6
  sheet: -0.05 (0.32), residues: 249
  loop :  0.04 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.013   0.002   PHE A 354 
 TYR   0.013   0.002   TYR A 121 
 ARG   0.002   0.000   ARG A 371 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  277 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8125 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 81
  average time/residue: 1.3198
  time to fit residues: 112.2083
Evaluate side-chains
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  370 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    0.2980
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0670
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN
A 141 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.139415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.110928 restraints weight = 4745.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.42
r_work: 0.3021 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.0825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5038  Z= 0.181
  Angle     :  0.582   8.579   6836  Z= 0.305
  Chirality :  0.049   0.418    761
  Planarity :  0.004   0.043    876
  Dihedral  : 13.060 102.720    873
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.63 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.19 (0.33), residues: 618
  helix:  0.27 (2.41), residues: 6
  sheet: -0.03 (0.31), residues: 247
  loop : -0.11 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 274 
 PHE   0.012   0.001   PHE A 354 
 TYR   0.011   0.001   TYR A 121 
 ARG   0.002   0.000   ARG A 224 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.760 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7622 (pm20)
REVERT: A  277 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: A  430 ARG cc_start: 0.7904 (mmt-90) cc_final: 0.7600 (mmt-90)
  outliers start: 14
  outliers final: 8
  residues processed: 82
  average time/residue: 1.5286
  time to fit residues: 130.6806
Evaluate side-chains
  75 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  160 MET
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  390 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0170
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN
A 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.138341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.107315 restraints weight = 4836.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.48
r_work: 0.3006 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5038  Z= 0.208
  Angle     :  0.574   9.463   6836  Z= 0.302
  Chirality :  0.048   0.400    761
  Planarity :  0.004   0.044    876
  Dihedral  : 10.588  99.472    867
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 15.82 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.18 (0.33), residues: 618
  helix:  0.26 (2.36), residues: 6
  sheet:  0.02 (0.31), residues: 232
  loop : -0.12 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.013   0.001   TYR A 121 
 ARG   0.003   0.000   ARG H  38 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A  277 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8017 (mt-10)
REVERT: A  368 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7562 (mt-10)
  outliers start: 19
  outliers final: 9
  residues processed: 80
  average time/residue: 1.4056
  time to fit residues: 118.5675
Evaluate side-chains
  75 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.138996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.110800 restraints weight = 4808.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.39
r_work: 0.3019 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5038  Z= 0.194
  Angle     :  0.554   9.681   6836  Z= 0.293
  Chirality :  0.048   0.413    761
  Planarity :  0.004   0.043    876
  Dihedral  :  9.742  96.879    867
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.95 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.23 (0.33), residues: 618
  helix:  0.27 (2.37), residues: 6
  sheet:  0.01 (0.31), residues: 232
  loop : -0.19 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.012   0.001   TYR A 121 
 ARG   0.001   0.000   ARG H  38 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.570 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7620 (pm20)
REVERT: A  277 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8007 (mt-10)
REVERT: A  368 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7550 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 78
  average time/residue: 1.3514
  time to fit residues: 109.9889
Evaluate side-chains
  79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 402 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.137564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.106270 restraints weight = 4778.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.48
r_work: 0.2984 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5038  Z= 0.257
  Angle     :  0.585   9.964   6836  Z= 0.309
  Chirality :  0.049   0.411    761
  Planarity :  0.004   0.044    876
  Dihedral  :  9.563  94.778    867
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.20 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.28 (0.33), residues: 618
  helix:  0.23 (2.38), residues: 6
  sheet: -0.03 (0.31), residues: 232
  loop : -0.21 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.014   0.002   PHE A 354 
 TYR   0.014   0.002   TYR A 121 
 ARG   0.002   0.000   ARG H  38 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.570 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7648 (pm20)
REVERT: A  277 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8064 (mt-10)
REVERT: A  337 CYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8495 (m)
REVERT: A  368 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7632 (mt-10)
  outliers start: 21
  outliers final: 12
  residues processed: 85
  average time/residue: 1.5644
  time to fit residues: 138.1412
Evaluate side-chains
  85 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  337 CYS
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.136339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.104744 restraints weight = 4805.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.48
r_work: 0.2959 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5038  Z= 0.302
  Angle     :  0.615  10.117   6836  Z= 0.325
  Chirality :  0.049   0.412    761
  Planarity :  0.004   0.045    876
  Dihedral  :  9.498  93.473    867
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.14 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.38 (0.33), residues: 618
  helix:  0.22 (2.41), residues: 6
  sheet: -0.16 (0.31), residues: 224
  loop : -0.23 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 178 
 HIS   0.004   0.001   HIS A 336 
 PHE   0.014   0.002   PHE A 354 
 TYR   0.014   0.002   TYR A 121 
 ARG   0.002   0.000   ARG H  38 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.530 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7627 (pm20)
REVERT: A  277 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8090 (mt-10)
