Starting phenix.real_space_refine
on Wed Mar  4 22:05:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7stk_25431/03_2026/7stk_25431_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7stk_25431/03_2026/7stk_25431.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7stk_25431/03_2026/7stk_25431_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7stk_25431/03_2026/7stk_25431_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7stk_25431/03_2026/7stk_25431.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7stk_25431/03_2026/7stk_25431.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3406 atoms to isotropic.
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     116      5.16       5
     C    8828      2.51       5
     N    2389      2.21       5
     O    2578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13911
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 815, 6579
          Classifications: {'peptide': 815}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 770}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 6621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 820, 6621
          Classifications: {'peptide': 820}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 773}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 376
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 1, 'TRANS': 46}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 335
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
          Chain breaks: 1
  Time building chain proxies: 2.86, per 1000 atoms: 0.21
  Number of scatterers: 13911
  At special positions: 0
  Unit cell: (133.92, 128.52, 177.12, 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     116     16.00
     O    2578      8.00
     N    2389      7.00
     C    8828      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=40, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 647 " - pdb=" SG  CYS A 860 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 682 " - pdb=" SG  CYS B 685 " distance=2.34
    Simple disulfide: pdb=" SG  CYS A 685 " - pdb=" SG  CYS B 682 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 786 " - pdb=" SG  CYS A 795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   8 " - pdb=" SG  CYS B  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 192 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 196 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 228 " - pdb=" SG  CYS B 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 259 " - pdb=" SG  CYS B 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 266 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 312 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 435 " - pdb=" SG  CYS B 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 647 " - pdb=" SG  CYS B 860 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 786 " - pdb=" SG  CYS B 795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS C  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  19 " - pdb=" SG  CYS C  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  61 " - pdb=" SG  CYS C  66 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS D  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D  66 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 527.6 milliseconds
  

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3256

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 32 sheets defined
      15.9% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 24
      removed outlier: 3.734A  pdb=" N   HIS A  21 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 47
      removed outlier: 3.905A  pdb=" N   ARG A  47 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 76
      removed outlier: 4.531A  pdb=" N   LEU A  75 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 137
      removed outlier: 3.555A  pdb=" N   ILE A 136 " --> pdb=" O   ASP A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 223
      No H-bonds generated for 'chain 'A' and resid 221 through 223'
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.709A  pdb=" N   CYS A 259 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 4.491A  pdb=" N   GLU A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 358
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.915A  pdb=" N   ILE A 439 " --> pdb=" O   CYS A 435 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLU A 443 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLU A 444 " --> pdb=" O   HIS A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 500
      removed outlier: 3.759A  pdb=" N   LEU A 500 " --> pdb=" O   PHE A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 3.746A  pdb=" N   GLU A 643 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 714
    Processing helix  chain 'A' and resid 863 through 870
    Processing helix  chain 'B' and resid 17 through 24
      removed outlier: 3.982A  pdb=" N   HIS B  21 " --> pdb=" O   THR B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 71 through 75
      removed outlier: 4.153A  pdb=" N   ASP B  74 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 223
      No H-bonds generated for 'chain 'B' and resid 221 through 223'
    Processing helix  chain 'B' and resid 255 through 268
      removed outlier: 3.609A  pdb=" N   CYS B 259 " --> pdb=" O   ASN B 255 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS B 266 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN B 268 " --> pdb=" O   PHE B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 316
      No H-bonds generated for 'chain 'B' and resid 314 through 316'
    Processing helix  chain 'B' and resid 323 through 328
    Processing helix  chain 'B' and resid 329 through 331
      No H-bonds generated for 'chain 'B' and resid 329 through 331'
    Processing helix  chain 'B' and resid 350 through 358
    Processing helix  chain 'B' and resid 378 through 382
      removed outlier: 4.515A  pdb=" N   PHE B 381 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 447
      removed outlier: 3.918A  pdb=" N   ILE B 439 " --> pdb=" O   CYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 643
    Processing helix  chain 'B' and resid 689 through 695
    Processing helix  chain 'B' and resid 704 through 715
    Processing helix  chain 'B' and resid 863 through 869
    Processing helix  chain 'C' and resid 8 through 19
      removed outlier: 3.801A  pdb=" N   VAL C  12 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 62
    Processing helix  chain 'C' and resid 67 through 72
      removed outlier: 3.593A  pdb=" N   LEU C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   GLU C  72 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 67 through 72'
    Processing helix  chain 'C' and resid 73 through 75
