Starting phenix.real_space_refine
on Wed Mar  4 06:38:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oge_20055/03_2026/6oge_20055_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oge_20055/03_2026/6oge_20055.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oge_20055/03_2026/6oge_20055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oge_20055/03_2026/6oge_20055.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oge_20055/03_2026/6oge_20055_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oge_20055/03_2026/6oge_20055_neut.cif"
  }
  resolution = 4.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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: 4
    Type Number    sf(0)   Gaussians
     S      81      5.16       5
     C    7189      2.51       5
     N    1963      2.21       5
     O    2261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11494
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 4755
          Classifications: {'peptide': 619}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 575}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1656
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202}
    Chain: "C"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1665
          Classifications: {'peptide': 222}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 208}
    Chain: "D"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1649
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201}
    Chain: "E"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1649
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 207}
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 2.55, per 1000 atoms: 0.22
  Number of scatterers: 11494
  At special positions: 0
  Unit cell: (116.49, 142.965, 145.083, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      81     16.00
     O    2261      8.00
     N    1963      7.00
     C    7189      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=34, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 204 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 199 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 227 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 235 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 252 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 264 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 315 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 475 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 520 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 531 " - pdb=" SG  CYS A 540 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 544 " - pdb=" SG  CYS A 560 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 563 " - pdb=" SG  CYS A 576 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 567 " - pdb=" SG  CYS A 584 " distance=2.13
    Simple disulfide: pdb=" SG  CYS A 587 " - pdb=" SG  CYS A 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 600 " - pdb=" SG  CYS A 623 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 626 " - pdb=" SG  CYS A 634 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 630 " - pdb=" SG  CYS A 642 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS C 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 140 " - pdb=" SG  CYS C 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 134 " - pdb=" SG  CYS D 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 203 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA F   3 " - " MAN F   4 "
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A  68 "
      " NAG A 702 " - " ASN A 187 "
      " NAG A 707 " - " ASN A 571 "
      " NAG A 708 " - " ASN A 530 "
      " NAG A 709 " - " ASN A 629 "
      " NAG F   1 " - " ASN A 259 "
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 511.6 milliseconds
  

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2744

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 27 sheets defined
      7.5% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 50
      removed outlier: 3.794A  pdb=" N   LEU A  46 " --> pdb=" O   HIS A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 77
      removed outlier: 4.089A  pdb=" N   ASP A  76 " --> pdb=" O   PHE A  73 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE A  77 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.960A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 4.117A  pdb=" N   CYS A 252 " --> pdb=" O   HIS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 365
    Processing helix  chain 'A' and resid 393 through 401
      removed outlier: 3.551A  pdb=" N   GLN A 398 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A 399 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE A 400 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   GLU A 401 " --> pdb=" O   GLN A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
      removed outlier: 3.640A  pdb=" N   GLN A 426 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 439
    Processing helix  chain 'A' and resid 481 through 486
      removed outlier: 4.418A  pdb=" N   PHE A 486 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.691A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 128
    Processing helix  chain 'B' and resid 182 through 187
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.976A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 191
    Processing helix  chain 'D' and resid 121 through 125
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.776A  pdb=" N   ASP E  31 " --> pdb=" O   ASN E  28 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   THR E  32 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 28 through 32'
    Processing helix  chain 'E' and resid 62 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.883A  pdb=" N   CYS A  26 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   VAL A 102 " --> pdb=" O   GLU A 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63
      removed outlier: 6.038A  pdb=" N   LEU A  60 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ALA A  87 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   LEU A  62 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU A 114 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   GLN A 156 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 322
      removed outlier: 3.965A  pdb=" N   ARG A 330 " --> pdb=" O   VAL A 322 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 376
      removed outlier: 6.346A  pdb=" N   LEU A 374 " --> pdb=" O   TYR A 411 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU A 410 " --> pdb=" O   THR A 444 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   GLN A 446 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ILE A 412 " --> pdb=" O   GLN A 446 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   LEU A 465 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 553 through 555
      removed outlier: 3.571A  pdb=" N   LEU A 561 " --> pdb=" O   TYR A 554 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 590 through 592
    Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 7
      removed outlier: 4.118A  pdb=" N   THR B  22 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.351A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 54
      removed outlier: 6.552A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   TYR B  49 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   VAL B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   THR B  85 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118
      removed outlier: 3.891A  pdb=" N   VAL B 133 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR B 173 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 153 through 155
      removed outlier: 3.866A  pdb=" N   TRP B 148 " --> pdb=" O   GLN B 155 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.739A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU C  78 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12
    Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 50
      removed outlier: 6.474A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   ASP C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   MET C  34 " --> pdb=" O   ASP C  50 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   THR C  33 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 120 through 124
      removed outlier: 6.411A  pdb=" N   TYR C 176 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124
      removed outlier: 6.411A  pdb=" N   TYR C 176 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 154
    Processing sheet with id=AC2, first strand: chain 'D' and resid 5 through 7
      removed outlier: 3.988A  pdb=" N   THR D  22 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS D  23 " --> pdb=" O   PHE D  71 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 11 through 13
      removed outlier: 6.811A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 48 through 49
    Processing sheet with id=AC5, first strand: chain 'D' and resid 62 through 63
    Processing sheet with id=AC6, first strand: chain 'E' and resid 17 through 23
      removed outlier: 4.076A  pdb=" N   SER E  71 " --> pdb=" O   TYR E  80 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 59 through 60
      removed outlier: 3.546A  pdb=" N   ARG E  50 " --> pdb=" O   ARG E  59 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ARG E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE E  34 " --> pdb=" O   ARG E  50 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 92 through 93
    Processing sheet with id=AC9, first strand: chain 'E' and resid 149 through 152
      removed outlier: 5.235A  pdb=" N   LYS E 150 " --> pdb=" O   LEU E 185 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   LEU E 185 " --> pdb=" O   LYS E 150 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR E 152 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)

    200 hydrogen bonds defined for protein.
