Starting phenix.real_space_refine
on Tue Jul 29 19:00:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oge_20055/07_2025/6oge_20055_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oge_20055/07_2025/6oge_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_20055/07_2025/6oge_20055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oge_20055/07_2025/6oge_20055.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oge_20055/07_2025/6oge_20055_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oge_20055/07_2025/6oge_20055_neut.cif"
  }
  resolution = 4.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.11, per 1000 atoms: 0.88
  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: 3.21
  Conformation dependent library (CDL) restraints added in 3.9 seconds
  

  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: 1.91
  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: 9.54

  Time building geometry restraints manager: 3.89 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:             13.850
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     40.990
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.570
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.020   0.004   TRP E 161 
 HIS   0.015   0.003   HIS E  35 
 PHE   0.053   0.004   PHE A 577 
 TYR   0.043   0.004   TYR E  80 
 ARG   0.008   0.001   ARG A 558 

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

*********************** 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  : 1.408 
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: 0.8547 (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: 0.8219 (m-80)
REVERT: B  186 TYR cc_start: 0.8405 (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: 0.3226
  time to fit residues: 132.8770
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  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 111 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 59 optimal weight:   20.0000
   chunk 115 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 70 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 133 optimal weight:    6.9990
   overall best weight:    2.9186

-------------------------------------------------------------------------------
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 178 GLN
A 319 ASN
A 329 GLN
B 155 GLN
B 166 GLN
D 138 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.077484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.054502 restraints weight = 56194.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.056547 restraints weight = 33017.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.057929 restraints weight = 22511.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.160  11809  Z= 0.198
  Angle     :  0.865  19.702  16110  Z= 0.443
  Chirality :  0.048   0.224   1810
  Planarity :  0.007   0.068   2074
  Dihedral  : 12.395  92.995   1788
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.10 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.11 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.20), residues: 1477
  helix: -4.15 (0.41), residues: 45
  sheet: -2.26 (0.28), residues: 295
  loop : -2.77 (0.17), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP E 110 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.037   0.002   PHE C  99A
 TYR   0.035   0.002   TYR B  96 
 ARG   0.009   0.001   ARG D  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01254 (    6)
  link_NAG-ASN         : angle       2.52214 (   18)
  link_BETA1-4         : bond        0.00482 (    2)
  link_BETA1-4         : angle       2.00947 (    6)
  link_ALPHA1-3        : bond        0.00256 (    1)
  link_ALPHA1-3        : angle       1.87155 (    3)
  hydrogen bonds       : bond        0.05421 (  187)
  hydrogen bonds       : angle       9.53231 (  438)
  SS BOND              : bond        0.01429 (   34)
  SS BOND              : angle       3.49929 (   68)
  covalent geometry    : bond        0.00430 (11766)
  covalent geometry    : angle       0.83135 (16015)

*********************** 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
  244 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 1.221 
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: A   75 GLN cc_start: 0.9237 (pt0) cc_final: 0.8861 (pm20)
REVERT: A  217 ARG cc_start: 0.9025 (ttp80) cc_final: 0.8682 (ptm160)
REVERT: A  226 ARG cc_start: 0.8056 (mmp80) cc_final: 0.7125 (ptp90)
REVERT: A  343 TYR cc_start: 0.8796 (m-80) cc_final: 0.8205 (m-10)
REVERT: A  403 LEU cc_start: 0.9101 (tp) cc_final: 0.8752 (mt)
REVERT: A  404 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8556 (mt-10)
REVERT: A  458 LEU cc_start: 0.9660 (tp) cc_final: 0.9426 (tt)
REVERT: B   42 LYS cc_start: 0.9690 (mmtt) cc_final: 0.9445 (mmtm)
REVERT: B   71 PHE cc_start: 0.8460 (m-10) cc_final: 0.8150 (m-10)
REVERT: B   78 LEU cc_start: 0.9410 (tp) cc_final: 0.8773 (mt)
REVERT: B   91 TYR cc_start: 0.8798 (p90) cc_final: 0.8556 (p90)
REVERT: B  105 GLU cc_start: 0.8196 (tp30) cc_final: 0.7815 (tp30)
REVERT: B  122 ASP cc_start: 0.9428 (p0) cc_final: 0.9151 (t0)
REVERT: B  138 ASN cc_start: 0.9410 (m-40) cc_final: 0.9123 (m-40)
REVERT: B  139 PHE cc_start: 0.9064 (p90) cc_final: 0.8221 (p90)
REVERT: B  149 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9081 (mmtm)
REVERT: B  155 GLN cc_start: 0.8624 (tp40) cc_final: 0.7806 (tm-30)
REVERT: B  173 TYR cc_start: 0.8788 (m-80) cc_final: 0.7912 (m-80)
REVERT: B  179 LEU cc_start: 0.9504 (tp) cc_final: 0.8885 (tp)
REVERT: C   34 MET cc_start: 0.8945 (mmm) cc_final: 0.8661 (mmm)
REVERT: C  100 PHE cc_start: 0.8357 (m-80) cc_final: 0.7820 (m-80)
REVERT: C  142 VAL cc_start: 0.9704 (t) cc_final: 0.9234 (t)
REVERT: C  144 ASP cc_start: 0.9081 (m-30) cc_final: 0.8769 (m-30)
REVERT: C  145 TYR cc_start: 0.7879 (p90) cc_final: 0.7531 (p90)
REVERT: C  214 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8396 (mmmt)
REVERT: D   11 LEU cc_start: 0.9437 (mt) cc_final: 0.9139 (mp)
REVERT: D   30 ASN cc_start: 0.9028 (m110) cc_final: 0.8397 (m-40)
REVERT: D  139 PHE cc_start: 0.7627 (p90) cc_final: 0.7355 (p90)
REVERT: D  140 TYR cc_start: 0.8553 (t80) cc_final: 0.8022 (t80)
REVERT: E   30 LYS cc_start: 0.8443 (pptt) cc_final: 0.8048 (pptt)
REVERT: E   50 ARG cc_start: 0.9590 (ttp-170) cc_final: 0.9349 (ttp-110)
REVERT: E   65 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8846 (mmtm)
REVERT: E  107 MET cc_start: 0.9499 (mtm) cc_final: 0.9162 (mtt)
REVERT: E  136 LYS cc_start: 0.8156 (tptt) cc_final: 0.7952 (mmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2701
  time to fit residues: 89.4528
Evaluate side-chains
  173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 133 optimal weight:    0.9980
   chunk 91 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 131 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  61 GLN
D 138 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.078159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.055302 restraints weight = 57519.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.057369 restraints weight = 33396.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.058790 restraints weight = 22614.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.160  11809  Z= 0.172
  Angle     :  0.822  19.668  16110  Z= 0.417
  Chirality :  0.047   0.235   1810
  Planarity :  0.006   0.066   2074
  Dihedral  : 10.915  83.024   1788
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.36 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.20), residues: 1477
  helix: -3.95 (0.47), residues: 46
  sheet: -2.07 (0.28), residues: 295
  loop : -2.59 (0.17), residues: 1136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP E 110 
 HIS   0.005   0.001   HIS C 200 
 PHE   0.048   0.002   PHE C  99A
 TYR   0.033   0.002   TYR B  96 
 ARG   0.008   0.001   ARG A  92 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00363 (    6)
  link_NAG-ASN         : angle       2.25658 (   18)
  link_BETA1-4         : bond        0.00164 (    2)
  link_BETA1-4         : angle       1.90277 (    6)
  link_ALPHA1-3        : bond        0.00735 (    1)
  link_ALPHA1-3        : angle       1.52018 (    3)
  hydrogen bonds       : bond        0.04116 (  187)
  hydrogen bonds       : angle       8.13186 (  438)
  SS BOND              : bond        0.01417 (   34)
  SS BOND              : angle       3.41592 (   68)
  covalent geometry    : bond        0.00395 (11766)
  covalent geometry    : angle       0.78891 (16015)

