Starting phenix.real_space_refine
on Wed Mar  4 13:56:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sk8_25176/03_2026/7sk8_25176_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sk8_25176/03_2026/7sk8_25176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sk8_25176/03_2026/7sk8_25176_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sk8_25176/03_2026/7sk8_25176_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sk8_25176/03_2026/7sk8_25176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sk8_25176/03_2026/7sk8_25176.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.083
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: 5
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4515      2.51       5
     N    1093      2.21       5
     O    1229      1.98       5
     H    6513      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13389
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5020
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 306, 5006
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 11, 'TRANS': 294}
      Conformer: "B"
        Number of residues, atoms: 306, 5006
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 11, 'TRANS': 294}
          bond proxies already assigned to first conformer: 5062
    Chain: "B"
      Number of atoms: 1040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 1040
          Classifications: {'peptide': 62}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
    Chain: "C"
      Number of atoms: 1653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 1653
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1934
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
    Chain: "E"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1618
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "F"
      Number of atoms: 1871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1871
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
    Chain: "A"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 253
          Unusual residues: {'CLR': 6, 'GJ9': 1, 'LMN': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 10
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   HIS A 121 " occ=0.50
      ... (29 atoms not shown)
      pdb=" HE1BHIS A 121 " occ=0.50
  Time building chain proxies: 2.92, per 1000 atoms: 0.22
  Number of scatterers: 13389
  At special positions: 0
  Unit cell: (71.28, 76.68, 153.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      39     16.00
     O    1229      8.00
     N    1093      7.00
     C    4515      6.00
     H    6513      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   9 " - pdb=" SG  CYS B  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  11 " - pdb=" SG  CYS B  50 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  25 " - pdb=" SG  CYS F  99 " distance=2.04

  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
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 474.7 milliseconds
  

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1578

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 14 sheets defined
      35.1% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 72
      removed outlier: 4.167A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 75
      No H-bonds generated for 'chain 'A' and resid 73 through 75'
    Processing helix  chain 'A' and resid 80 through 96
      removed outlier: 3.637A  pdb=" N   LEU A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR A  96 " --> pdb=" O   TRP A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 106
      removed outlier: 3.763A  pdb=" N   GLN A 106 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 148
      removed outlier: 3.773A  pdb=" N   TYR A 143 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE A 146 " --> pdb=" O   ARG A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 182
      Proline residue:  A 178  - end of helix
      removed outlier: 3.783A  pdb=" N   TYR A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 219
      removed outlier: 3.628A  pdb=" N   GLY A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 242
    Processing helix  chain 'A' and resid 243 through 249
    Processing helix  chain 'A' and resid 251 through 280
      removed outlier: 3.853A  pdb=" N   PHE A 255 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 286 through 305
      removed outlier: 3.635A  pdb=" N   ALA A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A 305 " --> pdb=" O   GLN A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 316
      removed outlier: 4.206A  pdb=" N   CYS A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      Proline residue:  A 312  - end of helix
    Processing helix  chain 'A' and resid 319 through 331
    Processing helix  chain 'B' and resid 19 through 23
    Processing helix  chain 'B' and resid 55 through 68
      removed outlier: 3.694A  pdb=" N   GLU B  60 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 34
    Processing helix  chain 'D' and resid 90 through 94
      removed outlier: 3.952A  pdb=" N   THR D  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 80 through 84
      removed outlier: 3.885A  pdb=" N   PHE E  84 " --> pdb=" O   PRO E  81 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 35
    Processing helix  chain 'F' and resid 90 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 33
      removed outlier: 5.843A  pdb=" N   VAL A  28 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ILE B  28 " --> pdb=" O   VAL A  28 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ASP A  30 " --> pdb=" O   ILE B  28 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   ASN B  30 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL A  32 " --> pdb=" O   ASN B  30 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   HIS B  25 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79
      removed outlier: 4.114A  pdb=" N   SER F 112 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 187
    Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 14
      removed outlier: 6.196A  pdb=" N   LEU C  12 " --> pdb=" O   GLU C 106 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   VAL C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   TYR C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 14
      removed outlier: 6.196A  pdb=" N   LEU C  12 " --> pdb=" O   GLU C 106 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   THR C  98 " --> pdb=" O   GLN C  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 10
    Processing sheet with id=AA8, first strand: chain 'D' and resid 13 through 14
      removed outlier: 6.076A  pdb=" N   GLY D  13 " --> pdb=" O   THR D 125 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE D  37 " --> pdb=" O   TYR D  53 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   TYR D  53 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   TRP D  39 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER D  62 " --> pdb=" O   TYR D  53 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 13 through 14
      removed outlier: 6.076A  pdb=" N   GLY D  13 " --> pdb=" O   THR D 125 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   TYR D 117 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 8
      removed outlier: 3.718A  pdb=" N   THR E  73 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
    Processing sheet with id=AB3, first strand: chain 'E' and resid 46 through 49
      removed outlier: 6.345A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR E  98 " --> pdb=" O   GLN E  91 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 6 through 10
    Processing sheet with id=AB5, first strand: chain 'F' and resid 61 through 63
      removed outlier: 6.690A  pdb=" N   TRP F  39 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   SER F  53 " --> pdb=" O   ILE F  37 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ILE F  37 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER F  36 " --> pdb=" O   VAL F 102 " (cutoff:3.500A)

    329 hydrogen bonds defined for protein.
