Starting phenix.real_space_refine (version: 1.21rc1)
on Wed Apr 26 14:03:41 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/04_2023/8adg_15362_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/04_2023/8adg_15362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/04_2023/8adg_15362.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/04_2023/8adg_15362.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/04_2023/8adg_15362_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/04_2023/8adg_15362_trim_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.051
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      32      5.16       5
     C    7440      2.51       5
     N    2019      2.21       5
     O    2317      1.98       5
     H   11375      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  232": "OD1" <-> "OD2"
    Residue "A ASP  447": "OD1" <-> "OD2"
    Residue "A TYR  609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  623": "OD1" <-> "OD2"
    Residue "A GLU  650": "OE1" <-> "OE2"
    Residue "A TYR  794": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  127": "OE1" <-> "OE2"
    Residue "B GLU  352": "OE1" <-> "OE2"
    Residue "D TYR  154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  183": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 23183
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 12167
          Classifications: {'peptide': 787}
          Link IDs: {'PTRANS': 29, 'TRANS': 757}
    Chain: "B"
      Number of atoms: 5393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 5393
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 11, 'TRANS': 349}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 845
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3348
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1292
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "F"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 138
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UX8:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 9.94, per 1000 atoms: 0.43
  Number of scatterers: 23183
  At special positions: 0
  Unit cell: (97.75, 133.45, 125.8, 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      32     16.00
     O    2317      8.00
     N    2019      7.00
     C    7440      6.00
     H   11375      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.04

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 18.35
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2756

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      27 helices and 15 sheets defined
      20.8% alpha, 26.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 45
    Processing helix  chain 'A' and resid 56 through 68
    Processing helix  chain 'A' and resid 107 through 117
    Processing helix  chain 'A' and resid 130 through 144
    Processing helix  chain 'A' and resid 190 through 196
      removed outlier: 4.590A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 233
      removed outlier: 4.094A  pdb=" N   ARG A 233 " --> pdb=" O   TYR A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 288
      removed outlier: 4.019A  pdb=" N   GLN A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LEU A 287 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR A 288 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 315
      removed outlier: 3.761A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 368
      removed outlier: 4.420A  pdb=" N   GLU A 368 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 392
    Processing helix  chain 'A' and resid 449 through 451
      No H-bonds generated for 'chain 'A' and resid 449 through 451'
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 543 through 551
      removed outlier: 3.607A  pdb=" N   TYR A 550 " --> pdb=" O   TRP A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 694
      No H-bonds generated for 'chain 'A' and resid 692 through 694'
    Processing helix  chain 'C' and resid 31 through 38
      removed outlier: 4.039A  pdb=" N   VAL C  35 " --> pdb=" O   TYR C  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 45
    Processing helix  chain 'D' and resid 48 through 61
    Processing helix  chain 'D' and resid 68 through 81
    Processing helix  chain 'D' and resid 85 through 98
    Processing helix  chain 'D' and resid 106 through 120
    Processing helix  chain 'D' and resid 138 through 153
    Processing helix  chain 'D' and resid 160 through 188
      removed outlier: 3.502A  pdb=" N   GLU D 187 " --> pdb=" O   GLU D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 204
      removed outlier: 3.669A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 224
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 228 through 241
      removed outlier: 3.529A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 45
      No H-bonds generated for 'chain 'E' and resid 43 through 45'
    Processing helix  chain 'E' and resid 52 through 58
    Processing sheet with id=  A, first strand: chain 'A' and resid 97 through 100
      removed outlier: 8.753A  pdb=" N   THR A  98 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   LEU A 165 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 8.349A  pdb=" N   SER A 100 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU A 167 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 321 through 329
      removed outlier: 6.251A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.623A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 9.753A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 12.062A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 9.466A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 424 through 431
      removed outlier: 3.524A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ALA A 770 " --> pdb=" O   PRO A 790 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   ILE A 772 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   ALA A 788 " --> pdb=" O   ILE A 772 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   LEU A 774 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   SER A 786 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   TRP A 776 " --> pdb=" O   VAL A 784 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   VAL A 784 " --> pdb=" O   TRP A 776 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   SER A 778 " --> pdb=" O   PRO A 782 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 72 through 79
      removed outlier: 6.593A  pdb=" N   LYS A  89 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   VAL A  75 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   GLN A  87 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   VAL A  77 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.460A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'A' and resid 348 through 355
      removed outlier: 7.487A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 48 through 50
      removed outlier: 3.655A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 71 through 75
      removed outlier: 3.676A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 122 through 125
    Processing sheet with id=  J, first strand: chain 'B' and resid 161 through 165
      removed outlier: 3.765A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 206 through 210
      removed outlier: 3.573A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 230 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN B 230 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.517A  pdb=" N   ALA B 269 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.543A  pdb=" N   LEU B 298 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'B' and resid 331 through 333
      removed outlier: 3.807A  pdb=" N   ALA B 358 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'E' and resid 32 through 35

