Starting phenix.real_space_refine
on Wed Mar  4 21:45:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a5s_11647/03_2026/7a5s_11647.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a5s_11647/03_2026/7a5s_11647.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a5s_11647/03_2026/7a5s_11647.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a5s_11647/03_2026/7a5s_11647.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a5s_11647/03_2026/7a5s_11647.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a5s_11647/03_2026/7a5s_11647.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.027
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      68      5.16       5
     C   10580      2.51       5
     N    2748      2.21       5
     O    3212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 168 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16608
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1634
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205}
    Chain: "L"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1694
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
    Chain: "A"
      Number of atoms: 4948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 624, 4948
          Classifications: {'peptide': 624}
          Link IDs: {'PTRANS': 31, 'TRANS': 592}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    I, M, B, G
  Time building chain proxies: 5.35, per 1000 atoms: 0.32
  Number of scatterers: 16608
  At special positions: 0
  Unit cell: (183.703, 190.225, 94.569, 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      68     16.00
     O    3212      8.00
     N    2748      7.00
     C   10580      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=26, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 144 " - pdb=" SG  CYS I 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M  23 " - pdb=" SG  CYS M  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 140 " - pdb=" SG  CYS M 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.04

  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
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 343 "
      " NAG G   1 " - " ASN B 343 "
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 808.9 milliseconds
  

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3932

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 40 sheets defined
      5.8% alpha, 34.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'L' and resid 127 through 134
      removed outlier: 3.689A  pdb=" N   LEU L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS L 132 " --> pdb=" O   ASP L 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER L 133 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY L 134 " --> pdb=" O   GLN L 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 127 through 134'
    Processing helix  chain 'L' and resid 189 through 193
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 3.964A  pdb=" N   LEU A 368 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 369'
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.237A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.759A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 127 through 134
      removed outlier: 3.690A  pdb=" N   LEU M 131 " --> pdb=" O   SER M 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS M 132 " --> pdb=" O   ASP M 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER M 133 " --> pdb=" O   GLU M 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY M 134 " --> pdb=" O   GLN M 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 127 through 134'
    Processing helix  chain 'M' and resid 189 through 193
    Processing helix  chain 'B' and resid 294 through 304
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 369
      removed outlier: 3.965A  pdb=" N   LEU B 368 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 369'
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 4.237A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.759A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 160 through 162
      No H-bonds generated for 'chain 'I' and resid 160 through 162'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.342A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS H 144 " --> pdb=" O   SER H 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER H 184 " --> pdb=" O   CYS H 144 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASP H 148 " --> pdb=" O   TYR H 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 111 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31
      removed outlier: 3.772A  pdb=" N   LYS L  36 " --> pdb=" O   TYR L  31 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER L 120 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN L 143 " --> pdb=" O   SER L 120 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 159 through 160
      removed outlier: 3.637A  pdb=" N   TYR L 198 " --> pdb=" O   PHE L 215 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS A  49 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 277 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN A 271 " --> pdb=" O   PHE A  55 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 63 through 67
      removed outlier: 4.369A  pdb=" N   LYS A 187 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.838A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 151 through 163
      removed outlier: 6.522A  pdb=" N   SER A 151 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TYR A 144 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   MET A 153 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY A 142 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   SER A 155 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 11.347A  pdb=" N   PHE A 140 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 9.837A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 11.223A  pdb=" N   ASP A 138 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 311 through 313
      removed outlier: 3.569A  pdb=" N   GLY A 311 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 324 through 328
      removed outlier: 3.761A  pdb=" N   VAL A 539 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR A 588 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR A 553 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP A 586 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLY A 566 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 435 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AC1, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AC2, first strand: chain 'A' and resid 664 through 667
      removed outlier: 6.263A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7
    Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU M  11 " --> pdb=" O   GLU M 111 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP M  41 " --> pdb=" O   LEU M  53 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31
      removed outlier: 3.773A  pdb=" N   LYS M  36 " --> pdb=" O   TYR M  31 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER M 120 " --> pdb=" O   ASN M 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN M 143 " --> pdb=" O   SER M 120 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 159 through 160
      removed outlier: 3.637A  pdb=" N   TYR M 198 " --> pdb=" O   PHE M 215 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS B  49 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 277 " --> pdb=" O   HIS B  49 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN B 271 " --> pdb=" O   PHE B  55 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 63 through 67
      removed outlier: 4.368A  pdb=" N   LYS B 187 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85
      removed outlier: 3.838A  pdb=" N   PHE B 168 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 163
      removed outlier: 6.522A  pdb=" N   SER B 151 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TYR B 144 " --> pdb=" O   SER B 151 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   MET B 153 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY B 142 " --> pdb=" O   MET B 153 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   SER B 155 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 11.347A  pdb=" N   PHE B 140 " --> pdb=" O   SER B 155 " (cutoff:3.500A)
      removed outlier: 9.838A  pdb=" N   PHE B 157 " --> pdb=" O   ASP B 138 " (cutoff:3.500A)
      removed outlier: 11.224A  pdb=" N   ASP B 138 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL B 159 " --> pdb=" O   CYS B 136 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLN B 134 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 313
      removed outlier: 3.569A  pdb=" N   GLY B 311 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 328
      removed outlier: 3.761A  pdb=" N   VAL B 539 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR B 588 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   THR B 553 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP B 586 " --> pdb=" O   THR B 553 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLY B 566 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE B 358 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ALA B 435 " --> pdb=" O   THR B 376 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AD8, first strand: chain 'B' and resid 664 through 667
      removed outlier: 6.264A  pdb=" N   ILE B 670 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL I 108 " --> pdb=" O   GLY I  98 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'I' and resid 124 through 128
      removed outlier: 4.343A  pdb=" N   GLY I 143 " --> pdb=" O   LEU I 128 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS I 144 " --> pdb=" O   SER I 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER I 184 " --> pdb=" O   CYS I 144 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP I 148 " --> pdb=" O   TYR I 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR I 180 " --> pdb=" O   ASP I 148 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'I' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR I 198 " --> pdb=" O   VAL I 215 " (cutoff:3.500A)

    528 hydrogen bonds defined for protein.