    893 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: 3.02

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6502
        1.03 -     1.23: 52
        1.23 -     1.42: 2993
        1.42 -     1.62: 3994
        1.62 -     1.82: 54
  Bond restraints: 13595
  Sorted by residual:
  bond pdb=" C1  LMN A 406 "
       pdb=" O5  LMN A 406 "
    ideal  model  delta    sigma   weight residual
    1.403  1.528 -0.125 2.00e-02 2.50e+03 3.92e+01
  bond pdb=" CBT LMN A 406 "
       pdb=" CCM LMN A 406 "
    ideal  model  delta    sigma   weight residual
    1.533  1.650 -0.117 2.00e-02 2.50e+03 3.43e+01
  bond pdb=" C4  LMN A 406 "
       pdb=" O4  LMN A 406 "
    ideal  model  delta    sigma   weight residual
    1.409  1.509 -0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" CBL LMN A 406 "
       pdb=" CBR LMN A 406 "
    ideal  model  delta    sigma   weight residual
    1.525  1.606 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" C3  LMN A 406 "
       pdb=" C4  LMN A 406 "
    ideal  model  delta    sigma   weight residual
    1.525  1.446  0.079 2.00e-02 2.50e+03 1.56e+01
  ... (remaining 13590 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 24009
        1.76 -     3.52: 243
        3.52 -     5.28: 66
        5.28 -     7.04: 21
        7.04 -     8.80: 7
  Bond angle restraints: 24346
  Sorted by residual:
  angle pdb=" C06 GJ9 A 408 "
        pdb=" N05 GJ9 A 408 "
        pdb=" C37 GJ9 A 408 "
      ideal   model   delta    sigma   weight residual
     121.17  112.37    8.80 3.00e+00 1.11e-01 8.60e+00
  angle pdb=" C08 GJ9 A 408 "
        pdb=" C09 GJ9 A 408 "
        pdb=" N10 GJ9 A 408 "
      ideal   model   delta    sigma   weight residual
     108.48  116.68   -8.20 3.00e+00 1.11e-01 7.47e+00
  angle pdb=" C22 CLR A 407 "
        pdb=" C23 CLR A 407 "
        pdb=" C24 CLR A 407 "
      ideal   model   delta    sigma   weight residual
     111.95  103.85    8.10 3.00e+00 1.11e-01 7.29e+00
  angle pdb=" C22 CLR A 401 "
        pdb=" C23 CLR A 401 "
        pdb=" C24 CLR A 401 "
      ideal   model   delta    sigma   weight residual
     111.95  103.98    7.97 3.00e+00 1.11e-01 7.06e+00
  angle pdb=" C22 CLR A 403 "
        pdb=" C23 CLR A 403 "
        pdb=" C24 CLR A 403 "
      ideal   model   delta    sigma   weight residual
     111.95  104.24    7.71 3.00e+00 1.11e-01 6.60e+00
  ... (remaining 24341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.51: 6488
       23.51 -    47.02: 330
       47.02 -    70.53: 54
       70.53 -    94.04: 6
       94.04 -   117.55: 9
  Dihedral angle restraints: 6887
    sinusoidal: 3822
      harmonic: 3065
  Sorted by residual:
  dihedral pdb=" CB  CYS E  24 "
           pdb=" SG  CYS E  24 "
           pdb=" SG  CYS E  89 "
           pdb=" CB  CYS E  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.44   43.56     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" O2  LMN A 406 "
           pdb=" C2  LMN A 406 "
           pdb=" C3  LMN A 406 "
           pdb=" O3  LMN A 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.11  177.56  117.55     1      3.00e+01 1.11e-03 1.56e+01
  dihedral pdb=" C1  LMN A 406 "
           pdb=" C2  LMN A 406 "
           pdb=" C3  LMN A 406 "
           pdb=" O3  LMN A 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.26   57.17  117.09     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 6884 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 985
       0.079 -    0.159: 86
       0.159 -    0.238: 3
       0.238 -    0.318: 15
       0.318 -    0.397: 9
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" C17 CLR A 405 "
            pdb=" C13 CLR A 405 "
            pdb=" C16 CLR A 405 "
            pdb=" C20 CLR A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.95   -0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" C17 CLR A 402 "
            pdb=" C13 CLR A 402 "
            pdb=" C16 CLR A 402 "
            pdb=" C20 CLR A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.95   -0.39 2.00e-01 2.50e+01 3.84e+00
  chirality pdb=" C17 CLR A 407 "
            pdb=" C13 CLR A 407 "
            pdb=" C16 CLR A 407 "
            pdb=" C20 CLR A 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.93   -0.38 2.00e-01 2.50e+01 3.53e+00
  ... (remaining 1095 not shown)

  Planarity restraints: 1939
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E   8 "    0.020 5.00e-02 4.00e+02   2.93e-02 1.37e+00
        pdb=" N   PRO E   9 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO E   9 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E   9 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 223 "    0.017 5.00e-02 4.00e+02   2.52e-02 1.01e+00
        pdb=" N   PRO A 224 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 224 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 224 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F  55 "   -0.016 5.00e-02 4.00e+02   2.44e-02 9.56e-01