REVERT: A  337 CYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8504 (m)
REVERT: A  368 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7659 (mt-10)
  outliers start: 19
  outliers final: 11
  residues processed: 82
  average time/residue: 1.4065
  time to fit residues: 120.8986
Evaluate side-chains
  80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  337 CYS
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    0.0980
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 18 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 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 = 0.3522 r_free = 0.3522 target = 0.139941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.111667 restraints weight = 4743.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.39
r_work: 0.3025 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5038  Z= 0.177
  Angle     :  0.554  10.389   6836  Z= 0.292
  Chirality :  0.047   0.398    761
  Planarity :  0.004   0.044    876
  Dihedral  :  8.850  90.518    867
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.27 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.25 (0.33), residues: 618
  helix:  0.29 (2.40), residues: 6
  sheet: -0.01 (0.32), residues: 232
  loop : -0.20 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.010   0.001   TYR A 121 
 ARG   0.002   0.000   ARG H  38 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.549 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7622 (pm20)
REVERT: A  277 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8029 (mt-10)
  outliers start: 16
  outliers final: 9
  residues processed: 84
  average time/residue: 1.1375
  time to fit residues: 100.1254
Evaluate side-chains
  80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 49 optimal weight:    0.3980
   chunk 31 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 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 = 0.3504 r_free = 0.3504 target = 0.138414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.106919 restraints weight = 4806.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.50
r_work: 0.2996 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2850
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5038  Z= 0.239
  Angle     :  0.585  10.677   6836  Z= 0.308
  Chirality :  0.048   0.395    761
  Planarity :  0.004   0.044    876
  Dihedral  :  8.800  87.737    867
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.46 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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 (0.33), residues: 618
  helix:  0.25 (2.38), residues: 6
  sheet: -0.12 (0.32), residues: 226
  loop : -0.19 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.013   0.002   PHE A 354 
 TYR   0.013   0.002   TYR A 121 
 ARG   0.004   0.000   ARG A 292 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.629 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7594 (pm20)
REVERT: A  277 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8016 (mt-10)
  outliers start: 15
  outliers final: 10
  residues processed: 79
  average time/residue: 1.4707
  time to fit residues: 122.2527
Evaluate side-chains
  80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 41 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 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 = 0.3523 r_free = 0.3523 target = 0.140056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.112175 restraints weight = 4724.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.41
r_work: 0.3028 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5038  Z= 0.189
  Angle     :  0.561  11.112   6836  Z= 0.295
  Chirality :  0.047   0.373    761
  Planarity :  0.004   0.044    876
  Dihedral  :  8.330  81.459    867
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.21 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.25 (0.33), residues: 618
  helix:  0.32 (2.40), residues: 6
  sheet: -0.01 (0.32), residues: 232
  loop : -0.19 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.011   0.001   TYR A 121 
 ARG   0.004   0.000   ARG A 292 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.538 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7548 (pm20)
REVERT: A  277 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7849 (mt-10)
  outliers start: 11
  outliers final: 9
  residues processed: 81
  average time/residue: 1.1799
  time to fit residues: 99.9691
Evaluate side-chains
  81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 54 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0870
   chunk 46 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.139915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.112053 restraints weight = 4826.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.39
r_work: 0.3063 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5038  Z= 0.185
  Angle     :  0.566  11.461   6836  Z= 0.295
  Chirality :  0.046   0.326    761
  Planarity :  0.004   0.044    876
  Dihedral  :  7.818  69.508    867
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.83 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.23 (0.33), residues: 618
  helix:  0.32 (2.38), residues: 6
  sheet:  0.02 (0.31), residues: 237
  loop : -0.19 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.011   0.001   TYR A 121 
 ARG   0.003   0.000   ARG A 292 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.543 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8600 (tt0) cc_final: 0.8386 (tt0)
REVERT: L  100 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7518 (pm20)
REVERT: A  277 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7848 (mt-10)
  outliers start: 15
  outliers final: 10
  residues processed: 79
  average time/residue: 1.1569
  time to fit residues: 95.7631
Evaluate side-chains
  79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 CYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  413 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0170
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0070
   chunk 59 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.141880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.115281 restraints weight = 4853.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.34
r_work: 0.3082 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5038  Z= 0.162
  Angle     :  0.541   8.689   6836  Z= 0.285
  Chirality :  0.045   0.170    761
  Planarity :  0.004   0.044    876
  Dihedral  :  6.820  52.220    867
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.40 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.19 (0.33), residues: 618
  helix:  0.40 (2.38), residues: 6
  sheet:  0.09 (0.32), residues: 237
  loop : -0.21 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.012   0.001   PHE A 354 
 TYR   0.010   0.001   TYR A 121 
 ARG   0.003   0.000   ARG A 292 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5352.68 seconds
wall clock time: 95 minutes 44.64 seconds (5744.64 seconds total)