*********************** 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
  243 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 239
  time to evaluate  : 1.248 
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: A   75 GLN cc_start: 0.9207 (pt0) cc_final: 0.8854 (pm20)
REVERT: A  168 LEU cc_start: 0.9133 (tp) cc_final: 0.8922 (tt)
REVERT: A  217 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8307 (tmm-80)
REVERT: A  258 PHE cc_start: 0.8280 (m-80) cc_final: 0.8033 (m-80)
REVERT: A  343 TYR cc_start: 0.8793 (m-80) cc_final: 0.8249 (m-10)
REVERT: A  403 LEU cc_start: 0.9024 (tp) cc_final: 0.8754 (mt)
REVERT: A  404 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8423 (mt-10)
REVERT: A  458 LEU cc_start: 0.9652 (tp) cc_final: 0.9422 (tt)
REVERT: B   71 PHE cc_start: 0.8506 (m-10) cc_final: 0.8169 (m-10)
REVERT: B   87 TYR cc_start: 0.8854 (m-80) cc_final: 0.8530 (m-80)
REVERT: B  122 ASP cc_start: 0.9388 (p0) cc_final: 0.9176 (t0)
REVERT: B  139 PHE cc_start: 0.8975 (p90) cc_final: 0.8138 (p90)
REVERT: B  145 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9052 (tppt)
REVERT: B  148 TRP cc_start: 0.7218 (m100) cc_final: 0.5526 (m100)
REVERT: B  149 LYS cc_start: 0.9357 (mtpp) cc_final: 0.8980 (mmtm)
REVERT: B  155 GLN cc_start: 0.8469 (tp40) cc_final: 0.7613 (tm-30)
REVERT: B  173 TYR cc_start: 0.8566 (m-80) cc_final: 0.7682 (m-80)
REVERT: B  179 LEU cc_start: 0.9492 (tp) cc_final: 0.8589 (tp)
REVERT: C   34 MET cc_start: 0.9019 (mmm) cc_final: 0.8215 (tpp)
REVERT: C   59 TYR cc_start: 0.8571 (p90) cc_final: 0.7531 (p90)
REVERT: C   92 CYS cc_start: 0.6248 (t) cc_final: 0.3693 (t)
REVERT: C  100 PHE cc_start: 0.8145 (m-80) cc_final: 0.7446 (m-80)
REVERT: C  142 VAL cc_start: 0.9738 (t) cc_final: 0.9233 (t)
REVERT: C  145 TYR cc_start: 0.7953 (p90) cc_final: 0.7532 (p90)
REVERT: C  214 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8372 (mmmt)
REVERT: D   11 LEU cc_start: 0.9380 (mt) cc_final: 0.9071 (mp)
REVERT: D  139 PHE cc_start: 0.7611 (p90) cc_final: 0.6941 (p90)
REVERT: D  140 TYR cc_start: 0.8482 (t80) cc_final: 0.7817 (t80)
REVERT: D  175 LEU cc_start: 0.9158 (tt) cc_final: 0.8923 (mp)
REVERT: E   30 LYS cc_start: 0.8392 (pptt) cc_final: 0.7963 (pptt)
REVERT: E   39 GLN cc_start: 0.8981 (tt0) cc_final: 0.8050 (tt0)
REVERT: E   50 ARG cc_start: 0.9530 (ttp-170) cc_final: 0.9294 (ttp-110)
REVERT: E   98 ARG cc_start: 0.8397 (ptt90) cc_final: 0.8137 (ptt-90)
  outliers start: 4
  outliers final: 1
  residues processed: 242
  average time/residue: 0.2591
  time to fit residues: 86.7714
Evaluate side-chains
  183 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 1 optimal weight:    0.3980
   chunk 13 optimal weight:    8.9990
   chunk 118 optimal weight:    0.0370
   chunk 97 optimal weight:    5.9990
   chunk 17 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    2.6662