    438 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.79

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 4474
        1.38 -     1.55: 7163
        1.55 -     1.71: 36
        1.71 -     1.88: 91
        1.88 -     2.04: 2
  Bond restraints: 11766
  Sorted by residual:
  bond pdb=" CB  CYS A 584 "
       pdb=" SG  CYS A 584 "
    ideal  model  delta    sigma   weight residual
    1.808  2.042 -0.234 3.30e-02 9.18e+02 5.04e+01
  bond pdb=" CA  THR A 575 "
       pdb=" C   THR A 575 "
    ideal  model  delta    sigma   weight residual
    1.521  1.581 -0.060 1.38e-02 5.25e+03 1.87e+01
  bond pdb=" N   CYS A 576 "
       pdb=" CA  CYS A 576 "
    ideal  model  delta    sigma   weight residual
    1.463  1.509 -0.046 1.27e-02 6.20e+03 1.31e+01
  bond pdb=" CB  CYS A 567 "
       pdb=" SG  CYS A 567 "
    ideal  model  delta    sigma   weight residual
    1.808  1.927 -0.119 3.30e-02 9.18e+02 1.30e+01
  bond pdb=" C   THR A 575 "
       pdb=" N   CYS A 576 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 1.42e-02 4.96e+03 1.05e+01
  ... (remaining 11761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.43: 15920
        5.43 -    10.86: 91
       10.86 -    16.29: 3
       16.29 -    21.72: 0
       21.72 -    27.15: 1
  Bond angle restraints: 16015
  Sorted by residual:
  angle pdb=" CA  CYS A 584 "
        pdb=" CB  CYS A 584 "
        pdb=" SG  CYS A 584 "
      ideal   model   delta    sigma   weight residual
     114.40  141.55  -27.15 2.30e+00 1.89e-01 1.39e+02
  angle pdb=" N   ASP A 582 "
        pdb=" CA  ASP A 582 "
        pdb=" C   ASP A 582 "
      ideal   model   delta    sigma   weight residual
     112.03  119.00   -6.97 1.31e+00 5.83e-01 2.83e+01
  angle pdb=" C   PRO A 606 "
        pdb=" N   ASP A 607 "
        pdb=" CA  ASP A 607 "
      ideal   model   delta    sigma   weight residual
     121.54  131.61  -10.07 1.91e+00 2.74e-01 2.78e+01
  angle pdb=" C   VAL D 150 "
        pdb=" N   ASP D 151 "
        pdb=" CA  ASP D 151 "
      ideal   model   delta    sigma   weight residual
     121.54  131.20   -9.66 1.91e+00 2.74e-01 2.56e+01
  angle pdb=" N   CYS A 584 "
        pdb=" CA  CYS A 584 "
        pdb=" CB  CYS A 584 "
      ideal   model   delta    sigma   weight residual
     110.07  117.31   -7.24 1.47e+00 4.63e-01 2.43e+01
  ... (remaining 16010 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.63: 6965
       22.63 -    45.27: 209
       45.27 -    67.90: 26
       67.90 -    90.53: 21
       90.53 -   113.16: 18
  Dihedral angle restraints: 7239
    sinusoidal: 2950
      harmonic: 4289
  Sorted by residual:
  dihedral pdb=" CA  HIS A 564 "
           pdb=" C   HIS A 564 "
           pdb=" N   PRO A 565 "
           pdb=" CA  PRO A 565 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.33  -41.67     0      5.00e+00 4.00e-02 6.95e+01
  dihedral pdb=" CB  CYS B  23 "
           pdb=" SG  CYS B  23 "
           pdb=" SG  CYS B  88 "
           pdb=" CB  CYS B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.76   57.24     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CA  GLU E 155 "
           pdb=" C   GLU E 155 "
           pdb=" N   PRO E 156 "
           pdb=" CA  PRO E 156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.78   31.22     0      5.00e+00 4.00e-02 3.90e+01
  ... (remaining 7236 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1388
       0.068 -    0.136: 381
       0.136 -    0.204: 36
       0.204 -    0.271: 3
       0.271 -    0.339: 2
  Chirality restraints: 1810
  Sorted by residual:
  chirality pdb=" C2  NAG A 707 "
            pdb=" C1  NAG A 707 "
            pdb=" C3  NAG A 707 "
            pdb=" N2  NAG A 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.15   -0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.57    0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" CA  ASP D 151 "
            pdb=" N   ASP D 151 "
            pdb=" C   ASP D 151 "
            pdb=" CB  ASP D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1807 not shown)

  Planarity restraints: 2080
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C  97 "   -0.057 5.00e-02 4.00e+02   8.56e-02 1.17e+01
        pdb=" N   PRO C  98 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO C  98 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO C  98 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 577 "   -0.018 2.00e-02 2.50e+03   2.32e-02 9.38e+00
        pdb=" CG  PHE A 577 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 577 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 577 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 577 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 577 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 577 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 155 "   -0.047 5.00e-02 4.00e+02   7.18e-02 8.24e+00
        pdb=" N   PRO E 156 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO E 156 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO E 156 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 2077 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1340
        2.74 -     3.28: 11128
        3.28 -     3.82: 20476
        3.82 -     4.36: 22846
        4.36 -     4.90: 37301
  Nonbonded interactions: 93091
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D 185 "
            pdb=" OH  TYR D 192 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" N   ARG E  87 "
            pdb=" OD2 ASP E  90 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" O   ASP B  82 "
            pdb=" OH  TYR B  86 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OG1 THR A 166 "
            pdb=" O   SER A 202 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ASP C  86 "
            pdb=" OH  TYR C  90 "
     model   vdw
     2.275 3.040
  ... (remaining 93086 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ 
 or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid  \ 
95 or resid 97 through 214))
  selection = (chain 'D' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ 
 or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid  \ 
95 or resid 97 through 214))
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 
2A or resid 55 or resid 59 or resid 64 through 68 or resid 70 or resid 72 or res \ 
id 74 through 77 or resid 79 through 92 or resid 94 or resid 97 or resid 99A thr \ 
ough 99B or resid 101 through 213))
  selection = (chain 'E' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 
3 or resid 56 or resid 60 or resid 65 through 69 or resid 71 or resid 73 or resi \ 
d 75 through 78 or resid 80 through 96 or resid 98 or resid 101 or resid 104 thr \ 
ough 105 or resid 108 through 220))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.410
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
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      :  0.008   0.234  11809  Z= 0.385
