Starting phenix.real_space_refine
on Fri Aug 22 20:56:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bmq_16121/08_2025/8bmq_16121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bmq_16121/08_2025/8bmq_16121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bmq_16121/08_2025/8bmq_16121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bmq_16121/08_2025/8bmq_16121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bmq_16121/08_2025/8bmq_16121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bmq_16121/08_2025/8bmq_16121.cif"
  }
  resolution = 3.6
  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=   0.010 sd=   0.098
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    5044      2.51       5
     N    1283      2.21       5
     O    1414      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7784
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2137
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 13, 'TRANS': 265}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2162
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 1321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1321
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 4, 'TRANS': 164}
    Chain: "D"
      Number of atoms: 2101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2101
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 9, 'TRANS': 251}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.58, per 1000 atoms: 0.20
  Number of scatterers: 7784
  At special positions: 0
  Unit cell: (79.716, 83.804, 128.772, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       6     15.00
     Mg      1     11.99
     O    1414      8.00
     N    1283      7.00
     C    5044      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.50
  Conformation dependent library (CDL) restraints added in 390.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1820

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      61.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 54
      removed outlier: 3.793A  pdb=" N   ASN A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 85
      removed outlier: 4.215A  pdb=" N   GLU A  84 " --> pdb=" O   TRP A  80 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS A  85 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 112
    Processing helix  chain 'A' and resid 116 through 131
      removed outlier: 3.904A  pdb=" N   LYS A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ALA A 125 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 145 through 160
      removed outlier: 4.217A  pdb=" N   VAL A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 194
    Processing helix  chain 'A' and resid 205 through 210
      removed outlier: 3.763A  pdb=" N   GLY A 209 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 3.822A  pdb=" N   PHE A 231 " --> pdb=" O   PRO A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.912A  pdb=" N   LEU A 237 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 258
    Processing helix  chain 'A' and resid 267 through 281
      removed outlier: 3.883A  pdb=" N   LEU A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 51
      removed outlier: 3.509A  pdb=" N   LEU B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.938A  pdb=" N   ASP B  82 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 98
      removed outlier: 3.800A  pdb=" N   LEU B  98 " --> pdb=" O   GLU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 4.119A  pdb=" N   GLY B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
      removed outlier: 3.959A  pdb=" N   PHE B 114 " --> pdb=" O   GLY B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 132
    Processing helix  chain 'B' and resid 142 through 146
      removed outlier: 3.724A  pdb=" N   LEU B 146 " --> pdb=" O   PRO B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 159
      removed outlier: 3.798A  pdb=" N   ARG B 153 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 192
    Processing helix  chain 'B' and resid 193 through 195
      No H-bonds generated for 'chain 'B' and resid 193 through 195'
    Processing helix  chain 'B' and resid 205 through 212
    Processing helix  chain 'B' and resid 228 through 232
    Processing helix  chain 'B' and resid 235 through 242
      removed outlier: 3.900A  pdb=" N   LEU B 239 " --> pdb=" O   ASP B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 260
      removed outlier: 3.616A  pdb=" N   ALA B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ALA B 259 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 281
    Processing helix  chain 'C' and resid 12 through 30
    Processing helix  chain 'C' and resid 43 through 54
      removed outlier: 3.974A  pdb=" N   GLY C  47 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 75
      removed outlier: 4.406A  pdb=" N   ALA C  62 " --> pdb=" O   TRP C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 101
      removed outlier: 3.894A  pdb=" N   THR C  86 " --> pdb=" O   PHE C  82 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLY C  92 " --> pdb=" O   THR C  88 " (cutoff:3.500A)
      Proline residue:  C  93  - end of helix
    Processing helix  chain 'C' and resid 106 through 121
    Processing helix  chain 'C' and resid 125 through 135
    Processing helix  chain 'C' and resid 137 through 145
      removed outlier: 3.538A  pdb=" N   ARG C 145 " --> pdb=" O   ALA C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 152
    Processing helix  chain 'C' and resid 152 through 172
