Starting phenix.real_space_refine
on Wed Feb 14 14:59:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frl_29400/02_2024/8frl_29400_updated.pdb"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.095
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       2      5.49       5
     S      40      5.16       5
     Cl      1      4.86       5
     C    5979      2.51       5
     N    1556      2.21       5
     O    1633      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  234": "OE1" <-> "OE2"
    Residue "B GLU   33": "OE1" <-> "OE2"
    Residue "F ARG  322": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 9211
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1876
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
    Chain: "B"
      Number of atoms: 1869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1869
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
    Chain: "F"
      Number of atoms: 2525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2525
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 303}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "G"
      Number of atoms: 2712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2712
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 12, 'TRANS': 325}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 194
          Unusual residues: {'JSG': 1, 'Y75': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'JSG:plan-7': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.44, per 1000 atoms: 0.59
  Number of scatterers: 9211
  At special positions: 0
  Unit cell: (105.6, 87.45, 141.075, 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)
     Cl      1     17.00
     S      40     16.00
     P       2     15.00
     O    1633      8.00
     N    1556      7.00
     C    5979      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  - 3.50
        Amino acid           : False - 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: 4.05
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      46 helices and 10 sheets defined
      52.5% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 58
    Processing helix  chain 'A' and resid 80 through 86
      removed outlier: 3.644A  pdb=" N   LYS A  86 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 111
      removed outlier: 3.793A  pdb=" N   ILE A 110 " --> pdb=" O   ASN A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 132
      removed outlier: 3.848A  pdb=" N   GLN A 124 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 138
      No H-bonds generated for 'chain 'A' and resid 136 through 138'
    Processing helix  chain 'A' and resid 148 through 162
      removed outlier: 3.724A  pdb=" N   ALA A 162 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 4.287A  pdb=" N   GLY A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ASP A 183 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 210
      removed outlier: 3.918A  pdb=" N   ALA A 210 " --> pdb=" O   ARG A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 234
    Processing helix  chain 'A' and resid 236 through 241
      removed outlier: 3.531A  pdb=" N   VAL A 241 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 58
    Processing helix  chain 'B' and resid 80 through 86
      removed outlier: 3.753A  pdb=" N   LYS B  86 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 113
      removed outlier: 3.567A  pdb=" N   ILE B 110 " --> pdb=" O   ASN B 106 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   THR B 113 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 132
      removed outlier: 3.621A  pdb=" N   GLN B 123 " --> pdb=" O   LYS B 119 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLN B 124 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 138
      No H-bonds generated for 'chain 'B' and resid 136 through 138'
    Processing helix  chain 'B' and resid 143 through 145
      No H-bonds generated for 'chain 'B' and resid 143 through 145'
    Processing helix  chain 'B' and resid 148 through 162
      removed outlier: 3.950A  pdb=" N   ALA B 162 " --> pdb=" O   ARG B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 193
    Processing helix  chain 'B' and resid 205 through 211
      removed outlier: 4.183A  pdb=" N   ALA B 210 " --> pdb=" O   ARG B 206 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE B 211 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 233
    Processing helix  chain 'B' and resid 236 through 241
    Processing helix  chain 'F' and resid 3 through 40
      removed outlier: 3.669A  pdb=" N   ARG F  30 " --> pdb=" O   MET F  26 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN F  40 " --> pdb=" O   GLY F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 54
      removed outlier: 3.544A  pdb=" N   ILE F  52 " --> pdb=" O   LEU F  48 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 56 through 81
      removed outlier: 4.019A  pdb=" N   LEU F  62 " --> pdb=" O   GLU F  58 " (cutoff:3.500A)
      Proline residue:  F  65  - end of helix
    Processing helix  chain 'F' and resid 86 through 89
      No H-bonds generated for 'chain 'F' and resid 86 through 89'
    Processing helix  chain 'F' and resid 95 through 118
      removed outlier: 3.806A  pdb=" N   LEU F 102 " --> pdb=" O   LEU F  98 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE F 103 " --> pdb=" O   GLY F  99 " (cutoff:3.500A)
      Proline residue:  F 104  - end of helix
    Processing helix  chain 'F' and resid 120 through 135
    Processing helix  chain 'F' and resid 140 through 143
    Processing helix  chain 'F' and resid 248 through 250
      No H-bonds generated for 'chain 'F' and resid 248 through 250'
    Processing helix  chain 'F' and resid 253 through 257
    Processing helix  chain 'F' and resid 263 through 273
    Processing helix  chain 'F' and resid 276 through 288