  Angle     :  1.199  27.151  16110  Z= 0.631
  Chirality :  0.058   0.339   1810
  Planarity :  0.009   0.086   2074
  Dihedral  : 13.401 113.165   4393
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.54 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.29 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.20 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.34 (0.19), residues: 1477
  helix: -4.66 (0.28), residues: 61
  sheet: -2.57 (0.29), residues: 279
  loop : -3.13 (0.16), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 558 
 TYR   0.043   0.004   TYR E  80 
 PHE   0.053   0.004   PHE A 577 
 TRP   0.020   0.004   TRP E 161 
 HIS   0.015   0.003   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00820 (11766)
  covalent geometry    : angle       1.15784 (16015)
  SS BOND              : bond        0.01876 (   34)
  SS BOND              : angle       4.31173 (   68)
  hydrogen bonds       : bond        0.31727 (  187)
  hydrogen bonds       : angle      13.37207 (  438)
  link_ALPHA1-3        : bond        0.00294 (    1)
  link_ALPHA1-3        : angle       4.15001 (    3)
  link_BETA1-4         : bond        0.00268 (    2)
  link_BETA1-4         : angle       2.28046 (    6)
  link_NAG-ASN         : bond        0.00702 (    6)
  link_NAG-ASN         : angle       4.27686 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 305
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.8731 (mpm) cc_final: 0.8499 (mpm)
REVERT: A  403 LEU cc_start: 0.9084 (tp) cc_final: 0.8734 (mp)
REVERT: A  404 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8253 (mt-10)
REVERT: B    2 ILE cc_start: 0.9121 (mt) cc_final: 0.8778 (mm)
REVERT: B   71 PHE cc_start: 0.8173 (m-10) cc_final: 0.7872 (m-10)
REVERT: B   87 TYR cc_start: 0.8920 (m-80) cc_final: 0.8706 (m-80)
REVERT: B   91 TYR cc_start: 0.8752 (p90) cc_final: 0.8533 (p90)
REVERT: B   97 THR cc_start: 0.8862 (p) cc_final: 0.8598 (p)
REVERT: B  105 GLU cc_start: 0.8045 (tp30) cc_final: 0.7672 (tp30)
REVERT: B  106 ILE cc_start: 0.9608 (tt) cc_final: 0.9212 (tt)
REVERT: B  122 ASP cc_start: 0.9545 (p0) cc_final: 0.9269 (t0)
REVERT: B  129 THR cc_start: 0.9359 (p) cc_final: 0.9109 (p)
REVERT: B  135 LEU cc_start: 0.9395 (tp) cc_final: 0.9033 (tp)
REVERT: B  139 PHE cc_start: 0.9135 (p90) cc_final: 0.8460 (p90)
REVERT: B  173 TYR cc_start: 0.8966 (m-80) cc_final: 0.8220 (m-80)
REVERT: B  186 TYR cc_start: 0.8406 (t80) cc_final: 0.8059 (t80)
REVERT: C   20 LEU cc_start: 0.8228 (mt) cc_final: 0.7982 (mt)
REVERT: C   34 MET cc_start: 0.8776 (mmm) cc_final: 0.8458 (mmm)
REVERT: C   79 TYR cc_start: 0.8115 (m-10) cc_final: 0.7424 (m-10)
REVERT: C   90 TYR cc_start: 0.8039 (m-10) cc_final: 0.7756 (m-80)
REVERT: C  100 PHE cc_start: 0.8093 (m-80) cc_final: 0.7646 (m-80)
REVERT: C  142 VAL cc_start: 0.9598 (t) cc_final: 0.9309 (t)
REVERT: C  178 LEU cc_start: 0.9489 (pp) cc_final: 0.9216 (pp)
REVERT: C  199 ASN cc_start: 0.8025 (t0) cc_final: 0.7646 (t0)
REVERT: C  201 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8850 (mmtt)
REVERT: C  214 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8385 (mmmt)
REVERT: D  139 PHE cc_start: 0.7938 (p90) cc_final: 0.7076 (p90)
REVERT: D  140 TYR cc_start: 0.8635 (t80) cc_final: 0.8057 (t80)
REVERT: D  168 SER cc_start: 0.8944 (p) cc_final: 0.8673 (t)
REVERT: D  175 LEU cc_start: 0.9125 (tt) cc_final: 0.8916 (mp)
REVERT: E   80 TYR cc_start: 0.8875 (m-80) cc_final: 0.8674 (m-10)
REVERT: E  219 GLU cc_start: 0.8992 (pt0) cc_final: 0.8500 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 307
  average time/residue: 0.1284
  time to fit residues: 52.7107
Evaluate side-chains
  175 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 174
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0470
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.9682

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

Flipped N/Q/H residues before XYZ refinement:
A  88 HIS
A 141 GLN
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 GLN
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 ASN
A 329 GLN
B 155 GLN
B 166 GLN
D 138 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.078594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.055433 restraints weight = 56109.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.057513 restraints weight = 32893.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.058908 restraints weight = 22408.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.059916 restraints weight = 16948.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.060522 restraints weight = 13759.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.147  11809  Z= 0.178
  Angle     :  0.853  19.212  16110  Z= 0.436
  Chirality :  0.048   0.229   1810
  Planarity :  0.007   0.068   2074
  Dihedral  : 11.996  89.856   1788
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.43 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.19 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.19), residues: 1477
  helix: -4.09 (0.43), residues: 45
  sheet: -2.21 (0.28), residues: 295
  loop : -2.77 (0.17), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 138 
 TYR   0.032   0.002   TYR B  96 
 PHE   0.044   0.002   PHE C  99A
 TRP   0.032   0.002   TRP E 110 
 HIS   0.007   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (11766)
  covalent geometry    : angle       0.81908 (16015)
  SS BOND              : bond        0.01295 (   34)
  SS BOND              : angle       3.52474 (   68)
  hydrogen bonds       : bond        0.04877 (  187)
  hydrogen bonds       : angle       9.22965 (  438)
  link_ALPHA1-3        : bond        0.00924 (    1)
  link_ALPHA1-3        : angle       1.55731 (    3)
  link_BETA1-4         : bond        0.00265 (    2)
  link_BETA1-4         : angle       2.28011 (    6)
  link_NAG-ASN         : bond        0.00762 (    6)
  link_NAG-ASN         : angle       2.39514 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 259
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9189 (pt0) cc_final: 0.8817 (pm20)
REVERT: A  343 TYR cc_start: 0.8745 (m-80) cc_final: 0.8178 (m-10)
REVERT: A  403 LEU cc_start: 0.9013 (tp) cc_final: 0.8716 (mt)
REVERT: A  458 LEU cc_start: 0.9648 (tp) cc_final: 0.9394 (tt)
REVERT: B   71 PHE cc_start: 0.8543 (m-10) cc_final: 0.8192 (m-10)
REVERT: B   91 TYR cc_start: 0.8711 (p90) cc_final: 0.8473 (p90)
REVERT: B  105 GLU cc_start: 0.8107 (tp30) cc_final: 0.7819 (tp30)
REVERT: B  122 ASP cc_start: 0.9370 (p0) cc_final: 0.9117 (t0)
REVERT: B  139 PHE cc_start: 0.9076 (p90) cc_final: 0.8210 (p90)
REVERT: B  148 TRP cc_start: 0.7358 (m100) cc_final: 0.5315 (m100)
REVERT: B  149 LYS cc_start: 0.9363 (mtpp) cc_final: 0.9054 (mmtm)
REVERT: B  155 GLN cc_start: 0.8619 (tp40) cc_final: 0.7899 (tm-30)
REVERT: B  173 TYR cc_start: 0.8680 (m-80) cc_final: 0.7760 (m-80)
REVERT: B  179 LEU cc_start: 0.9478 (tp) cc_final: 0.8649 (tp)