    1344 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: 3.97

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4594
        1.33 -     1.46: 3725
        1.46 -     1.58: 8629
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 17028
  Sorted by residual:
  bond pdb=" N   VAL B 595 "
       pdb=" CA  VAL B 595 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.040 1.14e-02 7.69e+03 1.25e+01
  bond pdb=" N   VAL A 595 "
       pdb=" CA  VAL A 595 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.040 1.14e-02 7.69e+03 1.24e+01
  bond pdb=" N   VAL A 534 "
       pdb=" CA  VAL A 534 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.039 1.15e-02 7.56e+03 1.13e+01
  bond pdb=" N   VAL B 534 "
       pdb=" CA  VAL B 534 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.15e-02 7.56e+03 1.11e+01
  bond pdb=" N   VAL B 551 "
       pdb=" CA  VAL B 551 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.22e-02 6.72e+03 1.07e+01
  ... (remaining 17023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 21616
        1.74 -     3.49: 1281
        3.49 -     5.23: 231
        5.23 -     6.98: 30
        6.98 -     8.72: 14
  Bond angle restraints: 23172
  Sorted by residual:
  angle pdb=" N   PRO A 217 "
        pdb=" CA  PRO A 217 "
        pdb=" C   PRO A 217 "
      ideal   model   delta    sigma   weight residual
     111.22  116.86   -5.64 1.40e+00 5.10e-01 1.62e+01
  angle pdb=" N   PRO B 217 "
        pdb=" CA  PRO B 217 "
        pdb=" C   PRO B 217 "
      ideal   model   delta    sigma   weight residual
     111.22  116.86   -5.64 1.40e+00 5.10e-01 1.62e+01
  angle pdb=" N   ASN B 536 "
        pdb=" CA  ASN B 536 "
        pdb=" C   ASN B 536 "
      ideal   model   delta    sigma   weight residual
     111.74  117.02   -5.28 1.35e+00 5.49e-01 1.53e+01
  angle pdb=" N   ASN A 536 "
        pdb=" CA  ASN A 536 "
        pdb=" C   ASN A 536 "
      ideal   model   delta    sigma   weight residual
     111.74  117.02   -5.28 1.35e+00 5.49e-01 1.53e+01
  angle pdb=" CA  GLY B 268 "
        pdb=" C   GLY B 268 "
        pdb=" O   GLY B 268 "
      ideal   model   delta    sigma   weight residual
     121.76  117.78    3.98 1.03e+00 9.43e-01 1.49e+01
  ... (remaining 23167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.03: 9283
       18.03 -    36.07: 661
       36.07 -    54.10: 162
       54.10 -    72.14: 30
       72.14 -    90.17: 10
  Dihedral angle restraints: 10146
    sinusoidal: 3986
      harmonic: 6160
  Sorted by residual:
  dihedral pdb=" CB  CYS B 538 "
           pdb=" SG  CYS B 538 "
           pdb=" SG  CYS B 590 "
           pdb=" CB  CYS B 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.17   90.17     1      1.00e+01 1.00e-02 9.63e+01
  dihedral pdb=" CB  CYS A 538 "
           pdb=" SG  CYS A 538 "
           pdb=" SG  CYS A 590 "
           pdb=" CB  CYS A 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.14   90.14     1      1.00e+01 1.00e-02 9.62e+01
  dihedral pdb=" C   ASP A 578 "
           pdb=" N   ASP A 578 "
           pdb=" CA  ASP A 578 "
           pdb=" CB  ASP A 578 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.80   11.20     0      2.50e+00 1.60e-01 2.01e+01
  ... (remaining 10143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 2015
       0.069 -    0.137: 474
       0.137 -    0.206: 61
       0.206 -    0.275: 20
       0.275 -    0.343: 6
  Chirality restraints: 2576
  Sorted by residual:
  chirality pdb=" CA  ASN B 536 "
            pdb=" N   ASN B 536 "
            pdb=" C   ASN B 536 "
            pdb=" CB  ASN B 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  chirality pdb=" CA  ASN A 536 "
            pdb=" N   ASN A 536 "
            pdb=" C   ASN A 536 "
            pdb=" CB  ASN A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CA  ASP A 578 "
            pdb=" N   ASP A 578 "
            pdb=" C   ASP A 578 "
            pdb=" CB  ASP A 578 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.80e+00
  ... (remaining 2573 not shown)

  Planarity restraints: 2976
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 548 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   GLY B 548 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLY B 548 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   THR B 549 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 548 "    0.018 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   GLY A 548 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   GLY A 548 "    0.023 2.00e-02 2.50e+03
        pdb=" N   THR A 549 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 571 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.81e+00
        pdb=" C   ASP A 571 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 571 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   THR A 572 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2973 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 6
        1.93 -     2.67: 277
        2.67 -     3.42: 20398
        3.42 -     4.16: 36938
        4.16 -     4.90: 65913
  Nonbonded interactions: 123532
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 273 "
            pdb=" OD2 ASP B 290 "
     model   vdw
     1.188 3.120
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OD2 ASP A 290 "
     model   vdw
     1.189 3.120
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" CG  ASP A 290 "
     model   vdw
     1.373 3.350
  nonbonded pdb=" NH2 ARG B 273 "
            pdb=" CG  ASP B 290 "
     model   vdw
     1.373 3.350
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OD1 ASP A 290 "
     model   vdw