      removed outlier: 3.545A  pdb=" N   VAL F 280 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET F 284 " --> pdb=" O   ILE F 281 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   MET F 285 " --> pdb=" O   ALA F 282 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA F 286 " --> pdb=" O   LEU F 283 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   VAL F 287 " --> pdb=" O   MET F 284 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA F 288 " --> pdb=" O   MET F 285 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 300 through 325
      Proline residue:  F 304  - end of helix
      removed outlier: 3.516A  pdb=" N   PHE F 307 " --> pdb=" O   ILE F 303 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE F 308 " --> pdb=" O   PRO F 304 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU F 312 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ARG F 322 " --> pdb=" O   ALA F 318 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 330 through 349
      Proline residue:  F 334  - end of helix
      removed outlier: 3.734A  pdb=" N   VAL F 339 " --> pdb=" O   ALA F 336 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE F 342 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA F 343 " --> pdb=" O   TYR F 340 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA F 344 " --> pdb=" O   GLY F 341 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU F 346 " --> pdb=" O   ALA F 343 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER F 348 " --> pdb=" O   ALA F 345 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 40
      removed outlier: 3.961A  pdb=" N   SER G  40 " --> pdb=" O   LEU G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 48 through 57
      removed outlier: 3.514A  pdb=" N   VAL G  55 " --> pdb=" O   ALA G  51 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 59 through 84
      Proline residue:  G  68  - end of helix
      removed outlier: 3.626A  pdb=" N   LEU G  82 " --> pdb=" O   GLY G  78 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 94
      removed outlier: 3.714A  pdb=" N   VAL G  94 " --> pdb=" O   VAL G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 98 through 122
      removed outlier: 3.558A  pdb=" N   SER G 108 " --> pdb=" O   TRP G 104 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL G 111 " --> pdb=" O   ARG G 107 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU G 112 " --> pdb=" O   SER G 108 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 124 through 136
      removed outlier: 3.710A  pdb=" N   GLU G 129 " --> pdb=" O   PRO G 125 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 232 through 237
      removed outlier: 4.398A  pdb=" N   HIS G 236 " --> pdb=" O   LYS G 233 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 247 through 260
      removed outlier: 3.710A  pdb=" N   TYR G 260 " --> pdb=" O   TYR G 256 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 265 through 275
    Processing helix  chain 'G' and resid 277 through 293
    Processing helix  chain 'G' and resid 301 through 327
      removed outlier: 3.715A  pdb=" N   LEU G 327 " --> pdb=" O   GLY G 323 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 333 through 353
      Proline residue:  G 340  - end of helix
    Processing sheet with id=  A, first strand: chain 'A' and resid 32 through 35
    Processing sheet with id=  B, first strand: chain 'A' and resid 222 through 227
      removed outlier: 6.517A  pdb=" N   ILE A 217 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLU A 226 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA A 215 " --> pdb=" O   GLU A 226 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   HIS A 214 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   VAL A 198 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ILE A 200 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 17 through 19
      removed outlier: 7.789A  pdb=" N   LYS A  19 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   LYS A  28 " --> pdb=" O   LYS A  19 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 32 through 35
    Processing sheet with id=  E, first strand: chain 'B' and resid 222 through 227
      removed outlier: 6.853A  pdb=" N   ILE B 217 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   GLU B 226 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ALA B 215 " --> pdb=" O   GLU B 226 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   HIS B 214 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   VAL B 198 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   LEU B  42 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ILE B 200 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 17 through 19
      removed outlier: 7.778A  pdb=" N   LYS B  19 " --> pdb=" O   LYS B  28 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   LYS B  28 " --> pdb=" O   LYS B  19 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'F' and resid 148 through 152
      removed outlier: 4.269A  pdb=" N   GLU F 148 " --> pdb=" O   ALA F 159 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ALA F 159 " --> pdb=" O   GLU F 148 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'F' and resid 192 through 194
    Processing sheet with id=  I, first strand: chain 'G' and resid 149 through 153
    Processing sheet with id=  J, first strand: chain 'G' and resid 162 through 164
      removed outlier: 3.867A  pdb=" N   GLN G 168 " --> pdb=" O   ASN G 164 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   GLN G 191 " --> pdb=" O   ASN G 203 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   VAL G 195 " --> pdb=" O   GLN G 199 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   GLN G 199 " --> pdb=" O   VAL G 195 " (cutoff:3.500A)

    451 hydrogen bonds defined for protein.
