Starting phenix.real_space_refine
on Tue Feb 11 09:40:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ez7_28729/02_2025/8ez7_28729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ez7_28729/02_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_28729/02_2025/8ez7_28729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ez7_28729/02_2025/8ez7_28729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ez7_28729/02_2025/8ez7_28729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ez7_28729/02_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-5592/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: 4.23, 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: 1.18
  Conformation dependent library (CDL) restraints added in 567.7 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: 0.60
  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: 1.60

  Time building geometry restraints manager: 1.37 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:             7.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     15.600
  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:15.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.290
-------------------------------------------------------------------------------
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  : 0.580 
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: 1.1791
  time to fit residues: 99.9683
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  : 0.584 
-------------------------------------------------------------------------------
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:    0.0050
   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:    0.4332

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.138879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.112099 restraints weight = 4824.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.34
r_work: 0.3034 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5038  Z= 0.174
  Angle     :  0.578   9.278   6836  Z= 0.303
  Chirality :  0.049   0.417    761
  Planarity :  0.004   0.043    876
  Dihedral  : 13.193 103.212    873
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.45
  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:  0.28 (2.42), residues: 6
  sheet: -0.02 (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  : 0.574 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7610 (pm20)
REVERT: A  277 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7957 (mt-10)
REVERT: A  430 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7608 (mmt-90)
  outliers start: 14
  outliers final: 8
  residues processed: 82
  average time/residue: 1.1984
  time to fit residues: 102.6382
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  : 0.582 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 54 optimal weight:    0.0570
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0980
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3532 r_free = 0.3532 target = 0.140619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.109478 restraints weight = 4809.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.49
r_work: 0.3030 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5038  Z= 0.175
  Angle     :  0.554   9.620   6836  Z= 0.291
  Chirality :  0.048   0.396    761
  Planarity :  0.004   0.044    876
  Dihedral  : 10.267  99.232    867
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.01 %
    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: -0.16 (0.33), residues: 618
  helix:  0.29 (2.34), residues: 6
  sheet:  0.04 (0.32), residues: 232
  loop : -0.12 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.012   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
  93 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A  277 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8016 (mt-10)
REVERT: A  430 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.7498 (mmt-90)
  outliers start: 18
  outliers final: 7
  residues processed: 85
  average time/residue: 1.0762
  time to fit residues: 95.8662
Evaluate side-chains
  74 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    0.4980
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0870
   chunk 10 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 52 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.140360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.113624 restraints weight = 4851.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.34
r_work: 0.3059 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1269

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= 0.169
  Angle     :  0.537   9.834   6836  Z= 0.283
  Chirality :  0.047   0.407    761
  Planarity :  0.004   0.042    876
  Dihedral  :  9.341  96.050    867
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.33 %
    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: -0.17 (0.33), residues: 618
  helix:  0.31 (2.36), residues: 6
  sheet:  0.07 (0.31), residues: 237
  loop : -0.16 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.011   0.001   TYR A 121 
 ARG   0.002   0.000   ARG A 292 

*********************** 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: 12
    poor density    : 72
  time to evaluate  : 0.517 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7579 (pm20)
REVERT: A  277 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: A  337 CYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8471 (m)
REVERT: A  430 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.7550 (mmt-90)
  outliers start: 12
  outliers final: 7
  residues processed: 80
  average time/residue: 1.1266
  time to fit residues: 94.3487
Evaluate side-chains
  77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
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  313 VAL
Chi-restraints excluded: chain A residue  337 CYS
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:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0770
   chunk 32 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.141654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114093 restraints weight = 4767.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.39
r_work: 0.3061 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1378

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= 0.167
  Angle     :  0.534  10.025   6836  Z= 0.281
  Chirality :  0.047   0.404    761
  Planarity :  0.004   0.042    876
  Dihedral  :  8.919  93.844    867
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.08 %
    Favored  : 78.91 %
  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: -0.12 (0.33), residues: 618
  helix:  0.34 (2.37), residues: 6
  sheet:  0.12 (0.31), residues: 237
  loop : -0.13 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   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 A 292 

*********************** 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
  89 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.593 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7559 (pm20)
REVERT: A  277 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7970 (mt-10)
REVERT: A  308 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8120 (mtmt)
  outliers start: 16
  outliers final: 10
  residues processed: 84
  average time/residue: 1.1297
  time to fit residues: 99.4909
Evaluate side-chains
  84 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
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  149 VAL
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  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:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.137583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.109181 restraints weight = 4786.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.38
r_work: 0.3011 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1215

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= 0.295
  Angle     :  0.604  10.182   6836  Z= 0.319
  Chirality :  0.049   0.410    761
  Planarity :  0.004   0.043    876
  Dihedral  :  9.205  92.760    867
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.14 %
    Favored  : 79.66 %
  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: -0.21 (0.33), residues: 618
  helix:  0.26 (2.40), residues: 6
  sheet: -0.01 (0.32), residues: 224
  loop : -0.15 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 178 
 HIS   0.004   0.001   HIS A 336 
 PHE   0.013   0.002   PHE A 354 
 TYR   0.014   0.002   TYR A 121 
 ARG   0.002   0.000   ARG A  85 