        pdb=" N   PRO F  56 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO F  56 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO F  56 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1936 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 385
        2.17 -     2.78: 25219
        2.78 -     3.38: 35246
        3.38 -     3.99: 47785
        3.99 -     4.60: 74527
  Nonbonded interactions: 183162
  Sorted by model distance:
  nonbonded pdb="HE22 GLN E  39 "
            pdb=" OE1 GLN F  42 "
     model   vdw
     1.560 2.450
  nonbonded pdb=" HH  TYR C  37 "
            pdb=" OE1 GLN C  90 "
     model   vdw
     1.632 2.450
  nonbonded pdb="HH12 ARG D  70 "
            pdb=" OD2 ASP D  93 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" O   ILE A 123 "
            pdb="HD22 ASN A 127 "
     model   vdw
     1.658 2.450
  nonbonded pdb=" OE1 GLN C 101 "
            pdb=" H   GLN C 101 "
     model   vdw
     1.702 2.450
  ... (remaining 183157 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 3 through 91 or resid 93 through 94 or resid 98 through 10 \ 
8))
  selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ 
r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 
13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ 
)) or resid 4 through 91 or resid 93 through 94 or resid 98 through 108))
}
ncs_group {
  reference = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ 
r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ 
G13 or name HG21 or name HG22 or name HG23)) or resid 6 through 31 or resid 33 o \ 
r resid 35 through 52 or resid 54 or resid 57 through 102 or resid 105 through 1 \ 
06 or resid 111 or resid 113 or resid 116 through 127))
  selection = (chain 'F' and (resid 5 through 31 or resid 33 or resid 35 through 52 or resid 5 \ 
4 or resid 57 through 102 or resid 105 or resid 109 or resid 114 or resid 116 or \ 
 resid 118 through 129))
}

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=0.50 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:             1.710
  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:             0.070
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     14.500
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
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      :  0.007   0.125   7089  Z= 0.344
  Angle     :  0.728   8.799   9692  Z= 0.306
  Chirality :  0.064   0.397   1098
  Planarity :  0.003   0.029   1143
  Dihedral  : 15.202 117.550   2882
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.30), residues: 824
  helix:  1.89 (0.34), residues: 240
  sheet: -0.80 (0.31), residues: 256
  loop : -0.81 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  22 
 TYR   0.012   0.001   TYR C  50 
 PHE   0.009   0.001   PHE A  55 
 TRP   0.007   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00711 ( 7082)
  covalent geometry    : angle       0.72620 ( 9678)
  SS BOND              : bond        0.00399 (    7)
  SS BOND              : angle       1.45989 (   14)
  hydrogen bonds       : bond        0.16559 (  323)
  hydrogen bonds       : angle       6.40515 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 GLU cc_start: 0.7623 (tt0) cc_final: 0.7417 (tt0)
REVERT: F  122 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7782 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2256
  time to fit residues: 26.9124
Evaluate side-chains
  84 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.119536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.102887 restraints weight = 27839.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.43
r_work: 0.2983 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
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 = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7089  Z= 0.153
  Angle     :  0.533   8.105   9692  Z= 0.276
  Chirality :  0.042   0.166   1098
  Planarity :  0.003   0.040   1143
  Dihedral  :  9.075  79.408   1429
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  5.59 %
    Favored  : 93.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.30), residues: 824
  helix:  2.07 (0.33), residues: 245
  sheet: -0.79 (0.31), residues: 256
  loop : -0.92 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  70 
 TYR   0.019   0.001   TYR D  53 
 PHE   0.017   0.001   PHE A 173 
 TRP   0.013   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7082)
  covalent geometry    : angle       0.53067 ( 9678)
  SS BOND              : bond        0.00591 (    7)
  SS BOND              : angle       1.27767 (   14)
  hydrogen bonds       : bond        0.05520 (  323)
  hydrogen bonds       : angle       5.05868 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7588 (mtmt)
REVERT: F  122 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7802 (mp10)
  outliers start: 4
  outliers final: 4
  residues processed: 92