    1257 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: 2.63

  Time building geometry restraints manager: 4.31 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1449
        1.32 -     1.44: 2476
        1.44 -     1.56: 5387
        1.56 -     1.68: 2
        1.68 -     1.81: 75
  Bond restraints: 9389
  Sorted by residual:
  bond pdb=" C7  JSG F 402 "
       pdb=" N2  JSG F 402 "
    ideal  model  delta    sigma   weight residual
    1.621  1.315  0.306 2.00e-02 2.50e+03 2.34e+02
  bond pdb=" C55 Y75 F 401 "
       pdb=" N27 Y75 F 401 "
    ideal  model  delta    sigma   weight residual
    1.526  1.327  0.199 2.00e-02 2.50e+03 9.93e+01
  bond pdb=" CDO JSG F 402 "
       pdb=" NAO JSG F 402 "
    ideal  model  delta    sigma   weight residual
    1.505  1.320  0.185 2.00e-02 2.50e+03 8.56e+01
  bond pdb=" C05 Y75 F 401 "
       pdb=" N04 Y75 F 401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.334  0.142 2.00e-02 2.50e+03 5.05e+01
  bond pdb=" C1  JSG F 402 "
       pdb=" O5  JSG F 402 "
    ideal  model  delta    sigma   weight residual
    1.533  1.395  0.138 2.00e-02 2.50e+03 4.74e+01
  ... (remaining 9384 not shown)

  Histogram of bond angle deviations from ideal:
       97.95 -   105.24: 151
      105.24 -   112.52: 4905
      112.52 -   119.81: 3223
      119.81 -   127.09: 4310
      127.09 -   134.37: 87
  Bond angle restraints: 12676
  Sorted by residual:
  angle pdb=" C02 Y75 F 401 "
        pdb=" N42 Y75 F 401 "
        pdb=" C44 Y75 F 401 "
      ideal   model   delta    sigma   weight residual
     109.67  125.80  -16.13 3.00e+00 1.11e-01 2.89e+01
  angle pdb=" N   ILE F 323 "
        pdb=" CA  ILE F 323 "
        pdb=" C   ILE F 323 "
      ideal   model   delta    sigma   weight residual
     111.05  104.65    6.40 1.25e+00 6.40e-01 2.62e+01
  angle pdb=" C26 Y75 F 401 "
        pdb=" N27 Y75 F 401 "
        pdb=" C55 Y75 F 401 "
      ideal   model   delta    sigma   weight residual
     109.44  122.14  -12.70 3.00e+00 1.11e-01 1.79e+01
  angle pdb=" C03 Y75 F 401 "
        pdb=" N04 Y75 F 401 "
        pdb=" C05 Y75 F 401 "
      ideal   model   delta    sigma   weight residual
     109.52  122.02  -12.50 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" N   ARG F 325 "
        pdb=" CA  ARG F 325 "
        pdb=" CB  ARG F 325 "
      ideal   model   delta    sigma   weight residual
     110.56  105.27    5.29 1.46e+00 4.69e-01 1.31e+01
  ... (remaining 12671 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.49: 5408
       29.49 -    58.98: 222
       58.98 -    88.47: 19
       88.47 -   117.96: 6
      117.96 -   147.45: 3
  Dihedral angle restraints: 5658
    sinusoidal: 2393
      harmonic: 3265
  Sorted by residual:
  dihedral pdb=" N04 Y75 F 401 "
           pdb=" C05 Y75 F 401 "
           pdb=" C06 Y75 F 401 "
           pdb=" N07 Y75 F 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.55  107.10  147.45     1      3.00e+01 1.11e-03 1.97e+01
  dihedral pdb=" C10 Y75 F 401 "
           pdb=" C08 Y75 F 401 "
           pdb=" C09 Y75 F 401 "
           pdb=" N07 Y75 F 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.18 -150.44 -140.38     1      3.00e+01 1.11e-03 1.89e+01
  dihedral pdb=" C12 Y75 F 401 "
           pdb=" C25 Y75 F 401 "
           pdb=" C26 Y75 F 401 "
           pdb=" N27 Y75 F 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.47  -64.71  134.18     1      3.00e+01 1.11e-03 1.81e+01
  ... (remaining 5655 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1193
       0.054 -    0.107: 211
       0.107 -    0.160: 30
       0.160 -    0.214: 8
       0.214 -    0.267: 1
  Chirality restraints: 1443
  Sorted by residual:
  chirality pdb=" CAN JSG F 402 "
            pdb=" CAL JSG F 402 "
            pdb=" CAP JSG F 402 "
            pdb=" NAO JSG F 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.80    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C2  JSG F 402 "
            pdb=" C1  JSG F 402 "
            pdb=" C3  JSG F 402 "