     1.766 3.120
  ... (remaining 123527 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}

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:             5.890
  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:             0.020
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     18.810
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  17058  Z= 0.370
  Angle     :  0.933   8.725  23236  Z= 0.569
  Chirality :  0.062   0.343   2576
  Planarity :  0.005   0.051   2974
  Dihedral  : 13.403  89.368   6136
  Min Nonbonded Distance : 1.188

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.94 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.66 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.17), residues: 2104
  helix: -2.03 (0.51), residues: 88
  sheet:  0.09 (0.20), residues: 698
  loop : -2.23 (0.15), residues: 1318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 328 
 TYR   0.019   0.002   TYR B 351 
 PHE   0.017   0.002   PHE H  29 
 TRP   0.027   0.002   TRP H  83 
 HIS   0.010   0.001   HIS L 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 (17028)
  covalent geometry    : angle       0.93115 (23172)
  SS BOND              : bond        0.00542 (   26)
  SS BOND              : angle       1.21436 (   52)
  hydrogen bonds       : bond        0.14456 (  520)
  hydrogen bonds       : angle       8.38848 ( 1344)
  link_BETA1-4         : bond        0.00292 (    2)
  link_BETA1-4         : angle       1.30212 (    6)
  link_NAG-ASN         : bond        0.00032 (    2)
  link_NAG-ASN         : angle       2.40095 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 200
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: -0.2022 (ttm) cc_final: -0.4005 (mtp)
REVERT: B  177 MET cc_start: -0.1960 (ttm) cc_final: -0.3965 (mtp)
  outliers start: 12
  outliers final: 2
  residues processed: 208
  average time/residue: 0.1510
  time to fit residues: 44.5061
Evaluate side-chains
  92 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:   20.0000
   chunk 200 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
H   1 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H  77 ASN
L   6 GLN
L  44 GLN
L 106 GLN
** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 164 ASN
A  66 HIS
A 115 GLN
A 146 HIS
A 164 ASN
A 218 GLN
A 239 GLN
A 245 HIS
A 271 GLN
A 321 GLN
A 370 ASN
A 493 GLN
A 540 ASN
A 542 ASN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN
A 641 ASN
A 658 ASN
A 675 GLN
M   6 GLN
M  44 GLN
M  95 GLN
M 106 GLN
** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 164 ASN
B  66 HIS
B 115 GLN
B 146 HIS
B 164 ASN
B 218 GLN
B 239 GLN
B 245 HIS
B 271 GLN
B 321 GLN
B 370 ASN
B 493 GLN
B 540 ASN
B 542 ASN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 613 GLN
B 641 ASN
B 658 ASN
B 675 GLN
I  39 GLN
I  77 ASN
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 48

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.103983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.075649 restraints weight = 55392.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072171 restraints weight = 53773.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.073269 restraints weight = 50810.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.073458 restraints weight = 35183.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.074131 restraints weight = 33224.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  17058  Z= 0.247
  Angle     :  0.754   8.736  23236  Z= 0.395
  Chirality :  0.049   0.148   2576
  Planarity :  0.005   0.041   2974
  Dihedral  :  5.946  49.270   2380
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.99 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.17), residues: 2104
  helix: -2.32 (0.55), residues: 86
  sheet:  0.32 (0.19), residues: 754
  loop : -2.13 (0.15), residues: 1264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 646 
 TYR   0.029   0.002   TYR B 612 
 PHE   0.025   0.002   PHE A  55 
 TRP   0.024   0.002   TRP I  83 
 HIS   0.005   0.001   HIS I 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 (17028)
  covalent geometry    : angle       0.75034 (23172)
  SS BOND              : bond        0.00485 (   26)
  SS BOND              : angle       1.59359 (   52)
  hydrogen bonds       : bond        0.04730 (  520)
  hydrogen bonds       : angle       7.03995 ( 1344)
  link_BETA1-4         : bond        0.00193 (    2)
  link_BETA1-4         : angle       1.24948 (    6)
  link_NAG-ASN         : bond        0.00079 (    2)
  link_NAG-ASN         : angle       1.83371 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 102
  time to evaluate  : 0.660 
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: H  149 TYR cc_start: 0.8666 (p90) cc_final: 0.8418 (p90)
REVERT: L  149 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6836 (tm-30)
REVERT: A  106 PHE cc_start: 0.8453 (m-80) cc_final: 0.8248 (m-10)
REVERT: A  153 MET cc_start: 0.7265 (ppp) cc_final: 0.7044 (ppp)
REVERT: A  177 MET cc_start: -0.2999 (ttm) cc_final: -0.3631 (mtp)
REVERT: B  153 MET cc_start: 0.7220 (ppp) cc_final: 0.6979 (ppp)
REVERT: B  177 MET cc_start: -0.2826 (ttm) cc_final: -0.3198 (mmm)
REVERT: B  471 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6390 (tp30)
  outliers start: 36
  outliers final: 21
  residues processed: 129
  average time/residue: 0.1194
  time to fit residues: 24.8241
Evaluate side-chains
  106 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain H residue  212 ASP
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue  195 HIS
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  199 ILE