      No H-bonds generated for 'chain 'C' and resid 73 through 75'
    Processing helix  chain 'D' and resid 8 through 18
    Processing helix  chain 'D' and resid 57 through 62
    Processing helix  chain 'D' and resid 67 through 74
      removed outlier: 3.590A  pdb=" N   LEU D  71 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR D  74 " --> pdb=" O   GLN D  70 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13
      removed outlier: 6.657A  pdb=" N   GLN A  34 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU A  63 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU A  36 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ARG A  65 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   MET A  98 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU A  93 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   GLU A 120 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ILE A  95 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ASN A 122 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   GLU A  97 " --> pdb=" O   ASN A 122 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   TYR A 144 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A 119 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.869A  pdb=" N   ILE A  82 " --> pdb=" O   ASN A 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173
    Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216
      removed outlier: 5.994A  pdb=" N   LEU A 213 " --> pdb=" O   CYS A 228 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   CYS A 228 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ASN A 215 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233
    Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248
    Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 293
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314
      removed outlier: 4.154A  pdb=" N   ILE A 314 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER A 339 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 318 through 321
      removed outlier: 6.382A  pdb=" N   LYS A 319 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 9.055A  pdb=" N   LYS A 369 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU A 340 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   ARG A 371 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ILE A 342 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   PHE A 427 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   TYR A 401 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   HIS A 429 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LEU A 403 " --> pdb=" O   HIS A 429 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 480
    Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 534
    Processing sheet with id=AB3, first strand: chain 'A' and resid 599 through 605
      removed outlier: 5.595A  pdb=" N   ASP A 600 " --> pdb=" O   LYS A 616 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   LYS A 616 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 759 through 762
      removed outlier: 4.166A  pdb=" N   GLY A 778 " --> pdb=" O   GLN A 635 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 819 through 822
    Processing sheet with id=AB6, first strand: chain 'A' and resid 859 through 862
      removed outlier: 3.605A  pdb=" N   LEU A 844 " --> pdb=" O   THR A 889 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   VAL A 886 " --> pdb=" O   TRP A 897 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   TRP A 897 " --> pdb=" O   VAL A 886 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ALA A 888 " --> pdb=" O   GLY A 895 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 880 through 882
      removed outlier: 3.717A  pdb=" N   PHE A 903 " --> pdb=" O   TYR A 882 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.544A  pdb=" N   VAL B  66 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   PHE B  96 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   LEU B  63 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   ARG B 118 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   VAL B  94 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   GLU B 120 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   PHE B  96 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   ASN B 122 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ILE B 145 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   GLU B 120 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LEU B 147 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29
      removed outlier: 3.569A  pdb=" N   ILE B  29 " --> pdb=" O   MET B  56 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173
    Processing sheet with id=AC2, first strand: chain 'B' and resid 212 through 216
      removed outlier: 6.172A  pdb=" N   LEU B 213 " --> pdb=" O   CYS B 228 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   CYS B 228 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   ASN B 215 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 246 through 248
    Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 294
    Processing sheet with id=AC5, first strand: chain 'B' and resid 318 through 321
      removed outlier: 8.493A  pdb=" N   HIS B 429 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ALA B 402 " --> pdb=" O   HIS B 429 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 335 through 336
    Processing sheet with id=AC7, first strand: chain 'B' and resid 472 through 473
    Processing sheet with id=AC8, first strand: chain 'B' and resid 477 through 479
    Processing sheet with id=AC9, first strand: chain 'B' and resid 530 through 534
      removed outlier: 3.667A  pdb=" N   GLY B 502 " --> pdb=" O   LEU B 569 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 599 through 604
      removed outlier: 7.084A  pdb=" N   LYS B 614 " --> pdb=" O   PRO B 601 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   SER B 603 " --> pdb=" O   ILE B 612 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE B 612 " --> pdb=" O   SER B 603 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 762
      removed outlier: 3.774A  pdb=" N   GLU B 760 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL B 630 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN B 788 " --> pdb=" O   ARG B 794 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 762
      removed outlier: 3.774A  pdb=" N   GLU B 760 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL B 630 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 819 through 822
      removed outlier: 3.522A  pdb=" N   CYS B 872 " --> pdb=" O   LEU B 830 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 856 through 862

    339 hydrogen bonds defined for protein.