            pdb=" N2  JSG F 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.78    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" C3B LMT G 401 "
            pdb=" C2B LMT G 401 "
            pdb=" C4B LMT G 401 "
            pdb=" O3B LMT G 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.29    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1440 not shown)

  Planarity restraints: 1570
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 Y75 F 401 "    0.041 2.00e-02 2.50e+03   3.00e-01 1.35e+03
        pdb=" C03 Y75 F 401 "   -0.372 2.00e-02 2.50e+03
        pdb=" C43 Y75 F 401 "   -0.383 2.00e-02 2.50e+03
        pdb=" C44 Y75 F 401 "    0.324 2.00e-02 2.50e+03
        pdb=" N42 Y75 F 401 "    0.003 2.00e-02 2.50e+03
        pdb=" O01 Y75 F 401 "    0.388 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 Y75 F 401 "   -0.022 2.00e-02 2.50e+03   7.16e-02 1.28e+02
        pdb=" C13 Y75 F 401 "   -0.014 2.00e-02 2.50e+03
        pdb=" C15 Y75 F 401 "    0.015 2.00e-02 2.50e+03
        pdb=" C16 Y75 F 401 "    0.023 2.00e-02 2.50e+03
        pdb=" C17 Y75 F 401 "    0.010 2.00e-02 2.50e+03
        pdb=" C18 Y75 F 401 "    0.057 2.00e-02 2.50e+03
        pdb=" C25 Y75 F 401 "   -0.027 2.00e-02 2.50e+03
        pdb=" C26 Y75 F 401 "   -0.125 2.00e-02 2.50e+03
        pdb=" S11 Y75 F 401 "    0.157 2.00e-02 2.50e+03
        pdb="CL14 Y75 F 401 "   -0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C03 Y75 F 401 "    0.071 2.00e-02 2.50e+03   5.93e-02 4.39e+01
        pdb=" C05 Y75 F 401 "    0.002 2.00e-02 2.50e+03
        pdb=" C06 Y75 F 401 "    0.047 2.00e-02 2.50e+03
        pdb=" N04 Y75 F 401 "   -0.100 2.00e-02 2.50e+03
        pdb=" O36 Y75 F 401 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1567 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.11: 2
        2.11 -     2.81: 2535
        2.81 -     3.51: 12288
        3.51 -     4.20: 22232
        4.20 -     4.90: 40262
  Nonbonded interactions: 77319
  Sorted by model distance:
  nonbonded pdb=" CBE JSG F 402 "
            pdb=" OBU JSG F 402 "
     model   vdw
     1.416 3.470
  nonbonded pdb=" CBC JSG F 402 "
            pdb=" OBS JSG F 402 "
     model   vdw
     1.421 3.470
  nonbonded pdb=" OD2 ASP G 161 "
            pdb=" NH1 ARG G 171 "
     model   vdw
     2.257 2.520
  nonbonded pdb=" O   ASP A  71 "
            pdb=" OD1 ASN A  72 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ARG F 166 "
            pdb=" NH2 ARG F 195 "
     model   vdw
     2.308 2.520
  ... (remaining 77314 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 10 through 247)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  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:          7.450
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     29.810
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
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      :  0.009   0.306   9389  Z= 0.620
  Angle     :  0.710  16.134  12676  Z= 0.320
  Chirality :  0.045   0.267   1443
  Planarity :  0.009   0.300   1570
  Dihedral  : 16.032 147.446   3558
  Min Nonbonded Distance : 1.416

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.24), residues: 1111
  helix: -0.84 (0.20), residues: 600
  sheet:  1.62 (0.56), residues: 109
  loop : -1.07 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 271 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.007   0.001   PHE A 133 
 TYR   0.007   0.001   TYR F 333 
 ARG   0.002   0.000   ARG A 152 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.007 
Fit side-chains
REVERT: B  240 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8452 (ttmt)
REVERT: G  208 MET cc_start: 0.7316 (tmm) cc_final: 0.6290 (tmm)
REVERT: G  233 LYS cc_start: 0.8123 (tttp) cc_final: 0.7758 (ttpt)
REVERT: G  240 ILE cc_start: 0.8732 (mt) cc_final: 0.8390 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2863
  time to fit residues: 39.8143
Evaluate side-chains