REVERT: C   34 MET cc_start: 0.8923 (mmm) cc_final: 0.8137 (tpp)
REVERT: C   59 TYR cc_start: 0.8566 (p90) cc_final: 0.7523 (p90)
REVERT: C   92 CYS cc_start: 0.6089 (t) cc_final: 0.3630 (t)
REVERT: C  100 PHE cc_start: 0.8230 (m-80) cc_final: 0.7554 (m-80)
REVERT: C  142 VAL cc_start: 0.9690 (t) cc_final: 0.9202 (t)
REVERT: C  144 ASP cc_start: 0.8973 (m-30) cc_final: 0.8682 (m-30)
REVERT: C  145 TYR cc_start: 0.7805 (p90) cc_final: 0.7449 (p90)
REVERT: C  199 ASN cc_start: 0.8054 (t0) cc_final: 0.7719 (t0)
REVERT: C  214 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8380 (mmmt)
REVERT: D   11 LEU cc_start: 0.9454 (mt) cc_final: 0.9173 (mp)
REVERT: D   30 ASN cc_start: 0.9009 (m110) cc_final: 0.8278 (m-40)
REVERT: D   70 ASP cc_start: 0.9540 (m-30) cc_final: 0.8599 (m-30)
REVERT: D  139 PHE cc_start: 0.7589 (p90) cc_final: 0.7332 (p90)
REVERT: D  140 TYR cc_start: 0.8523 (t80) cc_final: 0.7980 (t80)
REVERT: E   30 LYS cc_start: 0.8369 (pptt) cc_final: 0.7949 (pptt)
REVERT: E   39 GLN cc_start: 0.8874 (tt0) cc_final: 0.8404 (tt0)
REVERT: E   50 ARG cc_start: 0.9600 (ttp-170) cc_final: 0.9096 (ttp-110)
REVERT: E   65 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8859 (mmtm)
REVERT: E   98 ARG cc_start: 0.8474 (ptt90) cc_final: 0.8208 (ptt-90)
REVERT: E  107 MET cc_start: 0.9471 (mtm) cc_final: 0.9169 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1153
  time to fit residues: 41.2089
Evaluate side-chains
  177 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 130 optimal weight:    8.9990
   chunk 136 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0970
   chunk 108 optimal weight:    0.9990
   chunk 114 optimal weight:    5.9990
   chunk 137 optimal weight:   40.0000
   chunk 14 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
B  38 GLN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 ASN
C  61 GLN
D 138 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.077965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.054927 restraints weight = 57394.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.056932 restraints weight = 33889.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.058293 restraints weight = 23269.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.059244 restraints weight = 17668.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.059869 restraints weight = 14433.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.151  11809  Z= 0.190
  Angle     :  0.831  19.186  16110  Z= 0.421
  Chirality :  0.048   0.226   1810
  Planarity :  0.006   0.059   2074
  Dihedral  : 10.775  82.963   1788
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.10 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.43 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.54 (0.20), residues: 1477
  helix: -3.76 (0.50), residues: 45
  sheet: -2.05 (0.28), residues: 309
  loop : -2.58 (0.17), residues: 1123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 217 
 TYR   0.033   0.002   TYR B  96 
 PHE   0.046   0.002   PHE C  99A
 TRP   0.035   0.002   TRP E 110 
 HIS   0.006   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (11766)
  covalent geometry    : angle       0.79791 (16015)
  SS BOND              : bond        0.01362 (   34)
  SS BOND              : angle       3.45216 (   68)
  hydrogen bonds       : bond        0.04168 (  187)
  hydrogen bonds       : angle       8.08423 (  438)
  link_ALPHA1-3        : bond        0.00557 (    1)
  link_ALPHA1-3        : angle       1.51822 (    3)
  link_BETA1-4         : bond        0.00732 (    2)
  link_BETA1-4         : angle       1.99345 (    6)
  link_NAG-ASN         : bond        0.00318 (    6)
  link_NAG-ASN         : angle       2.28069 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 232
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9190 (pt0) cc_final: 0.8838 (pm20)
REVERT: A   78 GLN cc_start: 0.8522 (mp10) cc_final: 0.8213 (mp10)
REVERT: A  343 TYR cc_start: 0.8767 (m-80) cc_final: 0.8237 (m-10)
REVERT: A  403 LEU cc_start: 0.8982 (tp) cc_final: 0.8676 (mt)
REVERT: A  458 LEU cc_start: 0.9647 (tp) cc_final: 0.9432 (tt)
REVERT: B   71 PHE cc_start: 0.8511 (m-10) cc_final: 0.8171 (m-10)
REVERT: B   78 LEU cc_start: 0.9418 (tp) cc_final: 0.8848 (mt)
REVERT: B  122 ASP cc_start: 0.9385 (p0) cc_final: 0.9157 (t0)
REVERT: B  139 PHE cc_start: 0.8945 (p90) cc_final: 0.8122 (p90)
REVERT: B  145 LYS cc_start: 0.9373 (mmpt) cc_final: 0.9058 (tppt)
REVERT: B  148 TRP cc_start: 0.7182 (m100) cc_final: 0.5295 (m100)
REVERT: B  155 GLN cc_start: 0.8474 (tp40) cc_final: 0.7649 (tm-30)
REVERT: B  173 TYR cc_start: 0.8469 (m-80) cc_final: 0.7736 (m-80)
REVERT: B  179 LEU cc_start: 0.9464 (tp) cc_final: 0.8579 (tp)
REVERT: C   34 MET cc_start: 0.9037 (mmm) cc_final: 0.8232 (tpp)
REVERT: C   59 TYR cc_start: 0.8603 (p90) cc_final: 0.7639 (p90)
REVERT: C   79 TYR cc_start: 0.8670 (m-10) cc_final: 0.8172 (m-10)
REVERT: C   92 CYS cc_start: 0.6274 (t) cc_final: 0.3656 (t)
REVERT: C  142 VAL cc_start: 0.9739 (t) cc_final: 0.9283 (t)
REVERT: C  145 TYR cc_start: 0.7900 (p90) cc_final: 0.7516 (p90)
REVERT: C  214 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8381 (mmmt)
REVERT: D   11 LEU cc_start: 0.9416 (mt) cc_final: 0.9124 (mp)
REVERT: D  139 PHE cc_start: 0.7602 (p90) cc_final: 0.6960 (p90)
REVERT: D  140 TYR cc_start: 0.8459 (t80) cc_final: 0.7795 (t80)
REVERT: D  175 LEU cc_start: 0.9176 (tt) cc_final: 0.8933 (mp)
REVERT: E   30 LYS cc_start: 0.8413 (pptt) cc_final: 0.7970 (pptt)
REVERT: E   50 ARG cc_start: 0.9585 (ttp-170) cc_final: 0.9281 (ttp-110)
REVERT: E   98 ARG cc_start: 0.8408 (ptt90) cc_final: 0.8156 (ptt-90)
  outliers start: 5
  outliers final: 2
  residues processed: 235
  average time/residue: 0.1118
  time to fit residues: 36.7008
Evaluate side-chains
  174 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 172
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 117 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 130 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
** C  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.078272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.055198 restraints weight = 56996.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.057238 restraints weight = 33324.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.058602 restraints weight = 22755.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.059578 restraints weight = 17265.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.060219 restraints weight = 14084.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.152  11809  Z= 0.164
  Angle     :  0.794  19.094  16110  Z= 0.398
  Chirality :  0.047   0.245   1810
  Planarity :  0.005   0.053   2074
  Dihedral  :  9.811  78.785   1788
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.56 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.43 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.41 (0.20), residues: 1477