    843 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: 2.05

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4549
        1.34 -     1.46: 3051
        1.46 -     1.58: 6506
        1.58 -     1.70: 0
        1.70 -     1.82: 140
  Bond restraints: 14246
  Sorted by residual:
  bond pdb=" CA  GLU A 469 "
       pdb=" C   GLU A 469 "
    ideal  model  delta    sigma   weight residual
    1.523  1.501  0.022 1.35e-02 5.49e+03 2.64e+00
  bond pdb=" N   CYS A 468 "
       pdb=" CA  CYS A 468 "
    ideal  model  delta    sigma   weight residual
    1.455  1.473 -0.018 1.33e-02 5.65e+03 1.83e+00
  bond pdb=" CA  GLU A 471 "
       pdb=" C   GLU A 471 "
    ideal  model  delta    sigma   weight residual
    1.519  1.504  0.015 1.14e-02 7.69e+03 1.74e+00
  bond pdb=" C   CYS A 682 "
       pdb=" N   CYS A 683 "
    ideal  model  delta    sigma   weight residual
    1.332  1.315  0.018 1.40e-02 5.10e+03 1.58e+00
  bond pdb=" CA  GLU A 469 "
       pdb=" CB  GLU A 469 "
    ideal  model  delta    sigma   weight residual
    1.529  1.510  0.019 1.58e-02 4.01e+03 1.46e+00
  ... (remaining 14241 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 19176
        2.79 -     5.58: 114
        5.58 -     8.36: 9
        8.36 -    11.15: 0
       11.15 -    13.94: 1
  Bond angle restraints: 19300
  Sorted by residual:
  angle pdb=" N   GLU A 469 "
        pdb=" CA  GLU A 469 "
        pdb=" C   GLU A 469 "
      ideal   model   delta    sigma   weight residual
     111.33   97.39   13.94 1.21e+00 6.83e-01 1.33e+02
  angle pdb=" C   SER A 467 "
        pdb=" N   CYS A 468 "
        pdb=" CA  CYS A 468 "
      ideal   model   delta    sigma   weight residual
     122.49  115.96    6.53 1.55e+00 4.16e-01 1.77e+01
  angle pdb=" C   PHE B 714 "
        pdb=" N   VAL B 715 "
        pdb=" CA  VAL B 715 "
      ideal   model   delta    sigma   weight residual
     122.13  129.66   -7.53 1.85e+00 2.92e-01 1.66e+01
  angle pdb=" N   ASN A 470 "
        pdb=" CA  ASN A 470 "
        pdb=" C   ASN A 470 "
      ideal   model   delta    sigma   weight residual
     110.80  117.91   -7.11 2.13e+00 2.20e-01 1.11e+01
  angle pdb=" C   VAL A  99 "
        pdb=" N   HIS A 100 "
        pdb=" CA  HIS A 100 "
      ideal   model   delta    sigma   weight residual
     121.54  127.02   -5.48 1.91e+00 2.74e-01 8.23e+00
  ... (remaining 19295 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 7743
       17.46 -    34.92: 738
       34.92 -    52.38: 118
       52.38 -    69.84: 30
       69.84 -    87.30: 20
  Dihedral angle restraints: 8649
    sinusoidal: 3612
      harmonic: 5037
  Sorted by residual:
  dihedral pdb=" CB  CYS B 288 "
           pdb=" SG  CYS B 288 "
           pdb=" SG  CYS B 301 "
           pdb=" CB  CYS B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.70  -87.30     1      1.00e+01 1.00e-02 9.15e+01
  dihedral pdb=" CB  CYS D   7 "
           pdb=" SG  CYS D   7 "
           pdb=" SG  CYS D  62 "
           pdb=" CB  CYS D  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   12.44   80.56     1      1.00e+01 1.00e-02 8.02e+01
  dihedral pdb=" CB  CYS C   7 "
           pdb=" SG  CYS C   7 "
           pdb=" SG  CYS C  62 "
           pdb=" CB  CYS C  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   26.25   66.75     1      1.00e+01 1.00e-02 5.81e+01
  ... (remaining 8646 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1655
       0.050 -    0.101: 349
       0.101 -    0.151: 86
       0.151 -    0.202: 4
       0.202 -    0.252: 1
  Chirality restraints: 2095
  Sorted by residual:
  chirality pdb=" CA  CYS A 468 "
            pdb=" N   CYS A 468 "
            pdb=" C   CYS A 468 "
            pdb=" CB  CYS A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  ASN A 470 "
            pdb=" N   ASN A 470 "
            pdb=" C   ASN A 470 "
            pdb=" CB  ASN A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality pdb=" CB  ILE B 174 "
            pdb=" CA  ILE B 174 "
            pdb=" CG1 ILE B 174 "
            pdb=" CG2 ILE B 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.19e-01
  ... (remaining 2092 not shown)

  Planarity restraints: 2493
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 682 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.43e+00
        pdb=" C   CYS A 682 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   CYS A 682 "    0.014 2.00e-02 2.50e+03
        pdb=" N   CYS A 683 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "    0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A  43 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 467 "   -0.008 2.00e-02 2.50e+03   1.49e-02 2.23e+00
        pdb=" C   SER A 467 "    0.026 2.00e-02 2.50e+03
        pdb=" O   SER A 467 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   CYS A 468 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2490 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 486
        2.70 -     3.25: 14194
        3.25 -     3.80: 22891
        3.80 -     4.35: 29092
        4.35 -     4.90: 47041
  Nonbonded interactions: 113704
  Sorted by model distance:
  nonbonded pdb=" O   GLU D  59 "
