Starting phenix.real_space_refine
on Sun Dec 10 03:43:23 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twe_41667/12_2023/8twe_41667_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twe_41667/12_2023/8twe_41667.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twe_41667/12_2023/8twe_41667.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twe_41667/12_2023/8twe_41667.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twe_41667/12_2023/8twe_41667_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twe_41667/12_2023/8twe_41667_trim_updated.pdb"
  }
  resolution = 2.55
  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=  -0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4210      2.51       5
     N    1154      2.21       5
     O    1283      1.98       5
     H    6622      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 13305
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 6065
          Classifications: {'peptide': 387}
          Link IDs: {'PTRANS': 18, 'TRANS': 368}
    Chain: "B"
      Number of atoms: 6849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 6849
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 14, 'TRANS': 408}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 187
          Classifications: {'peptide': 11}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Planarities with less than four sites: {'MLL%COO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 204
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
  Time building chain proxies: 5.98, per 1000 atoms: 0.45
  Number of scatterers: 13305
  At special positions: 0
  Unit cell: (100.926, 89.178, 106.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     O    1283      8.00
     N    1154      7.00
     C    4210      6.00
     H    6622      1.00
    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: 10.53
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1620

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      40 helices and 9 sheets defined
      41.5% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 21
      removed outlier: 4.296A  pdb=" N   ARG A  21 " --> pdb=" O   ILE A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 42
      removed outlier: 5.274A  pdb=" N   SER A  36 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   THR A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 51 through 55
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.535A  pdb=" N   GLY A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   THR A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 98
      removed outlier: 5.493A  pdb=" N   HIS A  87 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      Proline residue:  A  91  - end of helix
      removed outlier: 3.530A  pdb=" N   SER A  95 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 116
    Processing helix  chain 'A' and resid 121 through 126
    Processing helix  chain 'A' and resid 128 through 136
    Processing helix  chain 'A' and resid 141 through 157
      removed outlier: 3.525A  pdb=" N   CYS A 148 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   GLY A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LEU A 150 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   PHE A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   SER A 152 " --> pdb=" O   CYS A 148 " (cutoff:3.500A)
      removed outlier: 5.460A  pdb=" N   VAL A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   CYS A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 160 through 175
    Processing helix  chain 'A' and resid 179 through 195
      removed outlier: 4.501A  pdb=" N   GLY A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL A 195 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 203
    Processing helix  chain 'A' and resid 205 through 214
    Processing helix  chain 'A' and resid 218 through 234
      removed outlier: 4.085A  pdb=" N   LEU A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 224 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL A 225 " --> pdb=" O   ARG A 221 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   GLU A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 243
      removed outlier: 4.187A  pdb=" N   GLU A 241 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 252
    Processing helix  chain 'A' and resid 257 through 265
    Processing helix  chain 'A' and resid 267 through 274
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 283 through 291
    Processing helix  chain 'A' and resid 296 through 311
      removed outlier: 3.852A  pdb=" N   LYS A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   LYS A 307 " --> pdb=" O   SER A 303 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   GLU A 308 " --> pdb=" O   HIS A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 324
    Processing helix  chain 'A' and resid 326 through 335
      removed outlier: 3.585A  pdb=" N   GLU A 332 " --> pdb=" O   PRO A 328 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 346
    Processing helix  chain 'A' and resid 349 through 356
      Proline residue:  A 354  - end of helix
    Processing helix  chain 'A' and resid 358 through 363
    Processing helix  chain 'A' and resid 365 through 373
    Processing helix  chain 'A' and resid 378 through 387
    Processing helix  chain 'A' and resid 389 through 392
      No H-bonds generated for 'chain 'A' and resid 389 through 392'
    Processing helix  chain 'B' and resid 27 through 29
      No H-bonds generated for 'chain 'B' and resid 27 through 29'
    Processing helix  chain 'B' and resid 146 through 148
      No H-bonds generated for 'chain 'B' and resid 146 through 148'
    Processing helix  chain 'B' and resid 222 through 224
      No H-bonds generated for 'chain 'B' and resid 222 through 224'
    Processing helix  chain 'B' and resid 282 through 285
      No H-bonds generated for 'chain 'B' and resid 282 through 285'
    Processing helix  chain 'B' and resid 327 through 329
      No H-bonds generated for 'chain 'B' and resid 327 through 329'
    Processing helix  chain 'B' and resid 333 through 338
    Processing helix  chain 'B' and resid 341 through 343
      No H-bonds generated for 'chain 'B' and resid 341 through 343'
    Processing helix  chain 'B' and resid 383 through 385
      No H-bonds generated for 'chain 'B' and resid 383 through 385'
    Processing helix  chain 'B' and resid 410 through 412
      No H-bonds generated for 'chain 'B' and resid 410 through 412'
    Processing helix  chain 'D' and resid 84 through 91
    Processing sheet with id=  A, first strand: chain 'B' and resid 31 through 36
      removed outlier: 6.147A  pdb=" N   GLY B  46 " --> pdb=" O   SER B  32 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   VAL B  34 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ALA B  44 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   PHE B  36 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LEU B  42 " --> pdb=" O   PHE B  36 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ARG B  51 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   GLN B  56 " --> pdb=" O   VAL B  73 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   VAL B  73 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 83 through 85
      removed outlier: 3.565A  pdb=" N   GLU B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 98 through 101
      removed outlier: 3.815A  pdb=" N   LYS B  98 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG B 170 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LYS B 123 " --> pdb=" O   PRO B 168 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   SER B 125 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ALA B 166 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ARG B 127 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   VAL B 164 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 129 through 132
    Processing sheet with id=  E, first strand: chain 'B' and resid 182 through 185
      removed outlier: 6.654A  pdb=" N   LEU B 202 " --> pdb=" O   ASN B 213 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   ASN B 213 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 267 through 269
      removed outlier: 3.779A  pdb=" N   ALA B 231 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 290 through 293
    Processing sheet with id=  H, first strand: chain 'B' and resid 348 through 350
    Processing sheet with id=  I, first strand: chain 'B' and resid 421 through 424
      removed outlier: 4.430A  pdb=" N   HIS B 421 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   GLN B 443 " --> pdb=" O   PHE B  14 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   PHE B  14 " --> pdb=" O   GLN B 443 " (cutoff:3.500A)