-------------------------------------------------------------------------------
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
A 632 HIS
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 ASN
** C  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.077642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.054826 restraints weight = 55880.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.056820 restraints weight = 32966.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.058196 restraints weight = 22617.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3603

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= 0.178
  Angle     :  0.793  19.302  16110  Z= 0.399
  Chirality :  0.046   0.236   1810
  Planarity :  0.006   0.051   2074
  Dihedral  :  9.884  79.531   1788
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.17 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.20), residues: 1477
  helix: -3.59 (0.52), residues: 46
  sheet: -1.95 (0.28), residues: 310
  loop : -2.46 (0.18), residues: 1121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 110 
 HIS   0.006   0.001   HIS B 189 
 PHE   0.049   0.002   PHE C  99A
 TYR   0.036   0.002   TYR B  96 
 ARG   0.007   0.001   ARG B  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00296 (    6)
  link_NAG-ASN         : angle       2.20777 (   18)
  link_BETA1-4         : bond        0.00184 (    2)
  link_BETA1-4         : angle       1.62123 (    6)
  link_ALPHA1-3        : bond        0.00358 (    1)
  link_ALPHA1-3        : angle       1.15516 (    3)
  hydrogen bonds       : bond        0.03725 (  187)
  hydrogen bonds       : angle       7.84437 (  438)
  SS BOND              : bond        0.01289 (   34)
  SS BOND              : angle       3.17007 (   68)
  covalent geometry    : bond        0.00402 (11766)
  covalent geometry    : angle       0.76332 (16015)

*********************** 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
  222 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.301 
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: A   75 GLN cc_start: 0.9230 (pt0) cc_final: 0.8837 (pm20)
REVERT: A  217 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8315 (tmm-80)
REVERT: A  258 PHE cc_start: 0.8360 (m-80) cc_final: 0.8054 (m-80)
REVERT: A  343 TYR cc_start: 0.8820 (m-80) cc_final: 0.8163 (m-10)
REVERT: A  348 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6585 (mm-30)
REVERT: A  403 LEU cc_start: 0.9003 (tp) cc_final: 0.8726 (mt)
REVERT: A  404 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8398 (mt-10)
REVERT: A  405 GLU cc_start: 0.8604 (tp30) cc_final: 0.8271 (tp30)
REVERT: A  458 LEU cc_start: 0.9658 (tp) cc_final: 0.9439 (tt)
REVERT: B   71 PHE cc_start: 0.8515 (m-10) cc_final: 0.8237 (m-10)
REVERT: B   73 LEU cc_start: 0.9573 (tt) cc_final: 0.9310 (pp)
REVERT: B   87 TYR cc_start: 0.8911 (m-80) cc_final: 0.8689 (m-80)
REVERT: B   91 TYR cc_start: 0.8897 (p90) cc_final: 0.8612 (p90)
REVERT: B  139 PHE cc_start: 0.8969 (p90) cc_final: 0.8187 (p90)
REVERT: B  145 LYS cc_start: 0.9412 (mmpt) cc_final: 0.9135 (tppt)
REVERT: B  148 TRP cc_start: 0.7538 (m100) cc_final: 0.4646 (m100)
REVERT: B  155 GLN cc_start: 0.8382 (tp40) cc_final: 0.7554 (tm-30)
REVERT: B  179 LEU cc_start: 0.9478 (tp) cc_final: 0.8659 (tp)
REVERT: C  142 VAL cc_start: 0.9739 (t) cc_final: 0.9335 (t)
REVERT: C  145 TYR cc_start: 0.7910 (p90) cc_final: 0.7386 (p90)
REVERT: C  214 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8381 (mmmt)
REVERT: D   11 LEU cc_start: 0.9343 (mt) cc_final: 0.9016 (mp)
REVERT: D  139 PHE cc_start: 0.7581 (p90) cc_final: 0.7209 (p90)
REVERT: D  140 TYR cc_start: 0.8444 (t80) cc_final: 0.7726 (t80)
REVERT: E   30 LYS cc_start: 0.8401 (pptt) cc_final: 0.7958 (pptt)
REVERT: E   39 GLN cc_start: 0.8732 (tt0) cc_final: 0.8047 (tt0)
REVERT: E   50 ARG cc_start: 0.9596 (ttp-170) cc_final: 0.9279 (ttp-110)
REVERT: E   65 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8918 (mmmt)
REVERT: E   98 ARG cc_start: 0.8333 (ptt90) cc_final: 0.7990 (ptt-90)
REVERT: E   99 TRP cc_start: 0.8423 (m-10) cc_final: 0.7991 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.2627
  time to fit residues: 80.0124
Evaluate side-chains
  169 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 111 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 106 optimal weight:    0.6980
   chunk 71 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   overall best weight:    4.5388