            pdb=" OG1 THR D  63 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" NH2 ARG A  14 "
            pdb=" O   VAL B 712 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O   SER B 878 "
            pdb=" OH  TYR B 882 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   PRO A  77 "
            pdb=" ND2 ASN A 108 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" O   GLN B 513 "
            pdb=" OH  TYR B 587 "
     model   vdw
     2.212 3.040
  ... (remaining 113699 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 518 or resid 528 through 905))
  selection = (chain 'B' and (resid 3 through 314 or resid 317 through 346 or resid 351 throug \ 
h 539 or resid 547 through 717 or resid 756 through 905))
}
ncs_group {
  reference = (chain 'C' and (resid 4 through 25 or resid 56 through 76))
  selection = chain 'D'
}

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:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.810
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
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      :  0.005   0.313  14286  Z= 0.218
  Angle     :  0.617  16.434  19380  Z= 0.326
  Chirality :  0.044   0.252   2095
  Planarity :  0.003   0.040   2493
  Dihedral  : 13.676  86.409   5273
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  7.12 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.70 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.96 (0.22), residues: 1686
  helix: -0.21 (0.39), residues: 201
  sheet: -0.16 (0.29), residues: 372
  loop : -0.89 (0.20), residues: 1113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 114 
 TYR   0.012   0.001   TYR B 708 
 PHE   0.022   0.001   PHE A  46 
 TRP   0.016   0.001   TRP A 414 
 HIS   0.008   0.001   HIS B 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14246)
  covalent geometry    : angle       0.59189 (19300)
  SS BOND              : bond        0.04955 (   40)
  SS BOND              : angle       2.76600 (   80)
  hydrogen bonds       : bond        0.25682 (  329)
  hydrogen bonds       : angle       9.43091 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.9095 (p90) cc_final: 0.8705 (p-80)
REVERT: A   88 PHE cc_start: 0.8597 (t80) cc_final: 0.8175 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 62
  average time/residue: 0.0927
  time to fit residues: 9.9331
Evaluate side-chains
  44 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0020
   chunk 149 optimal weight:    4.9990
   overall best weight:    0.9792

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 GLN
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 GLN
** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.070137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.045149 restraints weight = 78112.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.046850 restraints weight = 44916.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.047008 restraints weight = 31203.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.047286 restraints weight = 24207.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.047315 restraints weight = 23852.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14286  Z= 0.122
  Angle     :  0.586   8.709  19380  Z= 0.301
  Chirality :  0.045   0.180   2095
  Planarity :  0.004   0.045   2493
  Dihedral  :  4.240  27.699   1880
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.47 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  5.66 %
    Favored  : 93.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.91 (0.21), residues: 1686
  helix: -0.24 (0.36), residues: 218
  sheet:  0.08 (0.29), residues: 364
  loop : -0.94 (0.20), residues: 1104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 851 
 TYR   0.015   0.001   TYR B 800 
 PHE   0.015   0.001   PHE B 482 
 TRP   0.013   0.001   TRP B 414 
 HIS   0.004   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (14246)
  covalent geometry    : angle       0.58449 (19300)
  SS BOND              : bond        0.00234 (   40)
  SS BOND              : angle       0.84764 (   80)
  hydrogen bonds       : bond        0.05114 (  329)
  hydrogen bonds       : angle       7.03741 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8977 (p90) cc_final: 0.8553 (p-80)
REVERT: B  401 TYR cc_start: 0.8740 (t80) cc_final: 0.8459 (t80)
REVERT: B  831 MET cc_start: 0.7767 (mmm) cc_final: 0.7509 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 54
  average time/residue: 0.0929
  time to fit residues: 9.0021
Evaluate side-chains
  49 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  696 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 132 optimal weight:    0.3980
   chunk 41 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0470
   chunk 60 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 127 optimal weight:    6.9990
   overall best weight:    2.2884

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
A 313 GLN