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 192 optimal weight:    0.5980
   chunk 162 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 165 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 36 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 208 optimal weight:    0.9980
   chunk 173 optimal weight:    1.9990
   chunk 174 optimal weight:    0.2980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  95 GLN
** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** 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 = 0.4059 r_free = 0.4059 target = 0.105203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.076578 restraints weight = 56038.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.072821 restraints weight = 44885.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.073917 restraints weight = 49139.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.074015 restraints weight = 34891.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.074560 restraints weight = 30887.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17058  Z= 0.117
  Angle     :  0.592   7.378  23236  Z= 0.307
  Chirality :  0.045   0.145   2576
  Planarity :  0.004   0.045   2974
  Dihedral  :  5.506  49.608   2380
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.77 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.17), residues: 2104
  helix: -2.37 (0.50), residues: 100
  sheet:  0.57 (0.19), residues: 750
  loop : -1.80 (0.16), residues: 1254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG I  59 
 TYR   0.016   0.001   TYR I 180 
 PHE   0.024   0.001   PHE B 135 
 TRP   0.017   0.001   TRP I  83 
 HIS   0.004   0.001   HIS M 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (17028)
  covalent geometry    : angle       0.59124 (23172)
  SS BOND              : bond        0.00344 (   26)
  SS BOND              : angle       0.85428 (   52)
  hydrogen bonds       : bond        0.03723 (  520)
  hydrogen bonds       : angle       6.39643 ( 1344)
  link_BETA1-4         : bond        0.00382 (    2)
  link_BETA1-4         : angle       0.82958 (    6)
  link_NAG-ASN         : bond        0.00262 (    2)
  link_NAG-ASN         : angle       1.24108 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.612 
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: H    2 MET cc_start: 0.7356 (ppp) cc_final: 0.7029 (ttp)
REVERT: H  149 TYR cc_start: 0.8491 (p90) cc_final: 0.8283 (p90)
REVERT: L  149 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6839 (tm-30)
REVERT: A  153 MET cc_start: 0.7900 (ppp) cc_final: 0.6593 (pmm)
REVERT: A  177 MET cc_start: -0.3330 (ttm) cc_final: -0.4266 (mpp)
REVERT: B  128 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8968 (tp)
REVERT: B  153 MET cc_start: 0.7873 (ppp) cc_final: 0.6456 (pmm)
REVERT: B  471 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6281 (tp30)
REVERT: I    2 MET cc_start: 0.7790 (ppp) cc_final: 0.6932 (ppp)
  outliers start: 29
  outliers final: 20
  residues processed: 118
  average time/residue: 0.1119
  time to fit residues: 21.3262
Evaluate side-chains
  104 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue  195 HIS
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  173 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 197 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 125 optimal weight:    8.9990
   chunk 147 optimal weight:   20.0000
   chunk 166 optimal weight:    5.9990
   chunk 154 optimal weight:    0.6980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 GLN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 130 GLN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** 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 = 0.3960 r_free = 0.3960 target = 0.100038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.071332 restraints weight = 56145.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.069529 restraints weight = 47836.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.069736 restraints weight = 67684.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.070445 restraints weight = 39133.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.071055 restraints weight = 32508.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  17058  Z= 0.241
  Angle     :  0.664   8.914  23236  Z= 0.347
  Chirality :  0.047   0.148   2576
  Planarity :  0.005   0.044   2974
  Dihedral  :  5.777  58.471   2380
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.25 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.17), residues: 2104
  helix: -2.39 (0.55), residues: 88
  sheet:  0.53 (0.19), residues: 718
  loop : -1.88 (0.16), residues: 1298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.020   0.002   TYR I 180 
 PHE   0.017   0.002   PHE M 215 
 TRP   0.017   0.002   TRP H  83 
 HIS   0.011   0.001   HIS M 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (17028)
  covalent geometry    : angle       0.66191 (23172)
  SS BOND              : bond        0.00427 (   26)
  SS BOND              : angle       1.10991 (   52)
  hydrogen bonds       : bond        0.04393 (  520)
  hydrogen bonds       : angle       6.42857 ( 1344)
  link_BETA1-4         : bond        0.00044 (    2)
  link_BETA1-4         : angle       1.12580 (    6)
  link_NAG-ASN         : bond        0.00021 (    2)
  link_NAG-ASN         : angle       1.53478 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 87
  time to evaluate  : 0.579 
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: H    2 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7115 (ppp)
REVERT: L   31 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7377 (t80)