    242 hydrogen bonds defined for protein.
    657 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: 4.97

  Time building geometry restraints manager: 10.85 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6602
        1.03 -     1.23: 31
        1.23 -     1.42: 2812
        1.42 -     1.62: 3930
        1.62 -     1.81: 52
  Bond restraints: 13427
  Sorted by residual:
  bond pdb=" C   MLL C 309 "
       pdb=" OXT MLL C 309 "
    ideal  model  delta    sigma   weight residual
    1.231  1.364 -0.133 2.00e-02 2.50e+03 4.42e+01
  bond pdb=" CA  VAL A 129 "
       pdb=" CB  VAL A 129 "
    ideal  model  delta    sigma   weight residual
    1.534  1.543 -0.009 6.80e-03 2.16e+04 1.58e+00
  bond pdb=" CA  ILE A 206 "
       pdb=" CB  ILE A 206 "
    ideal  model  delta    sigma   weight residual
    1.539  1.533  0.006 5.40e-03 3.43e+04 1.17e+00
  bond pdb=" CB  TRP B 350 "
       pdb=" CG  TRP B 350 "
    ideal  model  delta    sigma   weight residual
    1.498  1.473  0.025 3.10e-02 1.04e+03 6.48e-01
  bond pdb=" CB  GLU B 190 "
       pdb=" CG  GLU B 190 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.70e-01
  ... (remaining 13422 not shown)