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 865 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.069385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.045430 restraints weight = 79121.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.045827 restraints weight = 52386.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.046210 restraints weight = 37171.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.046348 restraints weight = 34965.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.046410 restraints weight = 30950.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14286  Z= 0.178
  Angle     :  0.582   9.289  19380  Z= 0.298
  Chirality :  0.044   0.180   2095
  Planarity :  0.004   0.040   2493
  Dihedral  :  4.281  27.402   1879
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.88 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.40 %
    Favored  : 90.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.91 (0.22), residues: 1686
  helix: -0.15 (0.37), residues: 212
  sheet:  0.00 (0.29), residues: 364
  loop : -0.92 (0.20), residues: 1110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  83 
 TYR   0.014   0.001   TYR B 708 
 PHE   0.017   0.001   PHE A  88 
 TRP   0.013   0.001   TRP B 414 
 HIS   0.003   0.001   HIS B 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (14246)
  covalent geometry    : angle       0.58121 (19300)
  SS BOND              : bond        0.00212 (   40)
  SS BOND              : angle       0.79668 (   80)
  hydrogen bonds       : bond        0.04565 (  329)
  hydrogen bonds       : angle       6.64096 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8938 (p90) cc_final: 0.8545 (p-80)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0905
  time to fit residues: 8.0658
Evaluate side-chains
  53 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  696 LEU
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  709 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 148 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 140 optimal weight:    6.9990
   chunk 115 optimal weight:    3.9990
   chunk 135 optimal weight:    2.9990
   chunk 134 optimal weight:    0.7980
   chunk 93 optimal weight:    0.8980
   chunk 77 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0270
   chunk 136 optimal weight:    2.9990
   overall best weight:    1.0840

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 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 = 0.3838 r_free = 0.3838 target = 0.069894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.045531 restraints weight = 79060.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.046452 restraints weight = 51642.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.046488 restraints weight = 34026.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.046763 restraints weight = 34524.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.046732 restraints weight = 31998.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14286  Z= 0.111
  Angle     :  0.550  10.311  19380  Z= 0.281
  Chirality :  0.044   0.185   2095
  Planarity :  0.003   0.039   2493
  Dihedral  :  4.183  27.160   1879
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.23 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.92 %
    Favored  : 89.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.93 (0.21), residues: 1686
  helix: -0.38 (0.36), residues: 223
  sheet:  0.01 (0.29), residues: 364
  loop : -0.89 (0.20), residues: 1099

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 851 
 TYR   0.014   0.001   TYR B 708 
 PHE   0.016   0.001   PHE A  76 
 TRP   0.010   0.001   TRP B 414 
 HIS   0.004   0.001   HIS B 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (14246)
  covalent geometry    : angle       0.54914 (19300)
  SS BOND              : bond        0.00178 (   40)
  SS BOND              : angle       0.66266 (   80)
  hydrogen bonds       : bond        0.03836 (  329)
  hydrogen bonds       : angle       6.25587 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8874 (p90) cc_final: 0.8486 (p-80)
REVERT: B  401 TYR cc_start: 0.8783 (t80) cc_final: 0.8539 (t80)
REVERT: B  831 MET cc_start: 0.7643 (mmm) cc_final: 0.7308 (mmm)
  outliers start: 16
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0730
  time to fit residues: 7.8008
Evaluate side-chains
  59 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  696 LEU
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  709 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 152 optimal weight:   20.0000
   chunk 10 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0020
   chunk 123 optimal weight:    0.7980
   chunk 132 optimal weight:    0.9990
   chunk 163 optimal weight:    0.9980
   chunk 100 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 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 = 0.3840 r_free = 0.3840 target = 0.069921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.045913 restraints weight = 79264.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.046738 restraints weight = 52463.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.047262 restraints weight = 35826.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.047389 restraints weight = 35108.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.047344 restraints weight = 31175.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14286  Z= 0.107