      removed outlier: 4.720A  pdb=" N   VAL C 158 " --> pdb=" O   TRP C 154 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   TRP C 161 " --> pdb=" O   MET C 157 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU C 172 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 19
    Processing helix  chain 'D' and resid 20 through 37
      removed outlier: 3.923A  pdb=" N   PHE D  36 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU D  37 " --> pdb=" O   ILE D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 59
      removed outlier: 3.554A  pdb=" N   GLY D  59 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 70
      removed outlier: 4.217A  pdb=" N   PHE D  65 " --> pdb=" O   LYS D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 87
    Processing helix  chain 'D' and resid 102 through 129
      removed outlier: 3.793A  pdb=" N   ARG D 115 " --> pdb=" O   TYR D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 143
    Processing helix  chain 'D' and resid 144 through 150
    Processing helix  chain 'D' and resid 152 through 185
      removed outlier: 4.019A  pdb=" N   ILE D 156 " --> pdb=" O   ASN D 152 " (cutoff:3.500A)
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 191 through 199
      removed outlier: 4.136A  pdb=" N   LYS D 195 " --> pdb=" O   GLY D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 200 through 226
      Proline residue:  D 206  - end of helix
    Processing helix  chain 'D' and resid 245 through 262
      removed outlier: 3.856A  pdb=" N   VAL D 249 " --> pdb=" O   ASP D 245 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   THR D 256 " --> pdb=" O   CYS D 252 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89
      removed outlier: 6.301A  pdb=" N   ILE A 165 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   VAL A 213 " --> pdb=" O   GLN A 224 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   GLN A 224 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   VAL A 215 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 30
      removed outlier: 5.238A  pdb=" N   LEU B  26 " --> pdb=" O   ASN B   7 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE B  28 " --> pdb=" O   PHE B   5 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90
      removed outlier: 7.008A  pdb=" N   ALA B  90 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ILE B 167 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   VAL B 201 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU B 169 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ILE B  36 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS B 225 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   GLU B 219 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 35

    421 hydrogen bonds defined for protein.
    1185 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: 1.11

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2451
        1.34 -     1.46: 1198
        1.46 -     1.57: 4220
        1.57 -     1.69: 12
        1.69 -     1.81: 68
  Bond restraints: 7949
  Sorted by residual:
  bond pdb=" O3A ANP A 301 "
       pdb=" PB  ANP A 301 "
    ideal  model  delta    sigma   weight residual
    1.700  1.554  0.146 2.00e-02 2.50e+03 5.35e+01
  bond pdb=" O3A ANP B 301 "
       pdb=" PB  ANP B 301 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.25e+01
  bond pdb=" N3B ANP A 301 "
       pdb=" PG  ANP A 301 "
    ideal  model  delta    sigma   weight residual
    1.795  1.687  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" N3B ANP B 301 "
       pdb=" PG  ANP B 301 "
    ideal  model  delta    sigma   weight residual
    1.795  1.687  0.108 2.00e-02 2.50e+03 2.89e+01
  bond pdb=" O5' ANP A 301 "
       pdb=" PA  ANP A 301 "
    ideal  model  delta    sigma   weight residual
    1.655  1.577  0.078 2.00e-02 2.50e+03 1.52e+01
  ... (remaining 7944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.84: 10729
        3.84 -     7.68: 42
        7.68 -    11.52: 8
       11.52 -    15.36: 0
       15.36 -    19.20: 2
  Bond angle restraints: 10781
  Sorted by residual:
  angle pdb=" PB  ANP A 301 "
        pdb=" N3B ANP A 301 "
        pdb=" PG  ANP A 301 "
      ideal   model   delta    sigma   weight residual
     126.95  107.75   19.20 3.00e+00 1.11e-01 4.10e+01
  angle pdb=" PB  ANP B 301 "
        pdb=" N3B ANP B 301 "
        pdb=" PG  ANP B 301 "
      ideal   model   delta    sigma   weight residual
     126.95  107.82   19.13 3.00e+00 1.11e-01 4.06e+01
  angle pdb=" O1B ANP B 301 "
        pdb=" PB  ANP B 301 "
        pdb=" O2B ANP B 301 "
      ideal   model   delta    sigma   weight residual
     120.08  109.00   11.08 3.00e+00 1.11e-01 1.36e+01
  angle pdb=" C   LEU A 174 "
        pdb=" N   ASP A 175 "
        pdb=" CA  ASP A 175 "
      ideal   model   delta    sigma   weight residual
     120.65  125.64   -4.99 1.36e+00 5.41e-01 1.35e+01
  angle pdb=" O1B ANP A 301 "
        pdb=" PB  ANP A 301 "
        pdb=" O2B ANP A 301 "
      ideal   model   delta    sigma   weight residual
     120.08  109.21   10.87 3.00e+00 1.11e-01 1.31e+01
  ... (remaining 10776 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4255
       17.69 -    35.39: 383
       35.39 -    53.08: 72
       53.08 -    70.78: 31
       70.78 -    88.47: 14
  Dihedral angle restraints: 4755
    sinusoidal: 1931
      harmonic: 2824
  Sorted by residual:
  dihedral pdb=" CA  SER A 103 "
           pdb=" C   SER A 103 "
           pdb=" N   ASP A 104 "
           pdb=" CA  ASP A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ASP A 211 "
           pdb=" CB  ASP A 211 "