  Histogram of bond angle deviations from ideal:
      100.11 -   106.89: 204
      106.89 -   113.67: 16086
      113.67 -   120.45: 4313
      120.45 -   127.22: 3583
      127.22 -   134.00: 73
  Bond angle restraints: 24259
  Sorted by residual:
  angle pdb=" CA  VAL A 348 "
        pdb=" C   VAL A 348 "
        pdb=" N   ILE A 349 "
      ideal   model   delta    sigma   weight residual
     116.60  120.21   -3.61 1.45e+00 4.76e-01 6.21e+00
  angle pdb=" N   MLL C 309 "
        pdb=" CA  MLL C 309 "
        pdb=" CB  MLL C 309 "
      ideal   model   delta    sigma   weight residual
     110.50  114.49   -3.99 1.70e+00 3.46e-01 5.51e+00
  angle pdb=" CA  MLL C 309 "
        pdb=" C   MLL C 309 "
        pdb=" OXT MLL C 309 "
      ideal   model   delta    sigma   weight residual
     121.00  114.17    6.83 3.00e+00 1.11e-01 5.18e+00
  angle pdb=" N   THR B 226 "
        pdb=" CA  THR B 226 "
        pdb=" C   THR B 226 "
      ideal   model   delta    sigma   weight residual
     114.56  111.89    2.67 1.27e+00 6.20e-01 4.43e+00
  angle pdb=" N   VAL A 348 "
        pdb=" CA  VAL A 348 "
        pdb=" C   VAL A 348 "
      ideal   model   delta    sigma   weight residual
     109.34  113.56   -4.22 2.08e+00 2.31e-01 4.11e+00
  ... (remaining 24254 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 5878
       16.73 -    33.46: 208
       33.46 -    50.19: 70
       50.19 -    66.92: 21
       66.92 -    83.65: 18
  Dihedral angle restraints: 6195
    sinusoidal: 3337
      harmonic: 2858
  Sorted by residual:
  dihedral pdb=" CA  TRP B 311 "
           pdb=" C   TRP B 311 "
           pdb=" N   ASP B 312 "
           pdb=" CA  ASP B 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.42   19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  TRP B 203 "
           pdb=" C   TRP B 203 "
           pdb=" N   HIS B 204 "
           pdb=" CA  HIS B 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.85   18.15     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  THR B 114 "
           pdb=" C   THR B 114 "
           pdb=" N   ASN B 115 "
           pdb=" CA  ASN B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.85   17.15     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 6192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 635
       0.026 -    0.052: 261
       0.052 -    0.078: 80
       0.078 -    0.104: 42
       0.104 -    0.130: 29
  Chirality restraints: 1047
  Sorted by residual:
  chirality pdb=" CA  VAL B 308 "
            pdb=" N   VAL B 308 "
            pdb=" C   VAL B 308 "
            pdb=" CB  VAL B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  VAL B  34 "
            pdb=" N   VAL B  34 "
            pdb=" C   VAL B  34 "
            pdb=" CB  VAL B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE B 171 "
            pdb=" N   ILE B 171 "
            pdb=" C   ILE B 171 "
            pdb=" CB  ILE B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1044 not shown)

  Planarity restraints: 1980
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 206 "    0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO A 207 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 207 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 207 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 129 "   -0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO A 130 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 130 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 130 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 141 "    0.009 2.00e-02 2.50e+03   5.92e-03 1.05e+00
        pdb=" CG  PHE A 141 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 141 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 141 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 141 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 141 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 141 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1977 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.06: 230
        2.06 -     2.69: 21222
        2.69 -     3.33: 39547
        3.33 -     3.96: 51775
        3.96 -     4.60: 81023
  Nonbonded interactions: 193797
  Sorted by model distance:
  nonbonded pdb=" OXT MLL C 309 "
            pdb=" C10 MLL C 309 "
     model   vdw
     1.425 3.100
  nonbonded pdb=" OE1 GLU B  94 "
            pdb=" H   GLU B  94 "
     model   vdw
     1.642 1.850
  nonbonded pdb=" O   GLY A 357 "
            pdb=" HG1 THR A 361 "
     model   vdw
     1.645 1.850
  nonbonded pdb=" OD1 ASP B 196 "
            pdb=" H   ARG B 199 "
     model   vdw
     1.648 1.850
  nonbonded pdb=" OE1 GLU A 379 "
            pdb=" H   GLU A 379 "
     model   vdw
     1.659 1.850
  ... (remaining 193792 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.860
  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:             0.190
  Extract box with map and model:          32.360
  Check model and map are aligned:         0.200
  Set scattering table:                    0.120
  Process input model:                     45.290
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  100.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
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      :  0.003   0.133   6805  Z= 0.215
  Angle     :  0.477   6.830   9206  Z= 0.254
  Chirality :  0.038   0.130   1047
  Planarity :  0.003   0.030   1189
  Dihedral  : 10.129  83.646   2557
  Min Nonbonded Distance : 1.425