  Angle     :  0.558  12.129  19380  Z= 0.280
  Chirality :  0.044   0.188   2095
  Planarity :  0.003   0.039   2493
  Dihedral  :  4.108  26.708   1879
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.58 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 11.70 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.91 (0.21), residues: 1686
  helix: -0.47 (0.36), residues: 224
  sheet:  0.01 (0.29), residues: 364
  loop : -0.85 (0.20), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 114 
 TYR   0.014   0.001   TYR B 708 
 PHE   0.023   0.001   PHE A  88 
 TRP   0.012   0.001   TRP B 414 
 HIS   0.003   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (14246)
  covalent geometry    : angle       0.55530 (19300)
  SS BOND              : bond        0.00175 (   40)
  SS BOND              : angle       0.97781 (   80)
  hydrogen bonds       : bond        0.03654 (  329)
  hydrogen bonds       : angle       6.05226 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8900 (p90) cc_final: 0.8512 (p-80)
REVERT: A   69 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8249 (mm)
REVERT: A  294 MET cc_start: 0.8861 (ppp) cc_final: 0.8551 (tmm)
REVERT: B  401 TYR cc_start: 0.8819 (t80) cc_final: 0.8514 (t80)
REVERT: B  831 MET cc_start: 0.7892 (mmm) cc_final: 0.7602 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 52
  average time/residue: 0.0932
  time to fit residues: 8.6232
Evaluate side-chains
  58 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  696 LEU
Chi-restraints excluded: chain B residue  709 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 154 optimal weight:   10.0000
   chunk 100 optimal weight:   30.0000
   chunk 141 optimal weight:    4.9990
   chunk 146 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 132 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 83 optimal weight:    8.9990
   chunk 133 optimal weight:    0.9980
   chunk 130 optimal weight:    0.7980
   chunk 117 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 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 = 0.3844 r_free = 0.3844 target = 0.070022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.045778 restraints weight = 77943.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.046654 restraints weight = 50364.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.046885 restraints weight = 34243.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.047175 restraints weight = 33755.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.047152 restraints weight = 30510.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14286  Z= 0.100
  Angle     :  0.546  10.136  19380  Z= 0.275
  Chirality :  0.043   0.188   2095
  Planarity :  0.003   0.040   2493
  Dihedral  :  4.055  26.350   1879
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.23 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 12.47 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.84 (0.22), residues: 1686
  helix: -0.26 (0.37), residues: 218
  sheet:  0.05 (0.29), residues: 364
  loop : -0.84 (0.20), residues: 1104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  86 
 TYR   0.018   0.001   TYR C  69 
 PHE   0.013   0.001   PHE A 518 
 TRP   0.011   0.001   TRP A 414 
 HIS   0.002   0.000   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (14246)
  covalent geometry    : angle       0.54414 (19300)
  SS BOND              : bond        0.00165 (   40)
  SS BOND              : angle       0.91276 (   80)
  hydrogen bonds       : bond        0.03436 (  329)
  hydrogen bonds       : angle       5.84756 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8824 (p90) cc_final: 0.8424 (p-80)
REVERT: A   69 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8198 (mm)
REVERT: B  401 TYR cc_start: 0.8832 (t80) cc_final: 0.8541 (t80)
REVERT: B  831 MET cc_start: 0.7920 (mmm) cc_final: 0.7636 (mmm)
REVERT: D   60 GLN cc_start: 0.9044 (tt0) cc_final: 0.7927 (tm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 56
  average time/residue: 0.0876
  time to fit residues: 8.6951
Evaluate side-chains
  60 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  696 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 143 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 166 optimal weight:    0.9980
   chunk 120 optimal weight:    0.7980
   chunk 121 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 138 optimal weight:    0.0040
   chunk 141 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.1394

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.069930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.045412 restraints weight = 78652.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.046244 restraints weight = 49890.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.046350 restraints weight = 33995.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.046658 restraints weight = 34099.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.046671 restraints weight = 30521.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14286  Z= 0.110
  Angle     :  0.540  10.934  19380  Z= 0.272
  Chirality :  0.043   0.181   2095
  Planarity :  0.003   0.040   2493
  Dihedral  :  4.032  26.341   1879