-------------------------------------------------------------------------------
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**
A 484 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  61 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 = 0.3620 r_free = 0.3620 target = 0.076171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.053523 restraints weight = 56554.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.055479 restraints weight = 33238.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.056824 restraints weight = 22753.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.136  11809  Z= 0.226
  Angle     :  0.837  18.978  16110  Z= 0.419
  Chirality :  0.047   0.229   1810
  Planarity :  0.006   0.067   2074
  Dihedral  :  9.486  75.137   1788
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 21.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.05 %
    Favored  : 87.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.21), residues: 1477
  helix: -3.63 (0.47), residues: 46
  sheet: -1.94 (0.28), residues: 316
  loop : -2.40 (0.18), residues: 1115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP E 110 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.036   0.002   PHE C  99A
 TYR   0.031   0.002   TYR B  96 
 ARG   0.007   0.001   ARG B  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00319 (    6)
  link_NAG-ASN         : angle       2.33988 (   18)
  link_BETA1-4         : bond        0.00219 (    2)
  link_BETA1-4         : angle       1.39521 (    6)
  link_ALPHA1-3        : bond        0.00436 (    1)
  link_ALPHA1-3        : angle       1.28932 (    3)
  hydrogen bonds       : bond        0.03737 (  187)
  hydrogen bonds       : angle       7.81403 (  438)
  SS BOND              : bond        0.01299 (   34)
  SS BOND              : angle       3.17588 (   68)
  covalent geometry    : bond        0.00500 (11766)
  covalent geometry    : angle       0.80887 (16015)

*********************** 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
  204 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.330 
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: A   75 GLN cc_start: 0.9284 (pt0) cc_final: 0.8920 (pm20)
REVERT: A  141 GLN cc_start: 0.8381 (pt0) cc_final: 0.8025 (pp30)
REVERT: A  217 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8840 (ptm160)
REVERT: A  403 LEU cc_start: 0.9057 (tp) cc_final: 0.8719 (mt)
REVERT: A  404 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8389 (mt-10)
REVERT: B   33 VAL cc_start: 0.9336 (t) cc_final: 0.8844 (t)
REVERT: B   73 LEU cc_start: 0.9587 (tt) cc_final: 0.9307 (pp)
REVERT: B   87 TYR cc_start: 0.8935 (m-80) cc_final: 0.8721 (m-80)
REVERT: B   91 TYR cc_start: 0.8907 (p90) cc_final: 0.8685 (p90)
REVERT: B  139 PHE cc_start: 0.8941 (p90) cc_final: 0.8207 (p90)
REVERT: B  145 LYS cc_start: 0.9419 (mmpt) cc_final: 0.9109 (tppt)
REVERT: B  155 GLN cc_start: 0.8457 (tp40) cc_final: 0.7556 (tm-30)
REVERT: B  179 LEU cc_start: 0.9441 (tp) cc_final: 0.8834 (tp)
REVERT: B  185 ASP cc_start: 0.8783 (t0) cc_final: 0.8427 (t0)
REVERT: C  142 VAL cc_start: 0.9728 (t) cc_final: 0.9423 (m)
REVERT: C  145 TYR cc_start: 0.8018 (p90) cc_final: 0.7513 (p90)
REVERT: C  214 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8383 (mmmt)
REVERT: D   11 LEU cc_start: 0.9335 (mt) cc_final: 0.9127 (mp)
REVERT: D  139 PHE cc_start: 0.7555 (p90) cc_final: 0.6764 (p90)
REVERT: D  140 TYR cc_start: 0.8415 (t80) cc_final: 0.7678 (t80)
REVERT: D  175 LEU cc_start: 0.9297 (tt) cc_final: 0.9016 (mp)
REVERT: E   30 LYS cc_start: 0.8353 (pptt) cc_final: 0.7933 (pptt)
REVERT: E   39 GLN cc_start: 0.8699 (tt0) cc_final: 0.8114 (tt0)
REVERT: E   98 ARG cc_start: 0.8238 (ptt90) cc_final: 0.7818 (ptt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2622
  time to fit residues: 74.3070
Evaluate side-chains
  163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 126 optimal weight:   20.0000
   chunk 112 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 130 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 139 optimal weight:   30.0000
   chunk 96 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 135 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** 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 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
A 484 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 138 ASN
** E  35 HIS ** 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 = 0.3657 r_free = 0.3657 target = 0.078072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.054972 restraints weight = 55990.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.057045 restraints weight = 32562.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.058433 restraints weight = 22136.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4122

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= 0.155
  Angle     :  0.784  18.685  16110  Z= 0.390
  Chirality :  0.047   0.233   1810
  Planarity :  0.005   0.050   2074
  Dihedral  :  8.978  69.101   1788
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.56 %
    Favored  : 89.30 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.21), residues: 1477
  helix: -3.40 (0.51), residues: 46
  sheet: -2.01 (0.27), residues: 331
  loop : -2.31 (0.18), residues: 1100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 110 
 HIS   0.005   0.001   HIS D 198 
 PHE   0.044   0.002   PHE E 173 
 TYR   0.028   0.002   TYR B  96 
 ARG   0.005   0.001   ARG E  50 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    6)
  link_NAG-ASN         : angle       2.69391 (   18)
  link_BETA1-4         : bond        0.00242 (    2)
  link_BETA1-4         : angle       1.45005 (    6)
  link_ALPHA1-3        : bond        0.00739 (    1)
  link_ALPHA1-3        : angle       1.40699 (    3)
  hydrogen bonds       : bond        0.03459 (  187)
  hydrogen bonds       : angle       7.41248 (  438)
  SS BOND              : bond        0.01226 (   34)
  SS BOND              : angle       3.08881 (   68)
  covalent geometry    : bond        0.00353 (11766)
  covalent geometry    : angle       0.75384 (16015)