REVERT: A  153 MET cc_start: 0.7616 (ppp) cc_final: 0.6257 (pmm)
REVERT: A  353 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.7999 (p-90)
REVERT: M   31 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7007 (t80)
REVERT: B  128 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8860 (tp)
REVERT: B  153 MET cc_start: 0.7607 (ppp) cc_final: 0.6169 (pmm)
REVERT: B  353 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.7980 (p-90)
REVERT: B  471 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6260 (tp30)
REVERT: I  185 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8878 (m)
  outliers start: 53
  outliers final: 32
  residues processed: 123
  average time/residue: 0.1034
  time to fit residues: 20.8248
Evaluate side-chains
  115 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 75
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue  131 LEU
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  185 VAL
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 89 optimal weight:    0.0970
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 125 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   chunk 158 optimal weight:    0.4980
   chunk 55 optimal weight:    0.0030
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    4.9990
   chunk 119 optimal weight:    0.5980
   overall best weight:    0.3188

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 GLN
** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 ASN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 216 ASN
B 422 ASN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** 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 = 0.3981 r_free = 0.3981 target = 0.101506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.067232 restraints weight = 54219.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.067115 restraints weight = 32648.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.067108 restraints weight = 25007.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.067495 restraints weight = 25391.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.067647 restraints weight = 21640.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  17058  Z= 0.101
  Angle     :  0.561   7.708  23236  Z= 0.291
  Chirality :  0.044   0.166   2576
  Planarity :  0.004   0.038   2974
  Dihedral  :  5.156  57.927   2378
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.30 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.18), residues: 2104
  helix: -2.44 (0.50), residues: 100
  sheet:  0.64 (0.19), residues: 754
  loop : -1.78 (0.16), residues: 1250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  18 
 TYR   0.019   0.001   TYR B 204 
 PHE   0.028   0.001   PHE A 168 
 TRP   0.016   0.001   TRP H  83 
 HIS   0.003   0.001   HIS M 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (17028)
  covalent geometry    : angle       0.56014 (23172)
  SS BOND              : bond        0.00309 (   26)
  SS BOND              : angle       0.84537 (   52)
  hydrogen bonds       : bond        0.03320 (  520)
  hydrogen bonds       : angle       6.01438 ( 1344)
  link_BETA1-4         : bond        0.00311 (    2)
  link_BETA1-4         : angle       0.67994 (    6)
  link_NAG-ASN         : bond        0.00283 (    2)
  link_NAG-ASN         : angle       1.06593 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 83
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8018 (ppp) cc_final: 0.6800 (pmm)
REVERT: M   31 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7035 (t80)
REVERT: B  128 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9136 (tp)
REVERT: B  153 MET cc_start: 0.8007 (ppp) cc_final: 0.6724 (pmm)
REVERT: B  471 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6215 (tp30)
  outliers start: 31
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1044
  time to fit residues: 18.8379
Evaluate side-chains
  93 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  650 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 206 optimal weight:    2.9990
   chunk 167 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 129 optimal weight:    3.9990
   chunk 173 optimal weight:    2.9990
   chunk 185 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
H   1 GLN
L 130 GLN
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 GLN
A 422 ASN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
B 422 ASN
** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.098963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.065297 restraints weight = 54146.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.064214 restraints weight = 34945.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.064986 restraints weight = 26943.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.065289 restraints weight = 23410.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.065311 restraints weight = 20939.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  17058  Z= 0.193
  Angle     :  0.610   9.404  23236  Z= 0.318
  Chirality :  0.045   0.145   2576
  Planarity :  0.004   0.040   2974
  Dihedral  :  5.041  37.951   2378
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.82 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.17), residues: 2104
  helix: -2.38 (0.52), residues: 88
  sheet:  0.48 (0.19), residues: 738
  loop : -1.75 (0.16), residues: 1278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 403 
 TYR   0.015   0.002   TYR H  27 
 PHE   0.015   0.002   PHE B 106 
 TRP   0.014   0.001   TRP H  83 
 HIS   0.003   0.001   HIS B  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (17028)