*********************** 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
  92 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.512 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7591 (pm20)
REVERT: A  227 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8464 (mm-30)
REVERT: A  277 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7989 (mt-10)
REVERT: A  308 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8128 (mtmt)
  outliers start: 17
  outliers final: 11
  residues processed: 86
  average time/residue: 1.1275
  time to fit residues: 101.5758
Evaluate side-chains
  81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
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  370 LEU
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:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.133907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.105731 restraints weight = 4828.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.43
r_work: 0.2962 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5038  Z= 0.407
  Angle     :  0.669  10.357   6836  Z= 0.354
  Chirality :  0.052   0.416    761
  Planarity :  0.005   0.044    876
  Dihedral  :  9.612  91.413    867
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.08 %
    Favored  : 79.10 %
  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: -0.39 (0.33), residues: 618
  helix:  0.15 (2.40), residues: 6
  sheet: -0.14 (0.31), residues: 222
  loop : -0.26 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 178 
 HIS   0.004   0.001   HIS A 336 
 PHE   0.014   0.002   PHE A 354 
 TYR   0.015   0.002   TYR A 121 
 ARG   0.003   0.001   ARG A  85 

*********************** 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
  86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.550 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7607 (pm20)
REVERT: A  368 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7642 (mt-10)
  outliers start: 15
  outliers final: 12
  residues processed: 79
  average time/residue: 1.2032
  time to fit residues: 99.3859
Evaluate side-chains
  81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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  261 LYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  368 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.137514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.109182 restraints weight = 4786.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.42
r_work: 0.2992 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5038  Z= 0.231
  Angle     :  0.592  10.630   6836  Z= 0.312
  Chirality :  0.048   0.395    761
  Planarity :  0.004   0.044    876
  Dihedral  :  9.029  88.441    867
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  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: -0.35 (0.33), residues: 618
  helix:  0.16 (2.43), residues: 6
  sheet: -0.14 (0.32), residues: 226
  loop : -0.22 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.014   0.001   PHE A 354 
 TYR   0.012   0.001   TYR A 121 
 ARG   0.007   0.000   ARG L  61 

*********************** 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
  87 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.553 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7599 (pm20)
REVERT: A  277 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: A  308 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8144 (mtmt)
  outliers start: 15
  outliers final: 7
  residues processed: 83
  average time/residue: 1.2177
  time to fit residues: 105.4539
Evaluate side-chains
  77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0770
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.139403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.111375 restraints weight = 4731.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.38
r_work: 0.3022 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1395

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= 0.183
  Angle     :  0.569  11.030   6836  Z= 0.298
  Chirality :  0.047   0.378    761
  Planarity :  0.004   0.044    876
  Dihedral  :  8.433  82.812    867
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.40 %
    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: -0.21 (0.33), residues: 618
  helix:  0.35 (2.46), residues: 6
  sheet:  0.02 (0.32), residues: 232
  loop : -0.16 (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 191 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.010   0.001   TYR A 121 
 ARG   0.009   0.000   ARG L  61 

*********************** 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
  82 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.550 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7556 (pm20)
REVERT: A  277 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7957 (mt-10)
REVERT: A  308 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8177 (mtmt)
  outliers start: 12
  outliers final: 10
  residues processed: 77
  average time/residue: 1.2256
  time to fit residues: 98.5235
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  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  368 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 46 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 36 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
H  73 ASN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.141337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.114600 restraints weight = 4825.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.34
r_work: 0.3069 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1550

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= 0.162
  Angle     :  0.559  11.405   6836  Z= 0.290
  Chirality :  0.046   0.318    761
  Planarity :  0.004   0.043    876
  Dihedral  :  7.635  67.839    867
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.21 %
    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: -0.19 (0.33), residues: 618
  helix:  0.41 (2.39), residues: 6
  sheet: -0.02 (0.31), residues: 242
  loop : -0.11 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   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   0.009   0.000   ARG L  61 

********************** 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
  87 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.562 
Fit side-chains
REVERT: L  100 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7556 (pm20)
REVERT: A  277 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7772 (mt-10)
REVERT: A  308 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8153 (mtmt)
  outliers start: 13
  outliers final: 9
  residues processed: 80
  average time/residue: 1.1568
  time to fit residues: 96.7700
Evaluate side-chains
  76 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 13 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 59 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
H  73 ASN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.137851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.109404 restraints weight = 4808.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.44
r_work: 0.3023 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1393

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= 0.269
  Angle     :  0.604  10.493   6836  Z= 0.319
  Chirality :  0.047   0.213    761
  Planarity :  0.004   0.044    876
  Dihedral  :  7.485  52.594    867
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.02 %
    Favored  : 77.97 %
  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 (2.39), residues: 6
  sheet: -0.01 (0.32), residues: 226
  loop : -0.11 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 178 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.013   0.002   PHE A 354 
 TYR   0.014   0.002   TYR A 121 
 ARG   0.008   0.000   ARG L  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4489.90 seconds
wall clock time: 80 minutes 22.14 seconds (4822.14 seconds total)