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.29 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 13.30 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.75 (0.22), residues: 1686
  helix: -0.07 (0.38), residues: 209
  sheet:  0.06 (0.29), residues: 364
  loop : -0.78 (0.20), residues: 1113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.015   0.001   TYR B 708 
 PHE   0.025   0.001   PHE B 572 
 TRP   0.012   0.001   TRP A 414 
 HIS   0.002   0.000   HIS B 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (14246)
  covalent geometry    : angle       0.53832 (19300)
  SS BOND              : bond        0.00169 (   40)
  SS BOND              : angle       0.88616 (   80)
  hydrogen bonds       : bond        0.03363 (  329)
  hydrogen bonds       : angle       5.71686 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8856 (p90) cc_final: 0.8458 (p-80)
REVERT: A   69 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8211 (mm)
REVERT: B  401 TYR cc_start: 0.8865 (t80) cc_final: 0.8604 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 53
  average time/residue: 0.0922
  time to fit residues: 8.6693
Evaluate side-chains
  58 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  696 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 97 optimal weight:    0.1980
   chunk 89 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 131 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 165 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 162 optimal weight:    5.9990
   chunk 20 optimal weight:   30.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 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 = 0.3838 r_free = 0.3838 target = 0.069952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.045532 restraints weight = 78580.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.046561 restraints weight = 50366.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.046721 restraints weight = 33394.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.046961 restraints weight = 35401.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.046936 restraints weight = 31202.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14286  Z= 0.108
  Angle     :  0.548  10.858  19380  Z= 0.274
  Chirality :  0.043   0.180   2095
  Planarity :  0.003   0.040   2493
  Dihedral  :  4.033  26.272   1879
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.23 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 13.74 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.73 (0.22), residues: 1686
  helix: -0.04 (0.38), residues: 209
  sheet:  0.10 (0.29), residues: 362
  loop : -0.77 (0.20), residues: 1115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.019   0.001   TYR C  69 
 PHE   0.012   0.001   PHE A 518 
 TRP   0.014   0.001   TRP A 414 
 HIS   0.002   0.000   HIS B 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (14246)
  covalent geometry    : angle       0.54593 (19300)
  SS BOND              : bond        0.00167 (   40)
  SS BOND              : angle       0.87580 (   80)
  hydrogen bonds       : bond        0.03267 (  329)
  hydrogen bonds       : angle       5.63245 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.570 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8792 (p90) cc_final: 0.8399 (p-80)
REVERT: A   69 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8158 (mm)
REVERT: B  401 TYR cc_start: 0.8865 (t80) cc_final: 0.8593 (t80)
REVERT: B  806 MET cc_start: 0.8664 (mmm) cc_final: 0.8407 (ptp)
  outliers start: 16
  outliers final: 14
  residues processed: 55
  average time/residue: 0.0897
  time to fit residues: 8.6377
Evaluate side-chains
  59 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  696 LEU
Chi-restraints excluded: chain C residue    7 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 101 optimal weight:   10.0000
   chunk 110 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0020
   chunk 38 optimal weight:    6.9990
   chunk 133 optimal weight:    1.9990
   chunk 138 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 108 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 ASN
** B 343 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 = 0.3841 r_free = 0.3841 target = 0.070081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.046469 restraints weight = 79033.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.047156 restraints weight = 55718.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.047014 restraints weight = 38171.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.047276 restraints weight = 36161.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.047364 restraints weight = 33463.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14286  Z= 0.097
  Angle     :  0.545  10.508  19380  Z= 0.273
  Chirality :  0.043   0.182   2095
  Planarity :  0.003   0.040   2493
  Dihedral  :  3.981  26.165   1879
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.17 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 13.74 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.71 (0.22), residues: 1686
  helix: -0.01 (0.38), residues: 209
  sheet:  0.10 (0.29), residues: 367