    454 hydrogen bonds defined for protein.
    1290 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: 8.82

  Time building geometry restraints manager: 19.05 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: 11337
        1.03 -     1.23: 53
        1.23 -     1.42: 5210
        1.42 -     1.61: 6781
        1.61 -     1.81: 62
  Bond restraints: 23443
  Sorted by residual:
  bond pdb=" CG  PRO B  34 "
       pdb=" CD  PRO B  34 "
    ideal  model  delta    sigma   weight residual
    1.503  1.047  0.456 3.40e-02 8.65e+02 1.80e+02
  bond pdb=" C   UX8 F   3 "
       pdb=" O   UX8 F   3 "
    ideal  model  delta    sigma   weight residual
    1.231  1.395 -0.164 2.00e-02 2.50e+03 6.74e+01
  bond pdb=" CZ2 TRP F   1 "
       pdb=" HZ2 TRP F   1 "
    ideal  model  delta    sigma   weight residual
    0.930  1.090 -0.160 2.00e-02 2.50e+03 6.40e+01
  bond pdb=" CD1 TRP F   7 "
       pdb=" HD1 TRP F   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" CZ2 TRP F   7 "
       pdb=" HZ2 TRP F   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 23438 not shown)

  Histogram of bond angle deviations from ideal:
       78.61 -    90.07: 2
       90.07 -   101.53: 27
      101.53 -   112.99: 26854
      112.99 -   124.44: 14206
      124.44 -   135.90: 1064
  Bond angle restraints: 42153
  Sorted by residual:
  angle pdb=" N   PRO B  34 "
        pdb=" CD  PRO B  34 "
        pdb=" CG  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     103.20   78.61   24.59 1.50e+00 4.44e-01 2.69e+02
  angle pdb=" CA  PRO B  34 "
        pdb=" CB  PRO B  34 "
        pdb=" CG  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     104.50   87.73   16.77 1.90e+00 2.77e-01 7.79e+01
  angle pdb=" CA  PRO B  34 "
        pdb=" N   PRO B  34 "
        pdb=" CD  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     112.00  100.72   11.28 1.40e+00 5.10e-01 6.49e+01
  angle pdb=" CA  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB2 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     109.00   90.49   18.51 3.00e+00 1.11e-01 3.81e+01
  angle pdb=" CG  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB2 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     108.00   90.51   17.49 3.00e+00 1.11e-01 3.40e+01
  ... (remaining 42148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 8707
       17.96 -    35.91: 589
       35.91 -    53.87: 88
       53.87 -    71.82: 28
       71.82 -    89.78: 14
  Dihedral angle restraints: 9426
    sinusoidal: 4300
      harmonic: 5126
  Sorted by residual:
  dihedral pdb=" CD2 TRP F   1 "
           pdb=" CE2 TRP F   1 "
           pdb=" CZ2 TRP F   1 "
           pdb=" HZ2 TRP F   1 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.33  -54.67     0      5.00e+00 4.00e-02 1.20e+02
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.25   45.25     1      1.00e+01 1.00e-02 2.84e+01
  dihedral pdb=" CA  LEU A 699 "
           pdb=" C   LEU A 699 "
           pdb=" N   CYS A 700 "
           pdb=" CA  CYS A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.12  -19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 9423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 994
       0.029 -    0.058: 521
       0.058 -    0.087: 115
       0.087 -    0.116: 109
       0.116 -    0.145: 44
  Chirality restraints: 1783
  Sorted by residual:
  chirality pdb=" CA  ILE C  67 "
            pdb=" N   ILE C  67 "
            pdb=" C   ILE C  67 "
            pdb=" CB  ILE C  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE B 296 "
            pdb=" N   ILE B 296 "
            pdb=" C   ILE B 296 "
            pdb=" CB  ILE B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE E 104 "
            pdb=" N   ILE E 104 "
            pdb=" C   ILE E 104 "
            pdb=" CB  ILE E 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 1780 not shown)