  102 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 83 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    9.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 214 HIS
B 214 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9389  Z= 0.195
  Angle     :  0.543   6.762  12676  Z= 0.267
  Chirality :  0.042   0.215   1443
  Planarity :  0.004   0.043   1570
  Dihedral  : 12.392 155.446   1415
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  5.53 %
    Favored  : 93.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1111
  helix:  0.29 (0.20), residues: 602
  sheet:  1.42 (0.53), residues: 107
  loop : -1.03 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 271 
 HIS   0.003   0.001   HIS A  16 
 PHE   0.010   0.001   PHE B  32 
 TYR   0.009   0.001   TYR F   6 
 ARG   0.004   0.000   ARG F 195 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 ILE cc_start: 0.8268 (tt) cc_final: 0.8032 (tt)
REVERT: B  240 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8491 (ttmt)
REVERT: G  193 GLN cc_start: 0.7439 (tp40) cc_final: 0.7220 (tp40)
REVERT: G  208 MET cc_start: 0.7327 (tmm) cc_final: 0.6594 (tmm)
REVERT: G  233 LYS cc_start: 0.8090 (tttp) cc_final: 0.7688 (ttpt)
  outliers start: 5
  outliers final: 4
  residues processed: 109
  average time/residue: 0.2921
  time to fit residues: 41.5403
Evaluate side-chains
  109 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue  120 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0770
   chunk 89 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
G 193 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9389  Z= 0.202
  Angle     :  0.504   7.073  12676  Z= 0.247
  Chirality :  0.042   0.169   1443
  Planarity :  0.003   0.044   1570
  Dihedral  : 12.043 154.796   1415
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  8.34 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.25), residues: 1111
  helix:  0.74 (0.21), residues: 600
  sheet:  1.26 (0.49), residues: 117
  loop : -1.00 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 271 
 HIS   0.003   0.001   HIS G  10 
 PHE   0.012   0.001   PHE F  69 
 TYR   0.009   0.001   TYR F   6 
 ARG   0.003   0.000   ARG G 171 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 LYS cc_start: 0.8546 (mmtp) cc_final: 0.8251 (mmtp)
REVERT: A  138 ILE cc_start: 0.8293 (tt) cc_final: 0.8058 (tt)
REVERT: B  240 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8515 (ttmt)
REVERT: F  212 ARG cc_start: 0.6552 (mpt180) cc_final: 0.5994 (mtp180)
REVERT: G  208 MET cc_start: 0.7378 (tmm) cc_final: 0.6955 (tmm)
  outliers start: 6
  outliers final: 3
  residues processed: 113
  average time/residue: 0.2955
  time to fit residues: 44.3354
Evaluate side-chains
  107 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0020
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 95 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
A 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9389  Z= 0.181
  Angle     :  0.485   6.892  12676  Z= 0.238
  Chirality :  0.041   0.173   1443
  Planarity :  0.003   0.045   1570
  Dihedral  : 11.855 156.468   1415
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.43 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.25), residues: 1111
  helix:  1.03 (0.21), residues: 597
  sheet:  0.96 (0.47), residues: 123
  loop : -0.97 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 272 
 HIS   0.003   0.001   HIS G  10 
 PHE   0.010   0.001   PHE F  69 
 TYR   0.010   0.001   TYR F   6 
 ARG   0.003   0.000   ARG G 171 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASN cc_start: 0.7558 (p0) cc_final: 0.7272 (p0)
REVERT: A   67 GLU cc_start: 0.6973 (pm20) cc_final: 0.6599 (mp0)
REVERT: A  134 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8288 (mmtp)
REVERT: A  138 ILE cc_start: 0.8296 (tt) cc_final: 0.8052 (tt)
REVERT: B  240 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8514 (ttmt)
REVERT: F  233 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7812 (tt)
REVERT: F  326 ASP cc_start: 0.7997 (t0) cc_final: 0.7598 (t0)