*********************** 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
  221 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 1.191 
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   46 LEU cc_start: 0.9709 (mm) cc_final: 0.9126 (mm)
REVERT: A   56 VAL cc_start: 0.9692 (t) cc_final: 0.9343 (t)
REVERT: A   75 GLN cc_start: 0.9281 (pt0) cc_final: 0.8926 (pm20)
REVERT: A  141 GLN cc_start: 0.8312 (pt0) cc_final: 0.8034 (pp30)
REVERT: A  173 PHE cc_start: 0.9354 (m-80) cc_final: 0.9031 (m-80)
REVERT: A  258 PHE cc_start: 0.8203 (m-80) cc_final: 0.7891 (m-80)
REVERT: A  403 LEU cc_start: 0.8978 (tp) cc_final: 0.8692 (mt)
REVERT: A  404 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8319 (mt-10)
REVERT: A  405 GLU cc_start: 0.8831 (tp30) cc_final: 0.8437 (tp30)
REVERT: A  611 MET cc_start: 0.8730 (ptt) cc_final: 0.8331 (ptm)
REVERT: B   71 PHE cc_start: 0.8440 (m-10) cc_final: 0.8197 (m-10)
REVERT: B   87 TYR cc_start: 0.8876 (m-80) cc_final: 0.8668 (m-80)
REVERT: B  139 PHE cc_start: 0.9000 (p90) cc_final: 0.8297 (p90)
REVERT: B  142 ARG cc_start: 0.9024 (tpt90) cc_final: 0.8758 (tpt90)
REVERT: B  145 LYS cc_start: 0.9405 (mmpt) cc_final: 0.9145 (tppt)
REVERT: B  155 GLN cc_start: 0.8346 (tp40) cc_final: 0.7403 (tm-30)
REVERT: B  179 LEU cc_start: 0.9442 (tp) cc_final: 0.8815 (tp)
REVERT: B  185 ASP cc_start: 0.8986 (t0) cc_final: 0.8653 (t0)
REVERT: B  186 TYR cc_start: 0.8604 (t80) cc_final: 0.8374 (t80)
REVERT: C   64 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8733 (tttt)
REVERT: C  100 PHE cc_start: 0.8288 (m-80) cc_final: 0.7714 (m-80)
REVERT: C  142 VAL cc_start: 0.9729 (t) cc_final: 0.9396 (m)
REVERT: C  143 LYS cc_start: 0.9166 (tptp) cc_final: 0.8873 (tptp)
REVERT: C  145 TYR cc_start: 0.7878 (p90) cc_final: 0.7519 (p90)
REVERT: C  214 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8406 (mmmt)
REVERT: D  139 PHE cc_start: 0.7534 (p90) cc_final: 0.6819 (p90)
REVERT: D  140 TYR cc_start: 0.8373 (t80) cc_final: 0.7601 (t80)
REVERT: E    1 GLU cc_start: 0.7869 (tt0) cc_final: 0.7626 (tm-30)
REVERT: E   39 GLN cc_start: 0.8850 (tt0) cc_final: 0.8135 (tt0)
REVERT: E   50 ARG cc_start: 0.9039 (ttp-110) cc_final: 0.8788 (ttp-110)
REVERT: E   73 ASP cc_start: 0.8861 (m-30) cc_final: 0.8601 (m-30)
REVERT: E   98 ARG cc_start: 0.7593 (ptt90) cc_final: 0.6955 (ptt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2597
  time to fit residues: 79.3607
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  : 1.385 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 132 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 118 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 37 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0670
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.5924

-------------------------------------------------------------------------------
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
A 484 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
** C  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 138 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.077667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.054761 restraints weight = 56411.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.056789 restraints weight = 32875.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.058174 restraints weight = 22374.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134  11809  Z= 0.169
  Angle     :  0.799  19.589  16110  Z= 0.395
  Chirality :  0.047   0.262   1810
  Planarity :  0.005   0.056   2074
  Dihedral  :  8.640  63.950   1788
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 19.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.17 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.21), residues: 1477
  helix: -3.46 (0.51), residues: 46
  sheet: -1.70 (0.29), residues: 299
  loop : -2.33 (0.18), residues: 1132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP E  99 
 HIS   0.039   0.002   HIS E  35 
 PHE   0.039   0.002   PHE C  99A
 TYR   0.030   0.002   TYR B  96 
 ARG   0.011   0.001   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00328 (    6)
  link_NAG-ASN         : angle       2.56235 (   18)
  link_BETA1-4         : bond        0.00062 (    2)
  link_BETA1-4         : angle       1.25463 (    6)
  link_ALPHA1-3        : bond        0.00509 (    1)
  link_ALPHA1-3        : angle       1.36730 (    3)
  hydrogen bonds       : bond        0.03477 (  187)
  hydrogen bonds       : angle       7.32630 (  438)
  SS BOND              : bond        0.01235 (   34)
  SS BOND              : angle       2.94789 (   68)
  covalent geometry    : bond        0.00381 (11766)
  covalent geometry    : angle       0.77274 (16015)