  covalent geometry    : angle       0.60715 (23172)
  SS BOND              : bond        0.00380 (   26)
  SS BOND              : angle       1.29920 (   52)
  hydrogen bonds       : bond        0.04003 (  520)
  hydrogen bonds       : angle       6.06617 ( 1344)
  link_BETA1-4         : bond        0.00086 (    2)
  link_BETA1-4         : angle       0.95471 (    6)
  link_NAG-ASN         : bond        0.00088 (    2)
  link_NAG-ASN         : angle       1.37636 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 76
  time to evaluate  : 0.624 
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: L   31 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7075 (t80)
REVERT: A  153 MET cc_start: 0.8144 (ppp) cc_final: 0.7190 (pmm)
REVERT: A  168 PHE cc_start: 0.7674 (t80) cc_final: 0.7341 (t80)
REVERT: A  229 LEU cc_start: 0.9506 (mt) cc_final: 0.9244 (mp)
REVERT: A  353 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8013 (p-90)
REVERT: M   31 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.6992 (t80)
REVERT: B  128 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9188 (tp)
REVERT: B  153 MET cc_start: 0.8068 (ppp) cc_final: 0.7009 (pmm)
REVERT: B  353 TRP cc_start: 0.9003 (OUTLIER) cc_final: 0.8008 (p-90)
  outliers start: 48
  outliers final: 32
  residues processed: 113
  average time/residue: 0.1081
  time to fit residues: 19.7927
Evaluate side-chains
  108 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 71
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  131 LEU
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain M residue  217 ARG
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  145 LEU
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  183 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 169 optimal weight:    1.9990
   chunk 176 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 114 optimal weight:    0.7980
   chunk 126 optimal weight:    2.9990
   chunk 137 optimal weight:   30.0000
   chunk 96 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 ASN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN
I 196 GLN
** I 203 ASN ** 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 = 0.3954 r_free = 0.3954 target = 0.099993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.066655 restraints weight = 54182.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.066095 restraints weight = 36331.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.065883 restraints weight = 27410.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.066248 restraints weight = 26615.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.066403 restraints weight = 23139.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  17058  Z= 0.121
  Angle     :  0.564  10.233  23236  Z= 0.293
  Chirality :  0.045   0.185   2576
  Planarity :  0.004   0.037   2974
  Dihedral  :  4.798  36.064   2378
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.76 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.17), residues: 2104
  helix: -2.52 (0.47), residues: 100
  sheet:  0.52 (0.19), residues: 750
  loop : -1.65 (0.16), residues: 1254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M  60 
 TYR   0.013   0.001   TYR L  55 
 PHE   0.013   0.001   PHE A 135 
 TRP   0.015   0.001   TRP H  83 
 HIS   0.002   0.001   HIS L 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (17028)
  covalent geometry    : angle       0.56154 (23172)
  SS BOND              : bond        0.00492 (   26)
  SS BOND              : angle       1.19503 (   52)
  hydrogen bonds       : bond        0.03378 (  520)
  hydrogen bonds       : angle       5.85312 ( 1344)
  link_BETA1-4         : bond        0.00362 (    2)
  link_BETA1-4         : angle       0.92146 (    6)
  link_NAG-ASN         : bond        0.00209 (    2)
  link_NAG-ASN         : angle       1.19177 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 74
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   31 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7056 (t80)
REVERT: A  153 MET cc_start: 0.8264 (ppp) cc_final: 0.7220 (pmm)
REVERT: A  168 PHE cc_start: 0.7756 (t80) cc_final: 0.7401 (t80)
REVERT: A  229 LEU cc_start: 0.9555 (mt) cc_final: 0.9298 (mp)
REVERT: A  353 TRP cc_start: 0.8945 (OUTLIER) cc_final: 0.7866 (p-90)
REVERT: M   31 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7008 (t80)
REVERT: M   66 ASP cc_start: 0.7793 (m-30) cc_final: 0.7521 (t0)
REVERT: B  128 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9152 (tp)
REVERT: B  153 MET cc_start: 0.8305 (ppp) cc_final: 0.7365 (pmm)
REVERT: B  353 TRP cc_start: 0.8940 (OUTLIER) cc_final: 0.7857 (p-90)
  outliers start: 45
  outliers final: 28
  residues processed: 115
  average time/residue: 0.1027
  time to fit residues: 19.4372
Evaluate side-chains
  103 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 70
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  183 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 199 optimal weight:    3.9990
   chunk 128 optimal weight:    0.0970
   chunk 172 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0670
   chunk 153 optimal weight:    5.9990
   chunk 67 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 60 optimal weight:    0.6980
   chunk 170 optimal weight:    4.9990
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.100952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.067316 restraints weight = 54255.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.066690 restraints weight = 34363.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.067008 restraints weight = 26087.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.067397 restraints weight = 24241.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.067495 restraints weight = 21155.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  17058  Z= 0.097