  helix: -3.61 (0.51), residues: 46
  sheet: -2.03 (0.26), residues: 338
  loop : -2.46 (0.18), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  38 
 TYR   0.033   0.002   TYR B  96 
 PHE   0.051   0.002   PHE C  99A
 TRP   0.029   0.001   TRP E 110 
 HIS   0.006   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (11766)
  covalent geometry    : angle       0.76430 (16015)
  SS BOND              : bond        0.01313 (   34)
  SS BOND              : angle       3.18204 (   68)
  hydrogen bonds       : bond        0.03590 (  187)
  hydrogen bonds       : angle       7.49861 (  438)
  link_ALPHA1-3        : bond        0.00703 (    1)
  link_ALPHA1-3        : angle       1.25072 (    3)
  link_BETA1-4         : bond        0.00597 (    2)
  link_BETA1-4         : angle       1.57024 (    6)
  link_NAG-ASN         : bond        0.00336 (    6)
  link_NAG-ASN         : angle       2.13554 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LEU cc_start: 0.9658 (mm) cc_final: 0.9102 (mm)
REVERT: A   75 GLN cc_start: 0.9171 (pt0) cc_final: 0.8803 (pm20)
REVERT: A  161 LEU cc_start: 0.9073 (mp) cc_final: 0.8711 (mp)
REVERT: A  258 PHE cc_start: 0.8224 (m-80) cc_final: 0.7877 (m-80)
REVERT: A  343 TYR cc_start: 0.8807 (m-80) cc_final: 0.8275 (m-10)
REVERT: A  403 LEU cc_start: 0.8940 (tp) cc_final: 0.8647 (mt)
REVERT: A  405 GLU cc_start: 0.8606 (tp30) cc_final: 0.8381 (tp30)
REVERT: A  458 LEU cc_start: 0.9640 (tp) cc_final: 0.9421 (tt)
REVERT: B   71 PHE cc_start: 0.8425 (m-10) cc_final: 0.8116 (m-10)
REVERT: B   73 LEU cc_start: 0.9538 (tt) cc_final: 0.9293 (pp)
REVERT: B  139 PHE cc_start: 0.8974 (p90) cc_final: 0.8190 (p90)
REVERT: B  145 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9113 (tppt)
REVERT: B  148 TRP cc_start: 0.7385 (m100) cc_final: 0.5256 (m100)
REVERT: B  149 LYS cc_start: 0.9302 (mtpp) cc_final: 0.8917 (mmtm)
REVERT: B  155 GLN cc_start: 0.8406 (tp40) cc_final: 0.7540 (tm-30)
REVERT: B  179 LEU cc_start: 0.9466 (tp) cc_final: 0.8626 (tp)
REVERT: C  142 VAL cc_start: 0.9740 (t) cc_final: 0.9287 (t)
REVERT: C  145 TYR cc_start: 0.7850 (p90) cc_final: 0.7318 (p90)
REVERT: C  214 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8385 (mmmt)
REVERT: D   11 LEU cc_start: 0.9364 (mt) cc_final: 0.9154 (mp)
REVERT: D  139 PHE cc_start: 0.7463 (p90) cc_final: 0.7099 (p90)
REVERT: D  140 TYR cc_start: 0.8370 (t80) cc_final: 0.7638 (t80)
REVERT: E   30 LYS cc_start: 0.8386 (pptt) cc_final: 0.7953 (pptt)
REVERT: E   50 ARG cc_start: 0.9561 (ttp-170) cc_final: 0.9263 (ttp-110)
REVERT: E   65 LYS cc_start: 0.9183 (mmmt) cc_final: 0.8910 (mmmt)
REVERT: E   98 ARG cc_start: 0.8221 (ptt90) cc_final: 0.7745 (ptt-90)
REVERT: E   99 TRP cc_start: 0.8326 (m-10) cc_final: 0.7976 (m100)
REVERT: E  107 MET cc_start: 0.9357 (mtm) cc_final: 0.9092 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1161
  time to fit residues: 36.0358
Evaluate side-chains
  171 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 143 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 49 optimal weight:    8.9990
   chunk 109 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 113 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0980
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
A 632 HIS
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  61 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.079123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.056075 restraints weight = 54798.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.058161 restraints weight = 32087.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.059580 restraints weight = 21852.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.060530 restraints weight = 16442.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.061231 restraints weight = 13436.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.139  11809  Z= 0.150
  Angle     :  0.781  18.398  16110  Z= 0.388
  Chirality :  0.047   0.243   1810
  Planarity :  0.005   0.051   2074
  Dihedral  :  9.283  74.928   1788
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.36 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.41 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.27 (0.20), residues: 1477
  helix: -3.45 (0.52), residues: 46
  sheet: -1.96 (0.27), residues: 338
  loop : -2.35 (0.18), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  18 
 TYR   0.027   0.002   TYR B  96 
 PHE   0.044   0.002   PHE E 173 
 TRP   0.020   0.001   TRP E  99 
 HIS   0.010   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11766)
  covalent geometry    : angle       0.75480 (16015)
  SS BOND              : bond        0.01228 (   34)
  SS BOND              : angle       3.01391 (   68)
  hydrogen bonds       : bond        0.03280 (  187)
  hydrogen bonds       : angle       7.32167 (  438)
  link_ALPHA1-3        : bond        0.00841 (    1)
  link_ALPHA1-3        : angle       1.47322 (    3)
  link_BETA1-4         : bond        0.00294 (    2)
  link_BETA1-4         : angle       1.64349 (    6)
  link_NAG-ASN         : bond        0.00476 (    6)
  link_NAG-ASN         : angle       1.98800 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 220
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9180 (pt0) cc_final: 0.8876 (pm20)
REVERT: A  258 PHE cc_start: 0.8286 (m-80) cc_final: 0.7943 (m-80)
REVERT: A  343 TYR cc_start: 0.8806 (m-80) cc_final: 0.8258 (m-10)
REVERT: A  348 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6466 (mm-30)
REVERT: A  403 LEU cc_start: 0.8897 (tp) cc_final: 0.8579 (mt)
REVERT: A  405 GLU cc_start: 0.8473 (tp30) cc_final: 0.8175 (tp30)
REVERT: A  458 LEU cc_start: 0.9628 (tp) cc_final: 0.9379 (tt)
REVERT: B   33 VAL cc_start: 0.9260 (t) cc_final: 0.8856 (t)
REVERT: B   71 PHE cc_start: 0.8367 (m-10) cc_final: 0.8110 (m-10)
REVERT: B   73 LEU cc_start: 0.9545 (tt) cc_final: 0.9291 (pp)
REVERT: B  139 PHE cc_start: 0.8974 (p90) cc_final: 0.8251 (p90)
REVERT: B  145 LYS cc_start: 0.9398 (mmpt) cc_final: 0.9109 (tppt)
REVERT: B  155 GLN cc_start: 0.8360 (tp40) cc_final: 0.7436 (tm-30)
REVERT: B  179 LEU cc_start: 0.9452 (tp) cc_final: 0.8855 (tp)
REVERT: C  142 VAL cc_start: 0.9771 (t) cc_final: 0.9236 (p)
REVERT: C  144 ASP cc_start: 0.8858 (m-30) cc_final: 0.8576 (m-30)
REVERT: C  145 TYR cc_start: 0.7843 (p90) cc_final: 0.7474 (p90)
REVERT: C  214 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8451 (mmmt)
REVERT: D  139 PHE cc_start: 0.7734 (p90) cc_final: 0.7456 (p90)
REVERT: D  140 TYR cc_start: 0.8370 (t80) cc_final: 0.7585 (t80)
REVERT: E    1 GLU cc_start: 0.7705 (tt0) cc_final: 0.7460 (tm-30)
REVERT: E   30 LYS cc_start: 0.8371 (pptt) cc_final: 0.7913 (pptt)
REVERT: E   39 GLN cc_start: 0.8984 (tt0) cc_final: 0.8658 (tt0)
REVERT: E   98 ARG cc_start: 0.7963 (ptt90) cc_final: 0.6949 (ptt-90)
REVERT: E  110 TRP cc_start: 0.8811 (m100) cc_final: 0.8383 (m100)