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.80 %
    Favored  : 99.07 %
  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:  1.05 (0.31), residues: 816
  helix:  1.17 (0.30), residues: 340
  sheet:  0.47 (0.36), residues: 185
  loop :  0.50 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP B 203 
   HIS   0.002   0.001   HIS A 304 
   PHE   0.018   0.001   PHE A 141 
   TYR   0.012   0.001   TYR B 178 
   ARG   0.003   0.000   ARG B 298 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 81
  average time/residue: 2.9120
  time to fit residues: 247.5347
Evaluate side-chains
  43 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 1.139 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 0
  time to fit residues: 1.3978
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6805  Z= 0.301
  Angle     :  0.539   5.439   9206  Z= 0.288
  Chirality :  0.040   0.146   1047
  Planarity :  0.004   0.034   1189
  Dihedral  :  4.785  42.901    901
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  6.24 %
    Favored  : 92.96 %
  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:  0.88 (0.30), residues: 816
  helix:  1.20 (0.30), residues: 333
  sheet:  0.46 (0.39), residues: 166
  loop :  0.14 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP B 203 
   HIS   0.004   0.001   HIS A 304 
   PHE   0.018   0.002   PHE B 280 
   TYR   0.013   0.002   TYR B 178 
   ARG   0.004   0.000   ARG B 318 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 52
  average time/residue: 2.3759
  time to fit residues: 131.7173
Evaluate side-chains
  44 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 1.033 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.4427
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
D  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6805  Z= 0.266
  Angle     :  0.495   5.578   9206  Z= 0.263
  Chirality :  0.039   0.136   1047
  Planarity :  0.003   0.035   1189
  Dihedral  :  4.598  34.864    901
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  6.64 %
    Favored  : 92.30 %
  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:  0.89 (0.30), residues: 816
  helix:  1.40 (0.30), residues: 328
  sheet:  0.36 (0.39), residues: 166
  loop :  0.01 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP B 203 
   HIS   0.003   0.001   HIS B 425 
   PHE   0.014   0.001   PHE A 141 
   TYR   0.012   0.001   TYR B 178 
   ARG   0.002   0.000   ARG A  46 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 2
  residues processed: 49
  average time/residue: 2.1915
  time to fit residues: 115.1121
Evaluate side-chains
  40 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 1.115 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 2
  residues processed: 0
  time to fit residues: 1.3946
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9744

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6805  Z= 0.203
  Angle     :  0.468   5.328   9206  Z= 0.247
  Chirality :  0.039   0.137   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.451  31.522    901
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  6.91 %
    Favored  : 92.30 %
  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:  0.90 (0.30), residues: 816
  helix:  1.42 (0.30), residues: 329
  sheet:  0.30 (0.39), residues: 166
  loop :  0.04 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 203 
   HIS   0.002   0.001   HIS A 304 
   PHE   0.015   0.001   PHE A 141 
   TYR   0.011   0.001   TYR B 244 
   ARG   0.001   0.000   ARG B 158 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 47
  average time/residue: 2.1428
  time to fit residues: 108.7295
Evaluate side-chains
  39 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 1.277 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 2
  residues processed: 0
  time to fit residues: 1.3879
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 221 ASN
D  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6805  Z= 0.201
  Angle     :  0.460   5.127   9206  Z= 0.243
  Chirality :  0.038   0.134   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.361  29.050    901
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.04 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.89 (0.30), residues: 816
  helix:  1.50 (0.30), residues: 329
  sheet:  0.12 (0.39), residues: 172
  loop :  0.03 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B 203 
   HIS   0.002   0.001   HIS B  38 
   PHE   0.014   0.001   PHE A 141 
   TYR   0.011   0.001   TYR B 244 
   ARG   0.001   0.000   ARG B 158 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 44
  average time/residue: 2.4583
  time to fit residues: 115.7253
Evaluate side-chains
  39 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 1.133 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.3910
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0030
   chunk 19 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.3196