  Angle     :  0.531   7.899  23236  Z= 0.276
  Chirality :  0.044   0.154   2576
  Planarity :  0.004   0.036   2974
  Dihedral  :  4.473  33.583   2378
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.57 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.18), residues: 2104
  helix: -2.39 (0.46), residues: 100
  sheet:  0.69 (0.19), residues: 766
  loop : -1.52 (0.17), residues: 1238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 114 
 TYR   0.017   0.001   TYR H  27 
 PHE   0.016   0.001   PHE A 135 
 TRP   0.012   0.001   TRP H  83 
 HIS   0.004   0.000   HIS M 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (17028)
  covalent geometry    : angle       0.52988 (23172)
  SS BOND              : bond        0.00372 (   26)
  SS BOND              : angle       0.89116 (   52)
  hydrogen bonds       : bond        0.03013 (  520)
  hydrogen bonds       : angle       5.56512 ( 1344)
  link_BETA1-4         : bond        0.00314 (    2)
  link_BETA1-4         : angle       0.88656 (    6)
  link_NAG-ASN         : bond        0.00232 (    2)
  link_NAG-ASN         : angle       1.13883 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   31 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7103 (t80)
REVERT: A  153 MET cc_start: 0.8289 (ppp) cc_final: 0.7255 (pmm)
REVERT: A  168 PHE cc_start: 0.7832 (t80) cc_final: 0.7620 (t80)
REVERT: A  177 MET cc_start: -0.1288 (mmm) cc_final: -0.2071 (mpp)
REVERT: A  229 LEU cc_start: 0.9569 (mt) cc_final: 0.9355 (mp)
REVERT: M   66 ASP cc_start: 0.7761 (m-30) cc_final: 0.7485 (t0)
REVERT: B  128 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9123 (tp)
REVERT: B  153 MET cc_start: 0.8257 (ppp) cc_final: 0.7146 (pmm)
REVERT: B  177 MET cc_start: -0.1502 (mmm) cc_final: -0.2163 (mpp)
  outliers start: 31
  outliers final: 25
  residues processed: 107
  average time/residue: 0.1077
  time to fit residues: 19.1721
Evaluate side-chains
  96 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  183 SER
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 106 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0370
   chunk 104 optimal weight:    3.9990
   chunk 170 optimal weight:    5.9990
   chunk 39 optimal weight:    0.2980
   chunk 121 optimal weight:    4.9990
   chunk 138 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** L 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.101625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.073146 restraints weight = 56082.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.071324 restraints weight = 46035.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.071619 restraints weight = 61496.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.072516 restraints weight = 35593.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.072819 restraints weight = 29061.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.4474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  17058  Z= 0.102
  Angle     :  0.535   8.039  23236  Z= 0.276
  Chirality :  0.044   0.153   2576
  Planarity :  0.004   0.036   2974
  Dihedral  :  4.384  32.726   2378
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.68 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.18), residues: 2104
  helix: -2.42 (0.43), residues: 112
  sheet:  0.72 (0.19), residues: 770
  loop : -1.50 (0.17), residues: 1222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.013   0.001   TYR L  55 
 PHE   0.016   0.001   PHE A 135 
 TRP   0.012   0.001   TRP M 154 
 HIS   0.015   0.001   HIS L 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (17028)
  covalent geometry    : angle       0.53312 (23172)
  SS BOND              : bond        0.00352 (   26)
  SS BOND              : angle       0.89301 (   52)
  hydrogen bonds       : bond        0.03067 (  520)
  hydrogen bonds       : angle       5.45892 ( 1344)
  link_BETA1-4         : bond        0.00305 (    2)
  link_BETA1-4         : angle       0.94365 (    6)
  link_NAG-ASN         : bond        0.00187 (    2)
  link_NAG-ASN         : angle       1.19961 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 73
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   31 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7052 (t80)
REVERT: A  153 MET cc_start: 0.7868 (ppp) cc_final: 0.6795 (pmm)
REVERT: A  168 PHE cc_start: 0.7458 (t80) cc_final: 0.7252 (t80)
REVERT: A  177 MET cc_start: -0.1789 (mmm) cc_final: -0.2513 (mpp)
REVERT: A  192 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7875 (m-80)
REVERT: M   31 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7009 (t80)
REVERT: M   66 ASP cc_start: 0.7640 (m-30) cc_final: 0.7395 (t0)
REVERT: B  128 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8764 (tp)
REVERT: B  153 MET cc_start: 0.7835 (ppp) cc_final: 0.6717 (pmm)
REVERT: B  177 MET cc_start: -0.1664 (mmm) cc_final: -0.2341 (mpp)
  outliers start: 36
  outliers final: 27
  residues processed: 106
  average time/residue: 0.1115
  time to fit residues: 19.0050
Evaluate side-chains
  102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 71
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  183 SER
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 201 optimal weight:    3.9990
   chunk 140 optimal weight:   20.0000
   chunk 177 optimal weight:    8.9990
   chunk 195 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0170