  Planarity restraints: 3592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F   1 "   -0.129 2.00e-02 2.50e+03   1.84e-01 1.27e+03
        pdb=" CG  TRP F   1 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP F   1 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP F   1 "    0.014 2.00e-02 2.50e+03
        pdb=" NE1 TRP F   1 "    0.107 2.00e-02 2.50e+03
        pdb=" CE2 TRP F   1 "    0.108 2.00e-02 2.50e+03
        pdb=" CE3 TRP F   1 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F   1 "    0.183 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F   1 "    0.068 2.00e-02 2.50e+03
        pdb=" CH2 TRP F   1 "    0.159 2.00e-02 2.50e+03
        pdb=" HD1 TRP F   1 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE1 TRP F   1 "    0.155 2.00e-02 2.50e+03
        pdb=" HE3 TRP F   1 "   -0.078 2.00e-02 2.50e+03
        pdb=" HZ2 TRP F   1 "   -0.608 2.00e-02 2.50e+03
        pdb=" HZ3 TRP F   1 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "   -0.034 2.00e-02 2.50e+03   2.19e-02 1.92e+01
        pdb=" CG  TRP A 546 "    0.074 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "   -0.011 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 546 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 546 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 546 "    0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 546 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  33 "   -0.042 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO B  34 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B  34 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  34 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 3589 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 634
        2.15 -     2.76: 42761
        2.76 -     3.37: 61252
        3.37 -     3.99: 81679
        3.99 -     4.60: 128099
  Nonbonded interactions: 314425
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  38 "
            pdb=" H   GLU C  39 "
     model   vdw
     1.533 1.850
  nonbonded pdb=" OD1 ASN E  96 "
            pdb=" H   SER E  98 "
     model   vdw
     1.584 1.850
  nonbonded pdb=" HD1 HIS A 533 "
            pdb=" OD1 ASP A 568 "
     model   vdw
     1.614 1.850
  nonbonded pdb=" O   ARG A 661 "
            pdb=" HG  SER A 769 "
     model   vdw
     1.614 1.850
  nonbonded pdb="HE21 GLN B 319 "
            pdb=" O   GLY B 354 "
     model   vdw
     1.620 1.850
  ... (remaining 314420 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:                  0.010
  Normalize map: mean=0, sd=1:             3.050
  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:             0.350
  Extract box with map and model:          11.670
  Check model and map are aligned:         0.340
  Set scattering table:                    0.200
  Process input model:                     71.410
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.070
  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:12.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   99.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.456  12068  Z= 0.337
  Angle     :  0.622  24.587  16403  Z= 0.351
  Chirality :  0.044   0.145   1783
  Planarity :  0.004   0.058   2158
  Dihedral  : 14.028  89.781   4366
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer Outliers :  0.00 %
  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:  0.24 (0.21), residues: 1487
  helix:  2.32 (0.29), residues: 326
  sheet:  0.30 (0.25), residues: 445
  loop : -0.98 (0.21), residues: 716