REVERT: G  208 MET cc_start: 0.7392 (tmm) cc_final: 0.6941 (tmm)
  outliers start: 9
  outliers final: 5
  residues processed: 120
  average time/residue: 0.2553
  time to fit residues: 41.0970
Evaluate side-chains
  119 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  269 MET
Chi-restraints excluded: chain G residue  257 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0770
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9389  Z= 0.201
  Angle     :  0.492   7.291  12676  Z= 0.240
  Chirality :  0.041   0.163   1443
  Planarity :  0.003   0.044   1570
  Dihedral  : 11.800 156.971   1415
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.16 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.25), residues: 1111
  helix:  1.09 (0.21), residues: 599
  sheet:  0.65 (0.47), residues: 129
  loop : -0.89 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 272 
 HIS   0.003   0.001   HIS G  10 
 PHE   0.011   0.001   PHE F  69 
 TYR   0.010   0.001   TYR F   6 
 ARG   0.001   0.000   ARG A 152 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASN cc_start: 0.7624 (p0) cc_final: 0.7337 (p0)
REVERT: A  134 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8231 (mmtp)
REVERT: A  138 ILE cc_start: 0.8278 (tt) cc_final: 0.8031 (tt)
REVERT: B  240 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8511 (ttmt)
REVERT: F  233 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7770 (tt)
REVERT: F  326 ASP cc_start: 0.8027 (t0) cc_final: 0.7638 (t0)
REVERT: G  208 MET cc_start: 0.7390 (tmm) cc_final: 0.6960 (tmm)
REVERT: G  233 LYS cc_start: 0.8084 (tttp) cc_final: 0.7731 (ttpt)
  outliers start: 12
  outliers final: 6
  residues processed: 125
  average time/residue: 0.2822
  time to fit residues: 46.4310
Evaluate side-chains
  123 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  269 MET
Chi-restraints excluded: chain G residue  202 LEU
Chi-restraints excluded: chain G residue  257 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0670
   chunk 26 optimal weight:    0.0970
   chunk 106 optimal weight:    0.5980
   chunk 88 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0370
   chunk 8 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.2794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9389  Z= 0.131
  Angle     :  0.456   6.745  12676  Z= 0.226
  Chirality :  0.040   0.155   1443
  Planarity :  0.003   0.043   1570
  Dihedral  : 11.539 158.695   1415
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.68 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1111
  helix:  1.40 (0.22), residues: 598
  sheet:  0.75 (0.47), residues: 129
  loop : -0.87 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 150 
 HIS   0.002   0.000   HIS A  16 
 PHE   0.009   0.001   PHE B  32 
 TYR   0.007   0.001   TYR F   6 
 ARG   0.002   0.000   ARG B 206 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASN cc_start: 0.7515 (p0) cc_final: 0.7217 (p0)
REVERT: A   67 GLU cc_start: 0.7217 (pm20) cc_final: 0.6987 (mt-10)
REVERT: A  134 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8226 (mmtp)
REVERT: A  138 ILE cc_start: 0.8261 (tt) cc_final: 0.8026 (tt)
REVERT: B  240 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8504 (ttmt)
REVERT: F  212 ARG cc_start: 0.6615 (mpt180) cc_final: 0.6040 (mtp85)
REVERT: F  233 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7756 (tt)
REVERT: F  326 ASP cc_start: 0.8002 (t0) cc_final: 0.7536 (t0)
REVERT: G  208 MET cc_start: 0.7451 (tmm) cc_final: 0.7025 (tmm)
  outliers start: 12
  outliers final: 8
  residues processed: 124
  average time/residue: 0.2609
  time to fit residues: 43.1365
Evaluate side-chains
  118 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  269 MET
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue  193 GLN
Chi-restraints excluded: chain G residue  202 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    0.4980
   chunk 59 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    2.8988

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