*********************** 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
  212 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.258 
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   46 LEU cc_start: 0.9742 (mm) cc_final: 0.9163 (mm)
REVERT: A   75 GLN cc_start: 0.9275 (pt0) cc_final: 0.8895 (pm20)
REVERT: A  141 GLN cc_start: 0.8582 (pt0) cc_final: 0.8035 (pp30)
REVERT: A  403 LEU cc_start: 0.8974 (tp) cc_final: 0.8654 (mt)
REVERT: A  404 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8335 (mt-10)
REVERT: A  405 GLU cc_start: 0.8725 (tp30) cc_final: 0.8361 (tp30)
REVERT: A  611 MET cc_start: 0.8688 (ptt) cc_final: 0.8385 (ptm)
REVERT: B   71 PHE cc_start: 0.8513 (m-10) cc_final: 0.8220 (m-10)
REVERT: B   97 THR cc_start: 0.9048 (p) cc_final: 0.8716 (p)
REVERT: B  139 PHE cc_start: 0.9042 (p90) cc_final: 0.8332 (p90)
REVERT: B  142 ARG cc_start: 0.9029 (tpt90) cc_final: 0.8743 (tpt90)
REVERT: B  145 LYS cc_start: 0.9394 (mmpt) cc_final: 0.9122 (tppt)
REVERT: B  148 TRP cc_start: 0.7456 (m100) cc_final: 0.5274 (m100)
REVERT: B  155 GLN cc_start: 0.8345 (tp40) cc_final: 0.7644 (tm-30)
REVERT: B  179 LEU cc_start: 0.9422 (tp) cc_final: 0.8690 (tp)
REVERT: B  194 CYS cc_start: 0.5772 (t) cc_final: 0.3502 (t)
REVERT: C  100 PHE cc_start: 0.8488 (m-80) cc_final: 0.8151 (m-80)
REVERT: C  145 TYR cc_start: 0.7921 (p90) cc_final: 0.7577 (p90)
REVERT: C  214 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8438 (mmmt)
REVERT: D  139 PHE cc_start: 0.7034 (p90) cc_final: 0.6496 (p90)
REVERT: D  140 TYR cc_start: 0.8364 (t80) cc_final: 0.7606 (t80)
REVERT: E    1 GLU cc_start: 0.7911 (tt0) cc_final: 0.7681 (tm-30)
REVERT: E   39 GLN cc_start: 0.8878 (tt0) cc_final: 0.8186 (tt0)
REVERT: E   73 ASP cc_start: 0.8961 (m-30) cc_final: 0.8503 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2516
  time to fit residues: 74.5996
Evaluate side-chains
  164 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0980
   chunk 96 optimal weight:   20.0000
   chunk 41 optimal weight:    0.0970
   chunk 108 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 65 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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
A 484 GLN
** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
B 189 HIS
** C  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 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 = 0.3690 r_free = 0.3690 target = 0.079823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.056693 restraints weight = 54843.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.058783 restraints weight = 32076.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.060211 restraints weight = 21870.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.4736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.143  11809  Z= 0.146
  Angle     :  0.801  18.466  16110  Z= 0.394
  Chirality :  0.047   0.227   1810
  Planarity :  0.005   0.051   2074
  Dihedral  :  8.179  57.273   1788
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.82 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.21), residues: 1477
  helix: -3.49 (0.49), residues: 52
  sheet: -1.57 (0.28), residues: 326
  loop : -2.25 (0.18), residues: 1099

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.002   TRP E  99 
 HIS   0.028   0.001   HIS E  35 
 PHE   0.032   0.002   PHE E 173 
 TYR   0.026   0.002   TYR B  96 
 ARG   0.008   0.001   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00271 (    6)
  link_NAG-ASN         : angle       2.28275 (   18)
  link_BETA1-4         : bond        0.00329 (    2)
  link_BETA1-4         : angle       0.99891 (    6)
  link_ALPHA1-3        : bond        0.00570 (    1)
  link_ALPHA1-3        : angle       1.33272 (    3)
  hydrogen bonds       : bond        0.03314 (  187)
  hydrogen bonds       : angle       6.90534 (  438)
  SS BOND              : bond        0.01147 (   34)
  SS BOND              : angle       2.92525 (   68)
  covalent geometry    : bond        0.00332 (11766)
  covalent geometry    : angle       0.77650 (16015)