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 2.1122
  time to fit residues: 313.9467
Evaluate side-chains
  106 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.866 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.3691
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 61 optimal weight:    0.3980
   chunk 38 optimal weight:    0.4980
   chunk 75 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
A 561 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.0561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.062  12068  Z= 0.153
  Angle     :  0.478   6.688  16403  Z= 0.252
  Chirality :  0.042   0.141   1783
  Planarity :  0.003   0.039   2158
  Dihedral  :  4.072  19.077   1651
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer Outliers :  1.11 %
  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:  0.36 (0.22), residues: 1487
  helix:  2.41 (0.29), residues: 329
  sheet:  0.41 (0.24), residues: 448
  loop : -0.94 (0.22), residues: 710

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.967 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 11
  residues processed: 120
  average time/residue: 2.2066
  time to fit residues: 294.7946
Evaluate side-chains
  119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 2.033 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 5
  residues processed: 6
  average time/residue: 0.8270
  time to fit residues: 9.0662
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9980
   chunk 119 optimal weight:    0.0070
   chunk 132 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.0672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12068  Z= 0.212
  Angle     :  0.487   7.110  16403  Z= 0.256
  Chirality :  0.043   0.143   1783
  Planarity :  0.003   0.044   2158
  Dihedral  :  4.098  22.100   1651
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer Outliers :  1.03 %
  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:  0.28 (0.22), residues: 1487
  helix:  2.41 (0.29), residues: 327
  sheet:  0.32 (0.24), residues: 458
  loop : -0.99 (0.22), residues: 702

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 1.907 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 11
  residues processed: 119
  average time/residue: 2.1029
  time to fit residues: 278.0046
Evaluate side-chains
  117 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.789 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 5
  residues processed: 6
  average time/residue: 0.6640
  time to fit residues: 7.5206
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 132 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 134 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 127 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.0826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12068  Z= 0.224
  Angle     :  0.489   7.192  16403  Z= 0.257
  Chirality :  0.043   0.141   1783
  Planarity :  0.003   0.040   2158
  Dihedral  :  4.115  21.982   1651
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer Outliers :  1.35 %
  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:  0.26 (0.22), residues: 1487
  helix:  2.36 (0.29), residues: 327
  sheet:  0.34 (0.24), residues: 460
  loop : -1.02 (0.22), residues: 700

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.940 
Fit side-chains
  outliers start: 17
  outliers final: 12
  residues processed: 117
  average time/residue: 2.2547
  time to fit residues: 291.9030
Evaluate side-chains
  117 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 1.698 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 6
  residues processed: 6
  average time/residue: 0.3793
  time to fit residues: 5.7329
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 118 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 2 optimal weight:   20.0000
   chunk 105 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 121 optimal weight:    4.9990
   chunk 98 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 72 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12068  Z= 0.161
  Angle     :  0.461   6.620  16403  Z= 0.242
  Chirality :  0.042   0.142   1783
  Planarity :  0.003   0.071   2158
  Dihedral  :  3.997  18.906   1651
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer Outliers :  1.43 %
  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 (0.22), residues: 1487
  helix:  2.55 (0.29), residues: 326
  sheet:  0.38 (0.24), residues: 464
  loop : -0.95 (0.22), residues: 697

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.821 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 12
  residues processed: 120
  average time/residue: 2.1852
  time to fit residues: 294.2154
Evaluate side-chains
  119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 1.970 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 7
  residues processed: 5
  average time/residue: 0.4331
  time to fit residues: 5.8994
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9980
   chunk 118 optimal weight:    0.0670
   chunk 65 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   overall best weight:    1.4124

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12068  Z= 0.257
  Angle     :  0.504   7.532  16403  Z= 0.265
  Chirality :  0.043   0.144   1783
  Planarity :  0.004   0.065   2158
  Dihedral  :  4.125  17.050   1651
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer Outliers :  1.43 %
  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:  0.22 (0.22), residues: 1487
  helix:  2.33 (0.29), residues: 326
  sheet:  0.28 (0.24), residues: 459
  loop : -1.01 (0.22), residues: 702

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 1.822 
Fit side-chains
  outliers start: 18
  outliers final: 13
  residues processed: 118
  average time/residue: 2.2924
  time to fit residues: 299.2406
Evaluate side-chains
  119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.851 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 8
  residues processed: 5
  average time/residue: 0.7710
  time to fit residues: 7.2255
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0010
   chunk 79 optimal weight:    0.7980
   chunk 141 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0270
   chunk 87 optimal weight:    0.0770
   overall best weight:    0.5804