           pdb=" CG  ASP A 211 "
           pdb=" OD1 ASP A 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.09   55.09     1      2.00e+01 2.50e-03 1.03e+01
  dihedral pdb=" CA  THR B 197 "
           pdb=" C   THR B 197 "
           pdb=" N   VAL B 198 "
           pdb=" CA  VAL B 198 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.03  -15.97     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 4752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1027
       0.056 -    0.113: 190
       0.113 -    0.169: 23
       0.169 -    0.226: 1
       0.226 -    0.282: 2
  Chirality restraints: 1243
  Sorted by residual:
  chirality pdb=" C3' ANP B 301 "
            pdb=" C2' ANP B 301 "
            pdb=" C4' ANP B 301 "
            pdb=" O3' ANP B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C3' ANP A 301 "
            pdb=" C2' ANP A 301 "
            pdb=" C4' ANP A 301 "
            pdb=" O3' ANP A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  ILE B  21 "
            pdb=" CA  ILE B  21 "
            pdb=" CG1 ILE B  21 "
            pdb=" CG2 ILE B  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1240 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  47 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.98e+00
        pdb=" C   GLY C  47 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLY C  47 "    0.011 2.00e-02 2.50e+03
        pdb=" N   SER C  48 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C  92 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO C  93 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C  93 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  93 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 198 "   -0.008 2.00e-02 2.50e+03   1.62e-02 2.61e+00
        pdb=" C   VAL B 198 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL B 198 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 199 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 545
        2.73 -     3.27: 7949
        3.27 -     3.82: 12315
        3.82 -     4.36: 14288
        4.36 -     4.90: 25457
  Nonbonded interactions: 60554
  Sorted by model distance:
  nonbonded pdb=" O1B ANP B 301 "
            pdb=" O2G ANP B 301 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OD1 ASN D  40 "
            pdb=" N   TRP D  41 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OD1 ASP B 170 "
            pdb="MG    MG B 302 "
     model   vdw
     2.251 2.170
  nonbonded pdb=" O   PRO B 164 "
            pdb=" OH  TYR B 191 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OH  TYR D  30 "
            pdb=" OG1 THR D 256 "
     model   vdw
     2.253 3.040
  ... (remaining 60549 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.150
  Find NCS groups from input model:        0.050
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
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      :  0.006   0.146   7949  Z= 0.271
  Angle     :  0.756  19.200  10781  Z= 0.355
  Chirality :  0.046   0.282   1243
  Planarity :  0.004   0.041   1336
  Dihedral  : 15.483  88.472   2935
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.07 (0.27), residues: 975
  helix:  0.76 (0.23), residues: 547
  sheet: -0.74 (0.60), residues: 70
  loop : -1.07 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 263 
 TYR   0.027   0.002   TYR D  54 
 PHE   0.020   0.002   PHE D  86 
 TRP   0.010   0.001   TRP C  58 
 HIS   0.005   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 7949)
  covalent geometry    : angle       0.75615 (10781)
  hydrogen bonds       : bond        0.14996 (  421)
  hydrogen bonds       : angle       5.58643 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.309 
Fit side-chains
REVERT: B   82 ASP cc_start: 0.5799 (m-30) cc_final: 0.5558 (m-30)
REVERT: C  157 MET cc_start: 0.7164 (mtm) cc_final: 0.6944 (mtp)
REVERT: D  126 MET cc_start: 0.8272 (tpp) cc_final: 0.8029 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0791
  time to fit residues: 12.4079
Evaluate side-chains
  95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.166994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.148815 restraints weight = 9511.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.148730 restraints weight = 8756.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149334 restraints weight = 8312.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.149929 restraints weight = 7358.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.150172 restraints weight = 6659.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7949  Z= 0.128
  Angle     :  0.541   9.992  10781  Z= 0.271
  Chirality :  0.043   0.196   1243
  Planarity :  0.004   0.045   1336
  Dihedral  :  9.893  59.418   1107
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.22 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.42 (0.28), residues: 975
  helix:  1.18 (0.23), residues: 550
  sheet: -0.59 (0.62), residues: 70
  loop : -0.92 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 257 
 TYR   0.017   0.002   TYR D  54 
 PHE   0.010   0.001   PHE B 188 
 TRP   0.014   0.001   TRP A 276 
 HIS   0.004   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7949)
  covalent geometry    : angle       0.54125 (10781)
  hydrogen bonds       : bond        0.03819 (  421)
  hydrogen bonds       : angle       4.23596 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.220 
Fit side-chains
REVERT: D  126 MET cc_start: 0.8414 (tpp) cc_final: 0.8140 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0642
  time to fit residues: 9.3309