REVERT: E  155 GLU cc_start: 0.7905 (tp30) cc_final: 0.7595 (mm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1085
  time to fit residues: 34.0128
Evaluate side-chains
  159 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 119 optimal weight:    8.9990
   chunk 122 optimal weight:    0.4980
   chunk 99 optimal weight:   30.0000
   chunk 104 optimal weight:    1.9990
   chunk 134 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 93 optimal weight:   10.0000
   chunk 98 optimal weight:   30.0000
   chunk 73 optimal weight:    7.9990
   overall best weight:    3.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 GLN
E 171 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.077247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.054538 restraints weight = 58193.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.056578 restraints weight = 33753.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.057935 restraints weight = 22925.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.058920 restraints weight = 17298.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.059566 restraints weight = 14084.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.136  11809  Z= 0.198
  Angle     :  0.809  19.208  16110  Z= 0.403
  Chirality :  0.048   0.294   1810
  Planarity :  0.005   0.048   2074
  Dihedral  :  9.015  70.307   1788
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.71 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.03 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.20), residues: 1477
  helix: -3.36 (0.51), residues: 52
  sheet: -1.84 (0.27), residues: 318
  loop : -2.31 (0.18), residues: 1107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 188 
 TYR   0.025   0.002   TYR B  96 
 PHE   0.032   0.002   PHE C  99A
 TRP   0.011   0.002   TRP E 161 
 HIS   0.043   0.002   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (11766)
  covalent geometry    : angle       0.78065 (16015)
  SS BOND              : bond        0.01213 (   34)
  SS BOND              : angle       3.00438 (   68)
  hydrogen bonds       : bond        0.03495 (  187)
  hydrogen bonds       : angle       7.19140 (  438)
  link_ALPHA1-3        : bond        0.00507 (    1)
  link_ALPHA1-3        : angle       1.23177 (    3)
  link_BETA1-4         : bond        0.00080 (    2)
  link_BETA1-4         : angle       1.34310 (    6)
  link_NAG-ASN         : bond        0.00559 (    6)
  link_NAG-ASN         : angle       2.88126 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9214 (pt0) cc_final: 0.8904 (pm20)
REVERT: A  403 LEU cc_start: 0.8910 (tp) cc_final: 0.8525 (mt)
REVERT: B   33 VAL cc_start: 0.9259 (t) cc_final: 0.8859 (t)
REVERT: B   71 PHE cc_start: 0.8468 (m-10) cc_final: 0.8250 (m-10)
REVERT: B   73 LEU cc_start: 0.9575 (tt) cc_final: 0.9300 (pp)
REVERT: B  139 PHE cc_start: 0.8877 (p90) cc_final: 0.8114 (p90)
REVERT: B  142 ARG cc_start: 0.8973 (tpt90) cc_final: 0.8713 (tpt90)
REVERT: B  145 LYS cc_start: 0.9413 (mmpt) cc_final: 0.9134 (tppt)
REVERT: B  155 GLN cc_start: 0.8397 (tp40) cc_final: 0.7415 (tm-30)
REVERT: B  179 LEU cc_start: 0.9411 (tp) cc_final: 0.8746 (tp)
REVERT: C   31 ASP cc_start: 0.7937 (t70) cc_final: 0.7734 (t70)
REVERT: C  142 VAL cc_start: 0.9727 (t) cc_final: 0.9409 (m)
REVERT: C  145 TYR cc_start: 0.8025 (p90) cc_final: 0.7495 (p90)
REVERT: C  214 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8442 (mmmt)
REVERT: D  139 PHE cc_start: 0.7745 (p90) cc_final: 0.7417 (p90)
REVERT: D  140 TYR cc_start: 0.8410 (t80) cc_final: 0.7555 (t80)
REVERT: E   30 LYS cc_start: 0.8442 (pptt) cc_final: 0.7992 (pptt)
REVERT: E  155 GLU cc_start: 0.7931 (tp30) cc_final: 0.7672 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1070
  time to fit residues: 30.9216
Evaluate side-chains
  157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 136 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 137 optimal weight:   40.0000
   chunk 10 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 82 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.075715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.053042 restraints weight = 58351.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.054961 restraints weight = 34071.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.056254 restraints weight = 23375.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.057183 restraints weight = 17807.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.057804 restraints weight = 14595.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.126  11809  Z= 0.255
  Angle     :  0.874  20.511  16110  Z= 0.434
  Chirality :  0.049   0.249   1810
  Planarity :  0.006   0.053   2074
  Dihedral  :  8.854  63.895   1788
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 23.84
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.46 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.88 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.22 (0.20), residues: 1477
  helix: -3.56 (0.46), residues: 52
  sheet: -1.77 (0.28), residues: 306
  loop : -2.36 (0.18), residues: 1119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG E  38 
 TYR   0.032   0.002   TYR B  96 
 PHE   0.038   0.003   PHE C  99A
 TRP   0.030   0.003   TRP E 110 
 HIS   0.020   0.002   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 (11766)
  covalent geometry    : angle       0.84950 (16015)
  SS BOND              : bond        0.01205 (   34)
  SS BOND              : angle       2.95823 (   68)
  hydrogen bonds       : bond        0.04008 (  187)
  hydrogen bonds       : angle       7.53231 (  438)
  link_ALPHA1-3        : bond        0.00495 (    1)
  link_ALPHA1-3        : angle       1.59794 (    3)
  link_BETA1-4         : bond        0.00334 (    2)
  link_BETA1-4         : angle       1.29183 (    6)
  link_NAG-ASN         : bond        0.00421 (    6)
  link_NAG-ASN         : angle       2.78133 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9245 (pt0) cc_final: 0.8881 (pm20)
REVERT: A  403 LEU cc_start: 0.8987 (tp) cc_final: 0.8509 (mt)
REVERT: A  405 GLU cc_start: 0.8745 (tp30) cc_final: 0.8486 (tp30)
REVERT: B   73 LEU cc_start: 0.9579 (tt) cc_final: 0.9303 (pp)
REVERT: B  139 PHE cc_start: 0.8834 (p90) cc_final: 0.8031 (p90)
REVERT: B  142 ARG cc_start: 0.9075 (tpt90) cc_final: 0.8777 (tpt90)
REVERT: B  145 LYS cc_start: 0.9370 (mmpt) cc_final: 0.9088 (tppt)
REVERT: B  155 GLN cc_start: 0.8225 (tp40) cc_final: 0.7251 (tm-30)
REVERT: B  179 LEU cc_start: 0.9434 (tp) cc_final: 0.8773 (tp)
REVERT: C  100 PHE cc_start: 0.8263 (m-80) cc_final: 0.7811 (m-80)
REVERT: C  142 VAL cc_start: 0.9735 (t) cc_final: 0.9410 (m)
REVERT: C  145 TYR cc_start: 0.8164 (p90) cc_final: 0.7619 (p90)
REVERT: C  214 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8447 (mmmt)
REVERT: D   82 ASP cc_start: 0.9190 (m-30) cc_final: 0.8582 (m-30)