*********************** 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
  218 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.303 
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   44 ASP cc_start: 0.9486 (m-30) cc_final: 0.9280 (m-30)
REVERT: A   46 LEU cc_start: 0.9724 (mm) cc_final: 0.9139 (mm)
REVERT: A   74 LEU cc_start: 0.9374 (mt) cc_final: 0.9095 (tt)
REVERT: A   75 GLN cc_start: 0.9285 (pt0) cc_final: 0.8980 (pm20)
REVERT: A   96 LEU cc_start: 0.9234 (mt) cc_final: 0.8645 (mt)
REVERT: A  258 PHE cc_start: 0.8261 (m-80) cc_final: 0.7889 (m-80)
REVERT: A  301 TYR cc_start: 0.8149 (t80) cc_final: 0.7695 (t80)
REVERT: A  403 LEU cc_start: 0.8892 (tp) cc_final: 0.8650 (mt)
REVERT: A  404 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8317 (pt0)
REVERT: B   71 PHE cc_start: 0.8481 (m-10) cc_final: 0.8140 (m-10)
REVERT: B  139 PHE cc_start: 0.8902 (p90) cc_final: 0.8106 (p90)
REVERT: B  142 ARG cc_start: 0.9043 (tpt90) cc_final: 0.8784 (tpt90)
REVERT: B  145 LYS cc_start: 0.9401 (mmpt) cc_final: 0.9154 (tppt)
REVERT: B  148 TRP cc_start: 0.7251 (m100) cc_final: 0.5117 (m100)
REVERT: B  155 GLN cc_start: 0.8197 (tp40) cc_final: 0.7545 (tm-30)
REVERT: B  179 LEU cc_start: 0.9429 (tp) cc_final: 0.8631 (tp)
REVERT: B  185 ASP cc_start: 0.9240 (t0) cc_final: 0.8995 (t0)
REVERT: B  194 CYS cc_start: 0.5807 (t) cc_final: 0.5031 (t)
REVERT: C  100 PHE cc_start: 0.8284 (m-80) cc_final: 0.7647 (m-80)
REVERT: C  142 VAL cc_start: 0.9718 (t) cc_final: 0.9333 (m)
REVERT: C  145 TYR cc_start: 0.7802 (p90) cc_final: 0.7507 (p90)
REVERT: D   86 TYR cc_start: 0.7963 (m-80) cc_final: 0.6646 (m-80)
REVERT: D  139 PHE cc_start: 0.6774 (p90) cc_final: 0.6141 (p90)
REVERT: D  140 TYR cc_start: 0.8331 (t80) cc_final: 0.7459 (t80)
REVERT: D  142 ARG cc_start: 0.8809 (ttp-170) cc_final: 0.8543 (ttp-170)
REVERT: D  173 TYR cc_start: 0.6009 (m-10) cc_final: 0.5698 (m-10)
REVERT: E    1 GLU cc_start: 0.7777 (tt0) cc_final: 0.7436 (tm-30)
REVERT: E   30 LYS cc_start: 0.8325 (pptt) cc_final: 0.7869 (mttp)
REVERT: E   39 GLN cc_start: 0.8814 (tt0) cc_final: 0.8391 (tt0)
REVERT: E   73 ASP cc_start: 0.8907 (m-30) cc_final: 0.8473 (m-30)
REVERT: E  108 ASP cc_start: 0.6600 (p0) cc_final: 0.6051 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2452
  time to fit residues: 75.2644
Evaluate side-chains
  162 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 136 optimal weight:   20.0000
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 121 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 129 optimal weight:    5.9990
   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  97 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**
A 624 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
** C  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.075521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.053030 restraints weight = 57463.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.054951 restraints weight = 33726.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.056275 restraints weight = 23103.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.119  11809  Z= 0.254
  Angle     :  0.872  20.425  16110  Z= 0.432
  Chirality :  0.048   0.215   1810
  Planarity :  0.006   0.056   2074
  Dihedral  :  8.139  57.520   1788
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 23.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.66 %
    Favored  : 87.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.21), residues: 1477
  helix: -3.90 (0.39), residues: 61
  sheet: -1.57 (0.29), residues: 294
  loop : -2.32 (0.18), residues: 1122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP E 110 
 HIS   0.009   0.002   HIS E  35 
 PHE   0.032   0.003   PHE C  99A
 TYR   0.032   0.002   TYR B  96 
 ARG   0.007   0.001   ARG D  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00360 (    6)
  link_NAG-ASN         : angle       2.59403 (   18)
  link_BETA1-4         : bond        0.00073 (    2)
  link_BETA1-4         : angle       1.37602 (    6)
  link_ALPHA1-3        : bond        0.00364 (    1)
  link_ALPHA1-3        : angle       1.57163 (    3)
  hydrogen bonds       : bond        0.03901 (  187)
  hydrogen bonds       : angle       7.24410 (  438)
  SS BOND              : bond        0.01244 (   34)
  SS BOND              : angle       2.83292 (   68)
  covalent geometry    : bond        0.00558 (11766)
  covalent geometry    : angle       0.84972 (16015)

*********************** 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
  190 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.488 
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: 0.9264 (pt0) cc_final: 0.8900 (pm20)
REVERT: A  403 LEU cc_start: 0.8991 (tp) cc_final: 0.8468 (mt)
REVERT: A  404 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8423 (mt-10)
REVERT: A  405 GLU cc_start: 0.8989 (tp30) cc_final: 0.8613 (tp30)
REVERT: A  611 MET cc_start: 0.8335 (ptm) cc_final: 0.7555 (ppp)
REVERT: B  139 PHE cc_start: 0.8885 (p90) cc_final: 0.8110 (p90)
REVERT: B  142 ARG cc_start: 0.9069 (tpt90) cc_final: 0.8788 (tpt90)
REVERT: B  145 LYS cc_start: 0.9428 (mmpt) cc_final: 0.9149 (tppt)
REVERT: B  155 GLN cc_start: 0.8161 (tp40) cc_final: 0.7315 (tm-30)
REVERT: B  179 LEU cc_start: 0.9392 (tp) cc_final: 0.8854 (tp)
REVERT: C  145 TYR cc_start: 0.7883 (p90) cc_final: 0.7660 (p90)
REVERT: D   36 TYR cc_start: 0.8537 (m-80) cc_final: 0.8193 (m-80)
REVERT: D  139 PHE cc_start: 0.6943 (p90) cc_final: 0.6307 (p90)
REVERT: D  140 TYR cc_start: 0.8477 (t80) cc_final: 0.7694 (t80)
REVERT: D  173 TYR cc_start: 0.6458 (m-10) cc_final: 0.6178 (m-10)
REVERT: E   39 GLN cc_start: 0.8967 (tt0) cc_final: 0.8474 (tt0)
REVERT: E   50 ARG cc_start: 0.7824 (mtt180) cc_final: 0.6917 (mtt180)
REVERT: E   73 ASP cc_start: 0.8970 (m-30) cc_final: 0.8677 (m-30)
REVERT: E   98 ARG cc_start: 0.8269 (tmm160) cc_final: 0.7537 (ptm-80)
REVERT: E  107 MET cc_start: 0.6934 (tpt) cc_final: 0.5770 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2427
  time to fit residues: 65.7289
Evaluate side-chains
  152 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 61 optimal weight:    0.0870
   chunk 88 optimal weight:    0.5980
   chunk 68 optimal weight:    9.9990
   chunk 138 optimal weight:   10.0000
   chunk 101 optimal weight:   30.0000
   chunk 40 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    1.5364