Evaluate side-chains
  97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 25 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.151782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.121361 restraints weight = 10618.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124826 restraints weight = 6899.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.127164 restraints weight = 5174.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.128735 restraints weight = 4247.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.129638 restraints weight = 3699.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7949  Z= 0.165
  Angle     :  0.561   9.981  10781  Z= 0.281
  Chirality :  0.043   0.175   1243
  Planarity :  0.004   0.052   1336
  Dihedral  :  7.755  59.597   1107
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.14 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.36 (0.28), residues: 975
  helix:  1.11 (0.23), residues: 557
  sheet: -0.59 (0.64), residues: 70
  loop : -0.94 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 225 
 TYR   0.020   0.002   TYR D  54 
 PHE   0.013   0.001   PHE B  35 
 TRP   0.018   0.001   TRP A 276 
 HIS   0.004   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 7949)
  covalent geometry    : angle       0.56075 (10781)
  hydrogen bonds       : bond        0.03797 (  421)
  hydrogen bonds       : angle       4.17793 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ILE cc_start: 0.8453 (tp) cc_final: 0.8113 (tp)
REVERT: D  126 MET cc_start: 0.8452 (tpp) cc_final: 0.8128 (tpp)
  outliers start: 14
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0697
  time to fit residues: 10.7256
Evaluate side-chains
  104 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  153 VAL
Chi-restraints excluded: chain D residue  175 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 78 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.165020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.146343 restraints weight = 9564.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.146349 restraints weight = 8477.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.146922 restraints weight = 7811.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.147495 restraints weight = 6970.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.147977 restraints weight = 6432.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7949  Z= 0.142
  Angle     :  0.525   9.821  10781  Z= 0.264
  Chirality :  0.042   0.165   1243
  Planarity :  0.004   0.057   1336
  Dihedral  :  7.056  62.397   1107
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.53 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.48 (0.28), residues: 975
  helix:  1.23 (0.23), residues: 557
  sheet: -0.60 (0.63), residues: 70
  loop : -0.92 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 225 
 TYR   0.018   0.002   TYR D  17 
 PHE   0.015   0.001   PHE D  86 
 TRP   0.019   0.001   TRP A 276 
 HIS   0.003   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7949)
  covalent geometry    : angle       0.52491 (10781)
  hydrogen bonds       : bond        0.03428 (  421)
  hydrogen bonds       : angle       4.05334 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ILE cc_start: 0.8502 (tp) cc_final: 0.8151 (tp)
REVERT: C  100 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7222 (pp)
REVERT: D  190 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7101 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0716
  time to fit residues: 10.7720
Evaluate side-chains
  105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  153 VAL
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.154158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122607 restraints weight = 10834.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126125 restraints weight = 6994.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.128486 restraints weight = 5215.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.130184 restraints weight = 4280.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.131169 restraints weight = 3711.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7949  Z= 0.173
  Angle     :  0.555   9.916  10781  Z= 0.279
  Chirality :  0.043   0.162   1243
  Planarity :  0.004   0.058   1336
  Dihedral  :  6.929  61.757   1107
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.01 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.41 (0.28), residues: 975
  helix:  1.20 (0.23), residues: 556
  sheet: -0.73 (0.61), residues: 70
  loop : -0.98 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 225 
 TYR   0.020   0.002   TYR D  17 
 PHE   0.016   0.001   PHE D  86 
 TRP   0.021   0.001   TRP A 276 
 HIS   0.003   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 7949)
  covalent geometry    : angle       0.55451 (10781)
  hydrogen bonds       : bond        0.03617 (  421)
  hydrogen bonds       : angle       4.11435 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: C  100 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7138 (pp)
REVERT: D  196 ARG cc_start: 0.6498 (ttp-170) cc_final: 0.6014 (mtt-85)
  outliers start: 17
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0742
  time to fit residues: 11.7010
Evaluate side-chains
  112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  153 VAL