REVERT: D  139 PHE cc_start: 0.7669 (p90) cc_final: 0.7445 (p90)
REVERT: D  140 TYR cc_start: 0.8428 (t80) cc_final: 0.7633 (t80)
REVERT: D  173 TYR cc_start: 0.6468 (m-10) cc_final: 0.6086 (m-10)
REVERT: E   30 LYS cc_start: 0.8328 (pptt) cc_final: 0.7918 (pptt)
REVERT: E  104 PHE cc_start: 0.7895 (t80) cc_final: 0.7333 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1050
  time to fit residues: 28.4501
Evaluate side-chains
  150 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 112 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 107 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 ASN
** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 484 GLN
** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.075669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.053242 restraints weight = 59206.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.055138 restraints weight = 34948.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.056436 restraints weight = 24030.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.057323 restraints weight = 18287.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.057905 restraints weight = 15039.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.4630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.135  11809  Z= 0.224
  Angle     :  0.854  19.366  16110  Z= 0.422
  Chirality :  0.048   0.261   1810
  Planarity :  0.005   0.047   2074
  Dihedral  :  8.471  56.708   1788
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 22.56
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.78 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.63 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.22 (0.20), residues: 1477
  helix: -3.60 (0.46), residues: 61
  sheet: -1.69 (0.27), residues: 318
  loop : -2.37 (0.18), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  50 
 TYR   0.035   0.002   TYR B  96 
 PHE   0.042   0.002   PHE C  99A
 TRP   0.021   0.002   TRP E 110 
 HIS   0.018   0.002   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (11766)
  covalent geometry    : angle       0.82979 (16015)
  SS BOND              : bond        0.01196 (   34)
  SS BOND              : angle       2.95481 (   68)
  hydrogen bonds       : bond        0.03884 (  187)
  hydrogen bonds       : angle       7.46772 (  438)
  link_ALPHA1-3        : bond        0.00356 (    1)
  link_ALPHA1-3        : angle       1.43932 (    3)
  link_BETA1-4         : bond        0.00116 (    2)
  link_BETA1-4         : angle       1.11021 (    6)
  link_NAG-ASN         : bond        0.00354 (    6)
  link_NAG-ASN         : angle       2.63740 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9263 (pt0) cc_final: 0.8885 (pm20)
REVERT: A  403 LEU cc_start: 0.8994 (tp) cc_final: 0.8450 (mt)
REVERT: B   73 LEU cc_start: 0.9604 (tt) cc_final: 0.9297 (pp)
REVERT: B   97 THR cc_start: 0.9162 (p) cc_final: 0.8378 (p)
REVERT: B  139 PHE cc_start: 0.8918 (p90) cc_final: 0.8122 (p90)
REVERT: B  142 ARG cc_start: 0.9089 (tpt90) cc_final: 0.8781 (tpt90)
REVERT: B  145 LYS cc_start: 0.9410 (mmpt) cc_final: 0.9145 (tppt)
REVERT: B  155 GLN cc_start: 0.8123 (tp40) cc_final: 0.7140 (tm-30)
REVERT: B  179 LEU cc_start: 0.9398 (tp) cc_final: 0.8702 (tp)
REVERT: C   31 ASP cc_start: 0.7837 (t70) cc_final: 0.7593 (t70)
REVERT: C  100 PHE cc_start: 0.8428 (m-80) cc_final: 0.7932 (m-80)
REVERT: C  143 LYS cc_start: 0.8966 (tptp) cc_final: 0.8725 (tppt)
REVERT: C  144 ASP cc_start: 0.8708 (m-30) cc_final: 0.8123 (m-30)
REVERT: C  145 TYR cc_start: 0.8219 (p90) cc_final: 0.7632 (p90)
REVERT: C  214 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8446 (mmmt)
REVERT: D  139 PHE cc_start: 0.7750 (p90) cc_final: 0.7157 (p90)
REVERT: D  140 TYR cc_start: 0.8382 (t80) cc_final: 0.7634 (t80)
REVERT: D  173 TYR cc_start: 0.6426 (m-10) cc_final: 0.6067 (m-10)
REVERT: D  175 LEU cc_start: 0.9271 (tt) cc_final: 0.9012 (mp)
REVERT: E   30 LYS cc_start: 0.8313 (pptt) cc_final: 0.7912 (pptt)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1032
  time to fit residues: 26.5232
Evaluate side-chains
  148 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 144 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 124 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 GLN
A 275 ASN
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 484 GLN
** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
C 192 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.075979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.053391 restraints weight = 57021.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.055397 restraints weight = 33177.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.056768 restraints weight = 22557.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.057694 restraints weight = 16973.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.058314 restraints weight = 13822.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.131  11809  Z= 0.196
  Angle     :  0.818  18.867  16110  Z= 0.406
  Chirality :  0.048   0.261   1810
  Planarity :  0.005   0.048   2074
  Dihedral  :  8.017  56.554   1788
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.05 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.39 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.20), residues: 1477
  helix: -3.59 (0.46), residues: 61
  sheet: -1.55 (0.28), residues: 311
  loop : -2.33 (0.18), residues: 1105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 340 
 TYR   0.037   0.002   TYR B  96 
 PHE   0.033   0.002   PHE C  99A
 TRP   0.021   0.002   TRP E  99 
 HIS   0.016   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (11766)
  covalent geometry    : angle       0.79324 (16015)
  SS BOND              : bond        0.01156 (   34)
  SS BOND              : angle       2.90115 (   68)
  hydrogen bonds       : bond        0.03823 (  187)
  hydrogen bonds       : angle       7.25686 (  438)
  link_ALPHA1-3        : bond        0.00322 (    1)
  link_ALPHA1-3        : angle       1.52232 (    3)
  link_BETA1-4         : bond        0.00262 (    2)
  link_BETA1-4         : angle       1.08535 (    6)
  link_NAG-ASN         : bond        0.00320 (    6)
  link_NAG-ASN         : angle       2.59629 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9240 (pt0) cc_final: 0.8807 (pm20)
REVERT: A  301 TYR cc_start: 0.8029 (t80) cc_final: 0.7693 (t80)
REVERT: A  403 LEU cc_start: 0.9008 (tp) cc_final: 0.8498 (mt)
REVERT: B  139 PHE cc_start: 0.8984 (p90) cc_final: 0.8219 (p90)
REVERT: B  142 ARG cc_start: 0.9081 (tpt90) cc_final: 0.8790 (tpt90)
REVERT: B  145 LYS cc_start: 0.9404 (mmpt) cc_final: 0.9103 (tppt)
REVERT: B  149 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8439 (mmtt)
REVERT: B  155 GLN cc_start: 0.8126 (tp40) cc_final: 0.7178 (tm-30)
REVERT: B  179 LEU cc_start: 0.9396 (tp) cc_final: 0.8765 (tp)
REVERT: C   96 LEU cc_start: 0.8699 (tt) cc_final: 0.8417 (tt)