  average time/residue: 0.2088
  time to fit residues: 24.9989
Evaluate side-chains
  88 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 192 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.118426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.101158 restraints weight = 31276.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.68
r_work: 0.2934 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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      :  0.004   0.026   7089  Z= 0.161
  Angle     :  0.509   4.639   9692  Z= 0.267
  Chirality :  0.041   0.144   1098
  Planarity :  0.003   0.027   1143
  Dihedral  :  7.747  74.719   1429
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  7.64 %
    Favored  : 91.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.30), residues: 824
  helix:  2.09 (0.33), residues: 246
  sheet: -0.77 (0.32), residues: 256
  loop : -1.03 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  22 
 TYR   0.017   0.001   TYR D  53 
 PHE   0.013   0.001   PHE A 173 
 TRP   0.011   0.001   TRP F  50 
 HIS   0.004   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7082)
  covalent geometry    : angle       0.50690 ( 9678)
  SS BOND              : bond        0.00590 (    7)
  SS BOND              : angle       1.20199 (   14)
  hydrogen bonds       : bond        0.05188 (  323)
  hydrogen bonds       : angle       4.85847 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 GLU cc_start: 0.7690 (tt0) cc_final: 0.7473 (tt0)
REVERT: B   64 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7579 (mtpt)
REVERT: F  122 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7813 (mp10)
  outliers start: 3
  outliers final: 3
  residues processed: 94
  average time/residue: 0.1956
  time to fit residues: 23.8834
Evaluate side-chains
  90 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.118742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.102000 restraints weight = 29345.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.60
r_work: 0.2957 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7089  Z= 0.148
  Angle     :  0.497   4.240   9692  Z= 0.261
  Chirality :  0.041   0.145   1098
  Planarity :  0.003   0.027   1143
  Dihedral  :  7.675  71.721   1429
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.14 %
    Favored  : 90.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.30), residues: 824
  helix:  2.17 (0.33), residues: 241
  sheet: -0.77 (0.32), residues: 256
  loop : -1.01 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  22 
 TYR   0.015   0.001   TYR D  53 
 PHE   0.013   0.001   PHE A 173 
 TRP   0.011   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7082)
  covalent geometry    : angle       0.49567 ( 9678)
  SS BOND              : bond        0.00564 (    7)
  SS BOND              : angle       1.11714 (   14)
  hydrogen bonds       : bond        0.04838 (  323)
  hydrogen bonds       : angle       4.72552 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 GLU cc_start: 0.7650 (tt0) cc_final: 0.7448 (tt0)
REVERT: E   94 TYR cc_start: 0.8111 (m-80) cc_final: 0.7762 (m-80)
REVERT: F  122 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7789 (mp10)
  outliers start: 4
  outliers final: 4
  residues processed: 94
  average time/residue: 0.2091
  time to fit residues: 25.3030
Evaluate side-chains
  90 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 77 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.119552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.101096 restraints weight = 32549.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.70
r_work: 0.2949 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2809
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2809 r_free = 0.2809    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2809 r_free = 0.2809    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2809
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7089  Z= 0.128
  Angle     :  0.479   4.200   9692  Z= 0.252
  Chirality :  0.041   0.144   1098
  Planarity :  0.003   0.029   1143
  Dihedral  :  7.529  71.607   1429
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.55 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.30), residues: 824
  helix:  2.25 (0.33), residues: 241
  sheet: -0.76 (0.32), residues: 261
  loop : -0.97 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  25 
 TYR   0.013   0.001   TYR D  53 
 PHE   0.012   0.001   PHE A 173 
 TRP   0.010   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7082)
  covalent geometry    : angle       0.47763 ( 9678)
  SS BOND              : bond        0.00510 (    7)
  SS BOND              : angle       1.01388 (   14)
  hydrogen bonds       : bond        0.04540 (  323)
  hydrogen bonds       : angle       4.59778 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8790 (mpp) cc_final: 0.8563 (mpp)