Chi-restraints excluded: chain D residue  175 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 89 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.164660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146745 restraints weight = 9447.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.146555 restraints weight = 8471.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146890 restraints weight = 8115.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.147390 restraints weight = 7499.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.147628 restraints weight = 6940.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
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   0.034   7949  Z= 0.139
  Angle     :  0.525   9.808  10781  Z= 0.264
  Chirality :  0.042   0.161   1243
  Planarity :  0.004   0.058   1336
  Dihedral  :  6.791  61.023   1107
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.85 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.54 (0.28), residues: 975
  helix:  1.32 (0.23), residues: 555
  sheet: -0.62 (0.62), residues: 70
  loop : -0.95 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 225 
 TYR   0.022   0.002   TYR B  12 
 PHE   0.016   0.001   PHE D  86 
 TRP   0.023   0.001   TRP A 276 
 HIS   0.002   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7949)
  covalent geometry    : angle       0.52523 (10781)
  hydrogen bonds       : bond        0.03348 (  421)
  hydrogen bonds       : angle       4.02178 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8168 (tp)
REVERT: B  223 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7655 (tt)
REVERT: C  100 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7240 (pp)
REVERT: D  196 ARG cc_start: 0.6711 (ttp-170) cc_final: 0.6504 (mtt-85)
  outliers start: 18
  outliers final: 13
  residues processed: 114
  average time/residue: 0.0747
  time to fit residues: 12.0831
Evaluate side-chains
  113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  153 VAL
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3936 r_free = 0.3936 target = 0.165174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.147379 restraints weight = 9483.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.147092 restraints weight = 8572.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.147440 restraints weight = 8107.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147861 restraints weight = 7537.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.148174 restraints weight = 6993.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7949  Z= 0.129
  Angle     :  0.512   9.381  10781  Z= 0.258
  Chirality :  0.042   0.157   1243
  Planarity :  0.004   0.058   1336
  Dihedral  :  6.664  60.081   1107
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.21 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.63 (0.28), residues: 975
  helix:  1.37 (0.23), residues: 556
  sheet: -0.57 (0.62), residues: 70
  loop : -0.88 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 225 
 TYR   0.018   0.001   TYR D  17 
 PHE   0.017   0.001   PHE D  86 
 TRP   0.027   0.001   TRP A 276 
 HIS   0.002   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7949)
  covalent geometry    : angle       0.51164 (10781)
  hydrogen bonds       : bond        0.03245 (  421)
  hydrogen bonds       : angle       3.96832 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8160 (tp)
REVERT: B  223 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7636 (tt)
REVERT: C  100 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7265 (pp)
REVERT: D  196 ARG cc_start: 0.6770 (ttp-170) cc_final: 0.6471 (mtp180)
  outliers start: 22
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0692
  time to fit residues: 11.2087
Evaluate side-chains
  113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  153 VAL
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0870
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0470
   chunk 19 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.4656

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.168001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.149456 restraints weight = 9447.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149473 restraints weight = 8323.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.150194 restraints weight = 7563.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.150770 restraints weight = 6631.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.151179 restraints weight = 6096.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7949  Z= 0.102
  Angle     :  0.492   9.152  10781  Z= 0.249
  Chirality :  0.041   0.153   1243
  Planarity :  0.004   0.059   1336
  Dihedral  :  6.533  59.390   1107
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.81 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.82 (0.28), residues: 975
  helix:  1.56 (0.23), residues: 554
  sheet: -0.44 (0.63), residues: 70
  loop : -0.85 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 225 
 TYR   0.015   0.001   TYR D  17 
 PHE   0.017   0.001   PHE D  86 
 TRP   0.013   0.001   TRP A 276 
 HIS   0.002   0.000   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7949)
  covalent geometry    : angle       0.49175 (10781)
  hydrogen bonds       : bond        0.02995 (  421)
  hydrogen bonds       : angle       3.90614 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.197 
Fit side-chains
REVERT: B   66 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7897 (tp)
REVERT: B  223 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7627 (tt)
REVERT: C  157 MET cc_start: 0.7043 (mtp) cc_final: 0.6824 (mtp)
  outliers start: 16
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0644
  time to fit residues: 10.1160
Evaluate side-chains