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 ASN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12068  Z= 0.139
  Angle     :  0.453   7.436  16403  Z= 0.237
  Chirality :  0.042   0.140   1783
  Planarity :  0.003   0.075   2158
  Dihedral  :  3.938  15.999   1651
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer Outliers :  1.35 %
  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:  0.43 (0.22), residues: 1487
  helix:  2.62 (0.29), residues: 326
  sheet:  0.38 (0.24), residues: 464
  loop : -0.94 (0.22), residues: 697

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 1.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 11
  residues processed: 121
  average time/residue: 2.3285
  time to fit residues: 311.8432
Evaluate side-chains
  118 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 2.006 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 9
  residues processed: 2
  average time/residue: 0.4348
  time to fit residues: 3.9146
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 90 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B  41 GLN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12068  Z= 0.229
  Angle     :  0.491   7.281  16403  Z= 0.257
  Chirality :  0.043   0.143   1783
  Planarity :  0.004   0.077   2158
  Dihedral  :  4.039  16.462   1651
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer Outliers :  1.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.31 (0.22), residues: 1487
  helix:  2.49 (0.29), residues: 326
  sheet:  0.29 (0.24), residues: 465
  loop : -0.98 (0.22), residues: 696

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 1.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 13
  residues processed: 118
  average time/residue: 2.3496
  time to fit residues: 305.4099
Evaluate side-chains
  121 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 1.915 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 9
  residues processed: 4
  average time/residue: 0.3738
  time to fit residues: 4.5259
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 123 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9980
   chunk 135 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 119 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0050
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
A 286 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN
B 266 ASN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12068  Z= 0.157
  Angle     :  0.460   7.445  16403  Z= 0.241
  Chirality :  0.042   0.138   1783
  Planarity :  0.003   0.082   2158
  Dihedral  :  3.939  15.943   1651
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer Outliers :  1.35 %
  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:  0.46 (0.22), residues: 1487
  helix:  2.66 (0.29), residues: 326
  sheet:  0.44 (0.24), residues: 459
  loop : -0.94 (0.22), residues: 702

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 1.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 12
  residues processed: 121
  average time/residue: 2.3444
  time to fit residues: 314.6039
Evaluate side-chains
  120 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.900 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 8
  residues processed: 4
  average time/residue: 0.6986
  time to fit residues: 6.1266
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 139 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 146 optimal weight:    2.9990
   chunk 134 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B  41 GLN
B 266 ASN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12068  Z= 0.182
  Angle     :  0.470   7.456  16403  Z= 0.246
  Chirality :  0.042   0.139   1783
  Planarity :  0.003   0.085   2158
  Dihedral  :  3.950  15.996   1651
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer Outliers :  1.03 %
  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:  0.44 (0.22), residues: 1487
  helix:  2.64 (0.29), residues: 326
  sheet:  0.37 (0.24), residues: 464
  loop : -0.93 (0.22), residues: 697

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 10
  residues processed: 116
  average time/residue: 2.2908
  time to fit residues: 293.5094
Evaluate side-chains
  117 residues out of total 1263 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 1.844 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 8
  residues processed: 2
  average time/residue: 0.4033
  time to fit residues: 3.4966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0070
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
A 286 GLN
B  41 GLN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.170180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.124063 restraints weight = 35206.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.04
r_work: 0.3210 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12068  Z= 0.221
  Angle     :  0.490   7.568  16403  Z= 0.257
  Chirality :  0.043   0.138   1783
  Planarity :  0.004   0.080   2158
  Dihedral  :  4.054  16.309   1651
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer Outliers :  1.03 %
  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:  0.35 (0.22), residues: 1487
  helix:  2.53 (0.29), residues: 326
  sheet:  0.36 (0.24), residues: 455
  loop : -0.97 (0.22), residues: 706

===============================================================================
Job complete
usr+sys time: 6862.57 seconds
wall clock time: 121 minutes 6.69 seconds (7266.69 seconds total)