Flipped N/Q/H residues before XYZ refinement:
F 135 GLN
** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.066   9389  Z= 0.630
  Angle     :  0.706   8.177  12676  Z= 0.343
  Chirality :  0.052   0.194   1443
  Planarity :  0.005   0.047   1570
  Dihedral  : 12.493 156.181   1415
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.03 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.25), residues: 1111
  helix:  0.23 (0.20), residues: 606
  sheet:  0.27 (0.47), residues: 127
  loop : -1.10 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP G 272 
 HIS   0.005   0.001   HIS G  10 
 PHE   0.016   0.002   PHE F  69 
 TYR   0.018   0.002   TYR F   6 
 ARG   0.006   0.000   ARG A 152 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASN cc_start: 0.7749 (p0) cc_final: 0.7454 (p0)
REVERT: A  134 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8347 (mmtp)
REVERT: A  138 ILE cc_start: 0.8397 (tt) cc_final: 0.8151 (tt)
REVERT: B  240 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8400 (ttmt)
REVERT: F  233 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7755 (tt)
REVERT: F  326 ASP cc_start: 0.8040 (t0) cc_final: 0.7683 (t0)
REVERT: G  184 LYS cc_start: 0.7987 (mttp) cc_final: 0.6896 (mttp)
REVERT: G  208 MET cc_start: 0.7493 (tmm) cc_final: 0.7024 (tmm)
REVERT: G  233 LYS cc_start: 0.8138 (tttp) cc_final: 0.7723 (ttpt)
REVERT: G  257 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8308 (mtp)
  outliers start: 15
  outliers final: 10
  residues processed: 136
  average time/residue: 0.2619
  time to fit residues: 46.9303
Evaluate side-chains
  138 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue   73 MET
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  284 MET
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   70 SER
Chi-restraints excluded: chain G residue  257 MET
Chi-restraints excluded: chain G residue  328 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9389  Z= 0.206
  Angle     :  0.515   6.674  12676  Z= 0.254
  Chirality :  0.041   0.157   1443
  Planarity :  0.003   0.046   1570
  Dihedral  : 12.182 157.853   1415
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 13.87 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1111
  helix:  0.76 (0.21), residues: 602
  sheet:  0.37 (0.48), residues: 125
  loop : -1.04 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F 271 
 HIS   0.002   0.001   HIS G  10 
 PHE   0.011   0.001   PHE F  69 
 TYR   0.013   0.001   TYR F   6 
 ARG   0.002   0.000   ARG A 152 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASN cc_start: 0.7652 (p0) cc_final: 0.7345 (p0)
REVERT: A  138 ILE cc_start: 0.8328 (tt) cc_final: 0.8085 (tt)
REVERT: B  240 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8465 (ttmt)
REVERT: F  233 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7729 (tt)
REVERT: F  326 ASP cc_start: 0.8078 (t0) cc_final: 0.7726 (t0)
REVERT: G  208 MET cc_start: 0.7454 (tmm) cc_final: 0.6987 (tmm)
  outliers start: 7
  outliers final: 5
  residues processed: 110
  average time/residue: 0.2825
  time to fit residues: 41.1211
Evaluate side-chains
  109 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain G residue   66 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   chunk 89 optimal weight:    0.0270
   chunk 93 optimal weight:    0.0050
   chunk 64 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.3650

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9389  Z= 0.149
  Angle     :  0.472   6.771  12676  Z= 0.235
  Chirality :  0.040   0.143   1443
  Planarity :  0.003   0.044   1570
  Dihedral  : 11.836 160.168   1415
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 13.87 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1111
  helix:  1.26 (0.22), residues: 595
  sheet:  0.53 (0.48), residues: 123
  loop : -1.03 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 150 
 HIS   0.002   0.000   HIS G  10 
 PHE   0.010   0.001   PHE B  32 
 TYR   0.007   0.001   TYR F   6 