  109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain D residue   44 TYR
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0570
   chunk 10 optimal weight:    0.0770
   chunk 68 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 88 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
D  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.169680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.151411 restraints weight = 9467.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.151482 restraints weight = 8231.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.151977 restraints weight = 7658.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.152161 restraints weight = 6903.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.152273 restraints weight = 6523.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7949  Z= 0.097
  Angle     :  0.494   8.599  10781  Z= 0.248
  Chirality :  0.041   0.154   1243
  Planarity :  0.004   0.060   1336
  Dihedral  :  6.399  59.997   1107
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.57 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.98 (0.28), residues: 975
  helix:  1.66 (0.23), residues: 554
  sheet: -0.35 (0.64), residues: 70
  loop : -0.74 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 196 
 TYR   0.014   0.001   TYR D  17 
 PHE   0.017   0.001   PHE D  86 
 TRP   0.034   0.001   TRP A 276 
 HIS   0.002   0.000   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7949)
  covalent geometry    : angle       0.49363 (10781)
  hydrogen bonds       : bond        0.02834 (  421)
  hydrogen bonds       : angle       3.83872 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  275 LEU cc_start: 0.8655 (tp) cc_final: 0.8376 (tp)
REVERT: B   66 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8094 (tp)
REVERT: C  157 MET cc_start: 0.6983 (mtp) cc_final: 0.6767 (mtp)
  outliers start: 18
  outliers final: 13
  residues processed: 112
  average time/residue: 0.0628
  time to fit residues: 10.1119
Evaluate side-chains
  110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.3807 r_free = 0.3807 target = 0.153515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.121984 restraints weight = 10828.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.125482 restraints weight = 7010.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.127844 restraints weight = 5239.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.129290 restraints weight = 4289.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.130543 restraints weight = 3756.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7949  Z= 0.204
  Angle     :  0.596  10.428  10781  Z= 0.299
  Chirality :  0.044   0.147   1243
  Planarity :  0.004   0.060   1336
  Dihedral  :  6.579  59.081   1107
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.41 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.56 (0.28), residues: 975
  helix:  1.31 (0.23), residues: 556
  sheet: -0.73 (0.60), residues: 70
  loop : -0.86 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 184 
 TYR   0.018   0.002   TYR D  54 
 PHE   0.021   0.002   PHE D  86 
 TRP   0.026   0.001   TRP A 276 
 HIS   0.003   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 7949)
  covalent geometry    : angle       0.59615 (10781)
  hydrogen bonds       : bond        0.03756 (  421)
  hydrogen bonds       : angle       4.15875 ( 1185)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B   66 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8176 (tp)
  outliers start: 16
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0696
  time to fit residues: 11.0671
Evaluate side-chains
  110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  243 ASP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  175 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    0.0050
   chunk 43 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 84 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 88 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0980
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.3394

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.169004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.150664 restraints weight = 9348.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.150841 restraints weight = 8061.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.151320 restraints weight = 7470.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.151946 restraints weight = 6644.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.152343 restraints weight = 6158.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7949  Z= 0.099
  Angle     :  0.508   8.988  10781  Z= 0.254
  Chirality :  0.041   0.154   1243
  Planarity :  0.004   0.060   1336
  Dihedral  :  6.421  59.278   1107
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 17.25 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.93 (0.28), residues: 975
  helix:  1.64 (0.23), residues: 554
  sheet: -0.49 (0.62), residues: 70
  loop : -0.77 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 257 
 TYR   0.013   0.001   TYR D 251 
 PHE   0.017   0.001   PHE D  86 
 TRP   0.030   0.001   TRP A 276 
 HIS   0.002   0.000   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7949)
  covalent geometry    : angle       0.50755 (10781)
  hydrogen bonds       : bond        0.02905 (  421)
  hydrogen bonds       : angle       3.86736 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1044.27 seconds
wall clock time: 18 minutes 47.26 seconds (1127.26 seconds total)