REVERT: E   94 TYR cc_start: 0.8091 (m-80) cc_final: 0.7705 (m-80)
REVERT: F  122 GLN cc_start: 0.8452 (mm-40) cc_final: 0.7825 (mp10)
  outliers start: 4
  outliers final: 4
  residues processed: 93
  average time/residue: 0.2070
  time to fit residues: 24.8480
Evaluate side-chains
  92 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.118344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.099534 restraints weight = 33832.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 1.75
r_work: 0.2924 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7089  Z= 0.157
  Angle     :  0.499   4.276   9692  Z= 0.262
  Chirality :  0.041   0.142   1098
  Planarity :  0.003   0.029   1143
  Dihedral  :  7.711  82.684   1429
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 10.37 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.30), residues: 824
  helix:  2.18 (0.33), residues: 247
  sheet: -0.79 (0.32), residues: 261
  loop : -1.10 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  22 
 TYR   0.014   0.001   TYR D  53 
 PHE   0.011   0.001   PHE A 173 
 TRP   0.010   0.001   TRP F  50 
 HIS   0.004   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7082)
  covalent geometry    : angle       0.49762 ( 9678)
  SS BOND              : bond        0.00583 (    7)
  SS BOND              : angle       1.13948 (   14)
  hydrogen bonds       : bond        0.04694 (  323)
  hydrogen bonds       : angle       4.61699 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  122 GLN cc_start: 0.8489 (mm-40) cc_final: 0.7849 (mp10)
  outliers start: 5
  outliers final: 5
  residues processed: 91
  average time/residue: 0.2186
  time to fit residues: 25.8658
Evaluate side-chains
  91 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Chi-restraints excluded: chain F residue   15 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.118293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.101839 restraints weight = 28059.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.56
r_work: 0.2946 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7089  Z= 0.166
  Angle     :  0.507   4.278   9692  Z= 0.266
  Chirality :  0.041   0.143   1098
  Planarity :  0.003   0.030   1143
  Dihedral  :  7.816  84.833   1429
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.05 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.30), residues: 824
  helix:  2.13 (0.33), residues: 247
  sheet: -0.81 (0.32), residues: 261
  loop : -1.13 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  22 
 TYR   0.015   0.001   TYR D  53 
 PHE   0.011   0.001   PHE A  55 
 TRP   0.010   0.001   TRP F  50 
 HIS   0.004   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7082)
  covalent geometry    : angle       0.50586 ( 9678)
  SS BOND              : bond        0.00612 (    7)
  SS BOND              : angle       1.14776 (   14)
  hydrogen bonds       : bond        0.04744 (  323)
  hydrogen bonds       : angle       4.62860 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   48 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8476 (mp)
REVERT: F  122 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7799 (mp10)
  outliers start: 6
  outliers final: 5
  residues processed: 91
  average time/residue: 0.2086
  time to fit residues: 24.6370
Evaluate side-chains
  92 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain F residue   15 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 69 optimal weight:    0.4980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.119537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.102619 restraints weight = 28800.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.49
r_work: 0.2973 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    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 = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7089  Z= 0.125
  Angle     :  0.482   5.157   9692  Z= 0.252
  Chirality :  0.041   0.143   1098
  Planarity :  0.003   0.029   1143
  Dihedral  :  7.485  78.198   1429
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.32 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.30), residues: 824
  helix:  2.28 (0.33), residues: 247
  sheet: -0.75 (0.32), residues: 261
  loop : -1.03 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  22 
 TYR   0.012   0.001   TYR D  53 
 PHE   0.010   0.001   PHE A 173 
 TRP   0.009   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7082)
  covalent geometry    : angle       0.48018 ( 9678)
  SS BOND              : bond        0.00526 (    7)
  SS BOND              : angle       1.08599 (   14)
  hydrogen bonds       : bond        0.04371 (  323)
  hydrogen bonds       : angle       4.50692 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  122 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7749 (mp10)
  outliers start: 4
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1987