 ARG   0.002   0.000   ARG A 152 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASN cc_start: 0.7522 (p0) cc_final: 0.7241 (p0)
REVERT: A  138 ILE cc_start: 0.8291 (tt) cc_final: 0.8046 (tt)
REVERT: B  240 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8484 (ttmt)
REVERT: F  212 ARG cc_start: 0.6454 (mpt180) cc_final: 0.5921 (mtp85)
REVERT: F  233 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7737 (tt)
REVERT: F  326 ASP cc_start: 0.8051 (t0) cc_final: 0.7644 (t0)
REVERT: G  208 MET cc_start: 0.7409 (tmm) cc_final: 0.7112 (tmm)
  outliers start: 8
  outliers final: 5
  residues processed: 107
  average time/residue: 0.2865
  time to fit residues: 40.5691
Evaluate side-chains
  107 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 1.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  269 MET
Chi-restraints excluded: chain G residue   66 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 72 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 87 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 92 optimal weight:    8.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9389  Z= 0.215
  Angle     :  0.496   6.990  12676  Z= 0.245
  Chirality :  0.041   0.142   1443
  Planarity :  0.003   0.044   1570
  Dihedral  : 11.898 160.228   1415
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 14.29 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1111
  helix:  1.22 (0.21), residues: 598
  sheet:  0.71 (0.49), residues: 119
  loop : -1.01 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 272 
 HIS   0.002   0.001   HIS G  10 
 PHE   0.012   0.001   PHE F  69 
 TYR   0.010   0.001   TYR F   6 
 ARG   0.002   0.000   ARG A 152 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8231 (mttt) cc_final: 0.7666 (mmmt)
REVERT: A   20 ASN cc_start: 0.7570 (p0) cc_final: 0.7270 (p0)
REVERT: A   67 GLU cc_start: 0.7353 (pm20) cc_final: 0.7059 (mt-10)
REVERT: A  138 ILE cc_start: 0.8302 (tt) cc_final: 0.8048 (tt)
REVERT: B  240 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8475 (ttmt)
REVERT: F  212 ARG cc_start: 0.6425 (mpt180) cc_final: 0.5898 (mtp85)
REVERT: F  233 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7721 (tt)
REVERT: F  326 ASP cc_start: 0.8076 (t0) cc_final: 0.7669 (t0)
REVERT: G  184 LYS cc_start: 0.8042 (mttp) cc_final: 0.7256 (mttp)
REVERT: G  207 GLN cc_start: 0.7809 (tt0) cc_final: 0.7163 (tm-30)
REVERT: G  208 MET cc_start: 0.7525 (tmm) cc_final: 0.6932 (tmm)
REVERT: G  233 LYS cc_start: 0.8108 (tttp) cc_final: 0.7749 (ttpt)
  outliers start: 7
  outliers final: 5
  residues processed: 118
  average time/residue: 0.3510
  time to fit residues: 53.3843
Evaluate side-chains
  117 residues out of total 961 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain F residue   47 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  269 MET
Chi-restraints excluded: chain G residue   66 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    0.1980
   chunk 87 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 63 optimal weight:    8.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
G 193 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.136842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.100025 restraints weight = 10115.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.41
r_work: 0.2826 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9389  Z= 0.187
  Angle     :  0.486   6.841  12676  Z= 0.240
  Chirality :  0.041   0.135   1443
  Planarity :  0.003   0.045   1570
  Dihedral  : 11.929 160.837   1415
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.29 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1111
  helix:  1.26 (0.21), residues: 599
  sheet:  0.79 (0.49), residues: 119
  loop : -1.01 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 271 
 HIS   0.002   0.000   HIS G  10 
 PHE   0.011   0.001   PHE F  69 
 TYR   0.010   0.001   TYR F   6 
 ARG   0.002   0.000   ARG A 152 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2219.55 seconds
wall clock time: 41 minutes 19.85 seconds (2479.85 seconds total)