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6805  Z= 0.258
  Angle     :  0.477   5.146   9206  Z= 0.253
  Chirality :  0.039   0.136   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.402  28.137    901
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.04 %
    Favored  : 92.03 %
  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:  0.72 (0.30), residues: 816
  helix:  1.33 (0.30), residues: 335
  sheet:  0.05 (0.40), residues: 172
  loop : -0.06 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 203 
   HIS   0.003   0.001   HIS B  38 
   PHE   0.015   0.001   PHE A 141 
   TYR   0.012   0.001   TYR B 244 
   ARG   0.001   0.000   ARG B 158 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 44
  average time/residue: 2.3558
  time to fit residues: 110.7037
Evaluate side-chains
  38 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 1.021 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.3614
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6805  Z= 0.170
  Angle     :  0.449   5.160   9206  Z= 0.237
  Chirality :  0.038   0.133   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.309  28.244    901
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.44 %
    Favored  : 91.90 %
  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:  0.81 (0.30), residues: 816
  helix:  1.41 (0.30), residues: 335
  sheet:  0.08 (0.40), residues: 172
  loop : -0.02 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 203 
   HIS   0.002   0.001   HIS B 421 
   PHE   0.014   0.001   PHE A 141 
   TYR   0.010   0.001   TYR B 244 
   ARG   0.001   0.000   ARG A 318 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 41
  average time/residue: 2.2249
  time to fit residues: 98.2818
Evaluate side-chains
  39 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.996 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.5194
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 62 optimal weight:    0.4980
   chunk 71 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 438 ASN
D  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6805  Z= 0.178
  Angle     :  0.448   5.064   9206  Z= 0.236
  Chirality :  0.038   0.134   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.253  29.024    901
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.70 %
    Favored  : 91.50 %
  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:  0.80 (0.30), residues: 816
  helix:  1.42 (0.30), residues: 341
  sheet:  0.09 (0.40), residues: 172
  loop : -0.08 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B 203 
   HIS   0.002   0.001   HIS B  38 
   PHE   0.014   0.001   PHE A 141 
   TYR   0.017   0.001   TYR A  60 
   ARG   0.001   0.000   ARG B 257 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 42
  average time/residue: 2.3054
  time to fit residues: 103.9674
Evaluate side-chains
  39 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 1.226 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.3965
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   chunk 73 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6805  Z= 0.153
  Angle     :  0.443   5.089   9206  Z= 0.231
  Chirality :  0.038   0.133   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.193  32.135    901
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.57 %
    Favored  : 91.77 %
  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:  0.89 (0.30), residues: 816
  helix:  1.49 (0.30), residues: 341
  sheet:  0.12 (0.40), residues: 172
  loop : -0.02 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 203 
   HIS   0.002   0.001   HIS B 421 
   PHE   0.014   0.001   PHE A 141 
   TYR   0.022   0.001   TYR A  60 
   ARG   0.003   0.000   ARG B 127 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 42
  average time/residue: 2.1870
  time to fit residues: 99.0719
Evaluate side-chains
  40 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 1.127 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.5013
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 75 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6805  Z= 0.228
  Angle     :  0.464   5.767   9206  Z= 0.244
  Chirality :  0.038   0.134   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.314  37.423    901
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.70 %
    Favored  : 91.77 %
  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:  0.80 (0.30), residues: 816
  helix:  1.46 (0.30), residues: 340
  sheet: -0.03 (0.40), residues: 174
  loop : -0.05 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B 203 
   HIS   0.003   0.001   HIS B  38 
   PHE   0.014   0.001   PHE A 141 
   TYR   0.021   0.001   TYR A  60 
   ARG   0.001   0.000   ARG B 257 

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 41
  average time/residue: 2.4702
  time to fit residues: 108.9449
Evaluate side-chains
  40 residues out of total 753 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 1.634 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 2.3209
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.3980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 65 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 8 optimal weight:    0.1980
   chunk 12 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.083955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.056819 restraints weight = 36319.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 2.39
r_work: 0.2618 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2501 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6805  Z= 0.124
  Angle     :  0.438   5.659   9206  Z= 0.227
  Chirality :  0.038   0.135   1047
  Planarity :  0.003   0.034   1189
  Dihedral  :  4.169  39.252    901
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  7.84 %
    Favored  : 91.77 %
  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:  0.95 (0.31), residues: 816
  helix:  1.55 (0.30), residues: 341
  sheet:  0.08 (0.40), residues: 174
  loop :  0.04 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 203 
   HIS   0.002   0.000   HIS B 421 
   PHE   0.014   0.001   PHE A 141 
   TYR   0.023   0.001   TYR A  60 
   ARG   0.002   0.000   ARG B 127 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5241.13 seconds
wall clock time: 96 minutes 11.31 seconds (5771.31 seconds total)