  time to fit residues: 24.4998
Evaluate side-chains
  91 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.119132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.100309 restraints weight = 33771.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.75
r_work: 0.2931 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7089  Z= 0.136
  Angle     :  0.490   4.406   9692  Z= 0.257
  Chirality :  0.041   0.142   1098
  Planarity :  0.003   0.031   1143
  Dihedral  :  7.285  78.580   1429
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.87 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.30), residues: 824
  helix:  2.28 (0.33), residues: 247
  sheet: -0.72 (0.33), residues: 259
  loop : -1.04 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  25 
 TYR   0.013   0.001   TYR D  53 
 PHE   0.010   0.001   PHE A 173 
 TRP   0.009   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7082)
  covalent geometry    : angle       0.48854 ( 9678)
  SS BOND              : bond        0.00525 (    7)
  SS BOND              : angle       1.09616 (   14)
  hydrogen bonds       : bond        0.04426 (  323)
  hydrogen bonds       : angle       4.50300 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7491 (mtmt)
REVERT: C   80 GLN cc_start: 0.8551 (mm110) cc_final: 0.8262 (mm110)
REVERT: E   48 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8370 (mp)
REVERT: F  122 GLN cc_start: 0.8487 (mm-40) cc_final: 0.7856 (mp10)
  outliers start: 6
  outliers final: 5
  residues processed: 93
  average time/residue: 0.1985
  time to fit residues: 24.4177
Evaluate side-chains
  93 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain E residue   48 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:    0.0970
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.120212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.103239 restraints weight = 28966.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 1.50
r_work: 0.2990 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7089  Z= 0.114
  Angle     :  0.474   4.321   9692  Z= 0.249
  Chirality :  0.041   0.142   1098
  Planarity :  0.003   0.028   1143
  Dihedral  :  6.946  75.114   1429
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.14 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.30), residues: 824
  helix:  2.39 (0.33), residues: 247
  sheet: -0.70 (0.32), residues: 261
  loop : -1.00 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  25 
 TYR   0.011   0.001   TYR D  53 
 PHE   0.010   0.001   PHE A 173 
 TRP   0.009   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7082)
  covalent geometry    : angle       0.47239 ( 9678)
  SS BOND              : bond        0.00465 (    7)
  SS BOND              : angle       1.22328 (   14)
  hydrogen bonds       : bond        0.04170 (  323)
  hydrogen bonds       : angle       4.41973 (  893)

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

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

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1648 Ramachandran restraints generated.
    824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   48 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8345 (mp)
REVERT: F  122 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7736 (mp10)
  outliers start: 5
  outliers final: 4
  residues processed: 89
  average time/residue: 0.1884
  time to fit residues: 22.6102
Evaluate side-chains
  90 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   74 SER
Chi-restraints excluded: chain E residue   48 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    0.1980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.120719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.103993 restraints weight = 27612.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.47
r_work: 0.2983 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7089  Z= 0.116
  Angle     :  0.475   5.702   9692  Z= 0.249
  Chirality :  0.040   0.140   1098
  Planarity :  0.003   0.028   1143
  Dihedral  :  6.815  73.228   1429
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.87 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.30), residues: 824
  helix:  2.37 (0.33), residues: 249
  sheet: -0.66 (0.32), residues: 263
  loop : -0.96 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  25 
 TYR   0.011   0.001   TYR D  53 
 PHE   0.010   0.001   PHE A 173 
 TRP   0.008   0.001   TRP F  50 
 HIS   0.003   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7082)
  covalent geometry    : angle       0.47366 ( 9678)
  SS BOND              : bond        0.00468 (    7)
  SS BOND              : angle       1.17626 (   14)
  hydrogen bonds       : bond        0.04131 (  323)
  hydrogen bonds       : angle       4.39645 (  893)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3560.09 seconds
wall clock time: 60 minutes 57.33 seconds (3657.33 seconds total)