REVERT: C  100 PHE cc_start: 0.8472 (m-80) cc_final: 0.7980 (m-80)
REVERT: C  145 TYR cc_start: 0.8205 (p90) cc_final: 0.7644 (p90)
REVERT: C  214 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8477 (mmmt)
REVERT: D  139 PHE cc_start: 0.7733 (p90) cc_final: 0.7049 (p90)
REVERT: D  140 TYR cc_start: 0.8329 (t80) cc_final: 0.7497 (t80)
REVERT: D  173 TYR cc_start: 0.6475 (m-10) cc_final: 0.6136 (m-10)
REVERT: D  175 LEU cc_start: 0.9291 (tt) cc_final: 0.9033 (mp)
REVERT: E   30 LYS cc_start: 0.8348 (pptt) cc_final: 0.7908 (pptt)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1087
  time to fit residues: 28.0968
Evaluate side-chains
  146 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 129 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 115 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0370
   chunk 110 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 139 optimal weight:    9.9990
   overall best weight:    3.2066

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 ASN
A 446 GLN
A 484 GLN
** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.076344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.053737 restraints weight = 57536.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.055755 restraints weight = 33391.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.057126 restraints weight = 22663.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.058084 restraints weight = 17080.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.058702 restraints weight = 13892.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.132  11809  Z= 0.180
  Angle     :  0.802  18.673  16110  Z= 0.398
  Chirality :  0.048   0.280   1810
  Planarity :  0.005   0.047   2074
  Dihedral  :  7.719  56.659   1788
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 20.21
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.31 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.47 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.07 (0.20), residues: 1477
  helix: -3.56 (0.46), residues: 61
  sheet: -1.59 (0.28), residues: 326
  loop : -2.25 (0.18), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  98 
 TYR   0.033   0.002   TYR B  96 
 PHE   0.032   0.002   PHE C  99A
 TRP   0.015   0.002   TRP E  99 
 HIS   0.018   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11766)
  covalent geometry    : angle       0.77751 (16015)
  SS BOND              : bond        0.01130 (   34)
  SS BOND              : angle       2.82010 (   68)
  hydrogen bonds       : bond        0.03726 (  187)
  hydrogen bonds       : angle       7.13818 (  438)
  link_ALPHA1-3        : bond        0.00400 (    1)
  link_ALPHA1-3        : angle       1.53999 (    3)
  link_BETA1-4         : bond        0.00230 (    2)
  link_BETA1-4         : angle       1.10376 (    6)
  link_NAG-ASN         : bond        0.00290 (    6)
  link_NAG-ASN         : angle       2.55852 (   18)

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

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

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2954 Ramachandran restraints generated.
    1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.9179 (pt0) cc_final: 0.8835 (pm20)
REVERT: A  301 TYR cc_start: 0.8082 (t80) cc_final: 0.7724 (t80)
REVERT: A  403 LEU cc_start: 0.8985 (tp) cc_final: 0.8469 (mt)
REVERT: A  405 GLU cc_start: 0.8977 (tp30) cc_final: 0.8513 (tp30)
REVERT: A  448 LEU cc_start: 0.8188 (mt) cc_final: 0.7982 (mt)
REVERT: B   98 PHE cc_start: 0.8533 (m-80) cc_final: 0.8318 (m-10)
REVERT: B  139 PHE cc_start: 0.9007 (p90) cc_final: 0.8253 (p90)
REVERT: B  142 ARG cc_start: 0.9117 (tpt90) cc_final: 0.8823 (tpt90)
REVERT: B  145 LYS cc_start: 0.9405 (mmpt) cc_final: 0.9144 (tppt)
REVERT: B  155 GLN cc_start: 0.8085 (tp40) cc_final: 0.7190 (tm-30)
REVERT: B  179 LEU cc_start: 0.9399 (tp) cc_final: 0.8678 (tp)
REVERT: C   96 LEU cc_start: 0.8718 (tt) cc_final: 0.8399 (tt)
REVERT: C  100 PHE cc_start: 0.8473 (m-80) cc_final: 0.8215 (m-80)
REVERT: C  145 TYR cc_start: 0.8155 (p90) cc_final: 0.7620 (p90)
REVERT: C  176 TYR cc_start: 0.8792 (m-10) cc_final: 0.8582 (m-10)
REVERT: C  214 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8491 (mmmt)
REVERT: D  139 PHE cc_start: 0.7689 (p90) cc_final: 0.6688 (p90)
REVERT: D  140 TYR cc_start: 0.8334 (t80) cc_final: 0.7578 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 184
  average time/residue: 0.1054
  time to fit residues: 27.8053
Evaluate side-chains
  152 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 121 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 67 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0470
   chunk 50 optimal weight:    7.9990
   overall best weight:    2.8086

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 ASN
A 446 GLN
** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
C 192 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
D 137 ASN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.076757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.054064 restraints weight = 57137.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.056136 restraints weight = 33311.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.057526 restraints weight = 22479.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.058421 restraints weight = 16872.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.059101 restraints weight = 13797.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.131  11809  Z= 0.172
  Angle     :  0.799  18.019  16110  Z= 0.396
  Chirality :  0.047   0.221   1810
  Planarity :  0.005   0.047   2074
  Dihedral  :  7.554  56.447   1788
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.17 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.39 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.20), residues: 1477
  helix: -3.59 (0.46), residues: 61
  sheet: -1.58 (0.28), residues: 326
  loop : -2.20 (0.18), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E  98 
 TYR   0.032   0.002   TYR B  96 
 PHE   0.031   0.002   PHE C  99A
 TRP   0.021   0.002   TRP B  35 
 HIS   0.015   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (11766)
  covalent geometry    : angle       0.77325 (16015)
  SS BOND              : bond        0.01125 (   34)
  SS BOND              : angle       2.88367 (   68)
  hydrogen bonds       : bond        0.03662 (  187)
  hydrogen bonds       : angle       7.07488 (  438)
  link_ALPHA1-3        : bond        0.00403 (    1)
  link_ALPHA1-3        : angle       1.59265 (    3)
  link_BETA1-4         : bond        0.00286 (    2)
  link_BETA1-4         : angle       1.18905 (    6)
  link_NAG-ASN         : bond        0.00259 (    6)
  link_NAG-ASN         : angle       2.53226 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2176.76 seconds
wall clock time: 38 minutes 21.54 seconds (2301.54 seconds total)