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
A 484 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  61 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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.078476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.055547 restraints weight = 56758.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.057567 restraints weight = 32966.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.058918 restraints weight = 22404.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.4966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134  11809  Z= 0.151
  Angle     :  0.799  18.810  16110  Z= 0.394
  Chirality :  0.047   0.213   1810
  Planarity :  0.005   0.050   2074
  Dihedral  :  7.696  55.976   1788
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.95 %
    Favored  : 89.98 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.21), residues: 1477
  helix: -3.72 (0.42), residues: 61
  sheet: -1.55 (0.29), residues: 304
  loop : -2.25 (0.18), residues: 1112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP E  99 
 HIS   0.030   0.001   HIS E  35 
 PHE   0.029   0.002   PHE B  71 
 TYR   0.029   0.002   TYR B  87 
 ARG   0.009   0.001   ARG B  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00249 (    6)
  link_NAG-ASN         : angle       2.37689 (   18)
  link_BETA1-4         : bond        0.00159 (    2)
  link_BETA1-4         : angle       1.23761 (    6)
  link_ALPHA1-3        : bond        0.00326 (    1)
  link_ALPHA1-3        : angle       1.39303 (    3)
  hydrogen bonds       : bond        0.03347 (  187)
  hydrogen bonds       : angle       6.92883 (  438)
  SS BOND              : bond        0.01116 (   34)
  SS BOND              : angle       2.83140 (   68)
  covalent geometry    : bond        0.00348 (11766)
  covalent geometry    : angle       0.77554 (16015)

********************** 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
  189 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 1.213 
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: A   46 LEU cc_start: 0.9719 (mm) cc_final: 0.9133 (mm)
REVERT: A   75 GLN cc_start: 0.9221 (pt0) cc_final: 0.8868 (pm20)
REVERT: A  301 TYR cc_start: 0.8109 (t80) cc_final: 0.7688 (t80)
REVERT: A  403 LEU cc_start: 0.8946 (tp) cc_final: 0.8475 (mt)
REVERT: A  404 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8306 (mt-10)
REVERT: A  405 GLU cc_start: 0.8994 (tp30) cc_final: 0.8478 (tp30)
REVERT: A  611 MET cc_start: 0.8322 (ptm) cc_final: 0.7467 (ppp)
REVERT: B   97 THR cc_start: 0.9146 (p) cc_final: 0.8946 (p)
REVERT: B   98 PHE cc_start: 0.8115 (m-80) cc_final: 0.6944 (m-10)
REVERT: B  139 PHE cc_start: 0.8991 (p90) cc_final: 0.8178 (p90)
REVERT: B  142 ARG cc_start: 0.9121 (tpt90) cc_final: 0.8828 (tpt90)
REVERT: B  145 LYS cc_start: 0.9417 (mmpt) cc_final: 0.9169 (tppt)
REVERT: B  155 GLN cc_start: 0.8061 (tp40) cc_final: 0.7312 (tm-30)
REVERT: B  179 LEU cc_start: 0.9433 (tp) cc_final: 0.8777 (tp)
REVERT: C   99 PHE cc_start: 0.7698 (m-10) cc_final: 0.7492 (m-10)
REVERT: C  100 PHE cc_start: 0.8451 (m-80) cc_final: 0.7685 (m-80)
REVERT: C  145 TYR cc_start: 0.7816 (p90) cc_final: 0.7587 (p90)
REVERT: D  139 PHE cc_start: 0.6892 (p90) cc_final: 0.6219 (p90)
REVERT: D  140 TYR cc_start: 0.8571 (t80) cc_final: 0.7891 (t80)
REVERT: D  173 TYR cc_start: 0.6442 (m-10) cc_final: 0.6211 (m-10)
REVERT: E    1 GLU cc_start: 0.7910 (tt0) cc_final: 0.7639 (tm-30)
REVERT: E   39 GLN cc_start: 0.8936 (tt0) cc_final: 0.8461 (tt0)
REVERT: E  107 MET cc_start: 0.6877 (tpt) cc_final: 0.3411 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.2451
  time to fit residues: 65.5877
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  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 36 optimal weight:    0.1980
   chunk 120 optimal weight:   30.0000
   chunk 74 optimal weight:    8.9990
   chunk 42 optimal weight:    0.4980
   chunk 109 optimal weight:    8.9990
   chunk 113 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
A 484 GLN
A 624 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
** C  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 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 = 0.3640 r_free = 0.3640 target = 0.077183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.054488 restraints weight = 56522.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.056478 restraints weight = 32924.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.057840 restraints weight = 22402.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.125  11809  Z= 0.169
  Angle     :  0.785  18.961  16110  Z= 0.389
  Chirality :  0.046   0.214   1810
  Planarity :  0.005   0.048   2074
  Dihedral  :  7.450  56.774   1788
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 19.36
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.90 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.10 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.21), residues: 1477
  helix: -3.55 (0.46), residues: 61
  sheet: -1.34 (0.29), residues: 294
  loop : -2.26 (0.18), residues: 1122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP E 110 
 HIS   0.007   0.001   HIS E  35 
 PHE   0.031   0.002   PHE E 173 
 TYR   0.027   0.002   TYR B  96 
 ARG   0.005   0.001   ARG B  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    6)
  link_NAG-ASN         : angle       2.43240 (   18)
  link_BETA1-4         : bond        0.00225 (    2)
  link_BETA1-4         : angle       1.19191 (    6)
  link_ALPHA1-3        : bond        0.00422 (    1)
  link_ALPHA1-3        : angle       1.54767 (    3)
  hydrogen bonds       : bond        0.03421 (  187)
  hydrogen bonds       : angle       6.97670 (  438)
  SS BOND              : bond        0.01084 (   34)
  SS BOND              : angle       2.73936 (   68)
  covalent geometry    : bond        0.00383 (11766)
  covalent geometry    : angle       0.76216 (16015)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4319.23 seconds
wall clock time: 75 minutes 56.07 seconds (4556.07 seconds total)