   chunk 96 optimal weight:   10.0000
   chunk 132 optimal weight:   10.0000
   chunk 188 optimal weight:    3.9990
   chunk 91 optimal weight:    0.1980
   chunk 113 optimal weight:    2.9990
   overall best weight:    2.2424

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

Flipped N/Q/H residues before XYZ refinement:
** L 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 ASN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.098384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.069991 restraints weight = 55780.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.068303 restraints weight = 47682.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.068691 restraints weight = 62546.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.069164 restraints weight = 38259.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.069639 restraints weight = 32336.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069  17058  Z= 0.256
  Angle     :  0.646   6.697  23236  Z= 0.339
  Chirality :  0.046   0.147   2576
  Planarity :  0.004   0.037   2974
  Dihedral  :  4.891  36.250   2378
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.95 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.17), residues: 2104
  helix: -2.55 (0.44), residues: 100
  sheet:  0.51 (0.18), residues: 748
  loop : -1.72 (0.16), residues: 1256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  38 
 TYR   0.015   0.002   TYR B 380 
 PHE   0.015   0.002   PHE I 170 
 TRP   0.015   0.002   TRP H  83 
 HIS   0.007   0.001   HIS L 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 (17028)
  covalent geometry    : angle       0.64367 (23172)
  SS BOND              : bond        0.00495 (   26)
  SS BOND              : angle       1.27942 (   52)
  hydrogen bonds       : bond        0.04208 (  520)
  hydrogen bonds       : angle       5.88462 ( 1344)
  link_BETA1-4         : bond        0.00107 (    2)
  link_BETA1-4         : angle       1.26447 (    6)
  link_NAG-ASN         : bond        0.00049 (    2)
  link_NAG-ASN         : angle       1.44960 (    6)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 0.493 
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: L   31 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.6942 (t80)
REVERT: A  153 MET cc_start: 0.7846 (ppp) cc_final: 0.6716 (pmm)
REVERT: A  168 PHE cc_start: 0.7543 (t80) cc_final: 0.7262 (t80)
REVERT: A  177 MET cc_start: -0.1731 (mmm) cc_final: -0.2454 (mpp)
REVERT: A  192 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7787 (m-80)
REVERT: A  353 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.8088 (p-90)
REVERT: M   31 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.6937 (t80)
REVERT: B  128 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8833 (tp)
REVERT: B  153 MET cc_start: 0.7831 (ppp) cc_final: 0.6863 (pmm)
REVERT: B  177 MET cc_start: -0.1768 (mmm) cc_final: -0.2427 (mpp)
REVERT: B  353 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.8090 (p-90)
  outliers start: 35
  outliers final: 25
  residues processed: 98
  average time/residue: 0.1130
  time to fit residues: 17.6603
Evaluate side-chains
  95 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 64
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  183 SER
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 203 optimal weight:    0.6980
   chunk 152 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9990
   chunk 182 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 163 optimal weight:    0.5980
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** L 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 ASN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN
** B 564 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 = 0.3967 r_free = 0.3967 target = 0.100166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.071574 restraints weight = 55691.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.069047 restraints weight = 47764.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.069559 restraints weight = 55922.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.069698 restraints weight = 38378.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.070472 restraints weight = 31699.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.4732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17058  Z= 0.117
  Angle     :  0.550   7.488  23236  Z= 0.286
  Chirality :  0.044   0.151   2576
  Planarity :  0.004   0.034   2974
  Dihedral  :  4.584  34.873   2378
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 16.33 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.17), residues: 2104
  helix: -2.74 (0.40), residues: 112
  sheet:  0.61 (0.19), residues: 752
  loop : -1.62 (0.16), residues: 1240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M  60 
 TYR   0.012   0.001   TYR L  55 
 PHE   0.016   0.001   PHE B 135 
 TRP   0.026   0.001   TRP A 258 
 HIS   0.008   0.001   HIS L 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (17028)
  covalent geometry    : angle       0.54851 (23172)
  SS BOND              : bond        0.00383 (   26)
  SS BOND              : angle       0.88184 (   52)
  hydrogen bonds       : bond        0.03302 (  520)
  hydrogen bonds       : angle       5.57112 ( 1344)
  link_BETA1-4         : bond        0.00248 (    2)
  link_BETA1-4         : angle       0.95708 (    6)
  link_NAG-ASN         : bond        0.00172 (    2)
  link_NAG-ASN         : angle       1.22713 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2298.85 seconds
wall clock time: 40 minutes 43.33 seconds (2443.33 seconds total)