  loop : -0.76 (0.20), residues: 1110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.029   0.001   TYR D  16 
 PHE   0.013   0.001   PHE A 518 
 TRP   0.015   0.001   TRP A 414 
 HIS   0.002   0.000   HIS B 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (14246)
  covalent geometry    : angle       0.54347 (19300)
  SS BOND              : bond        0.00200 (   40)
  SS BOND              : angle       0.86474 (   80)
  hydrogen bonds       : bond        0.03140 (  329)
  hydrogen bonds       : angle       5.52744 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.536 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8760 (p90) cc_final: 0.8370 (p-80)
REVERT: A   69 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8150 (mm)
REVERT: B  401 TYR cc_start: 0.8705 (t80) cc_final: 0.8425 (t80)
  outliers start: 16
  outliers final: 14
  residues processed: 55
  average time/residue: 0.0917
  time to fit residues: 8.9241
Evaluate side-chains
  60 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  696 LEU
Chi-restraints excluded: chain C residue    7 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 70 optimal weight:    0.4980
   chunk 88 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 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 = 0.3836 r_free = 0.3836 target = 0.069866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.045582 restraints weight = 78852.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.046054 restraints weight = 53605.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.046247 restraints weight = 39615.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.046444 restraints weight = 34841.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.046513 restraints weight = 31874.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14286  Z= 0.115
  Angle     :  0.565  11.273  19380  Z= 0.281
  Chirality :  0.043   0.188   2095
  Planarity :  0.003   0.040   2493
  Dihedral  :  4.010  26.240   1879
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.35 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.93 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.71 (0.22), residues: 1686
  helix:  0.02 (0.38), residues: 209
  sheet:  0.10 (0.29), residues: 367
  loop : -0.77 (0.20), residues: 1110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.028   0.001   TYR D  16 
 PHE   0.012   0.001   PHE A 518 
 TRP   0.017   0.001   TRP A 414 
 HIS   0.002   0.000   HIS A 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (14246)
  covalent geometry    : angle       0.56350 (19300)
  SS BOND              : bond        0.00179 (   40)
  SS BOND              : angle       0.85429 (   80)
  hydrogen bonds       : bond        0.03194 (  329)
  hydrogen bonds       : angle       5.50887 (  843)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A   32 HIS cc_start: 0.8831 (p90) cc_final: 0.8398 (p-80)
REVERT: A   69 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8194 (mm)
REVERT: B  401 TYR cc_start: 0.8834 (t80) cc_final: 0.8531 (t80)
  outliers start: 15
  outliers final: 14
  residues processed: 53
  average time/residue: 0.0860
  time to fit residues: 8.1101
Evaluate side-chains
  60 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   11 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  696 LEU
Chi-restraints excluded: chain C residue    7 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0970
   chunk 57 optimal weight:    0.9990
   chunk 165 optimal weight:    0.6980
   chunk 144 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 132 optimal weight:    0.0870
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 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 = 0.3847 r_free = 0.3847 target = 0.070264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.046602 restraints weight = 78298.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.047025 restraints weight = 51454.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.047271 restraints weight = 34501.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.047377 restraints weight = 33907.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.047432 restraints weight = 30970.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14286  Z= 0.091
  Angle     :  0.555  11.148  19380  Z= 0.277
  Chirality :  0.043   0.183   2095
  Planarity :  0.003   0.040   2493
  Dihedral  :  3.939  26.029   1879
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.23 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 14.06 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.73 (0.22), residues: 1686
  helix: -0.02 (0.38), residues: 210
  sheet:  0.05 (0.28), residues: 381
  loop : -0.77 (0.20), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 804 
 TYR   0.028   0.001   TYR D  16 
 PHE   0.019   0.001   PHE B 572 
 TRP   0.019   0.001   TRP A 414 
 HIS   0.002   0.000   HIS A 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 (14246)
  covalent geometry    : angle       0.55419 (19300)
  SS BOND              : bond        0.00163 (   40)
  SS BOND              : angle       0.80539 (   80)
  hydrogen bonds       : bond        0.02979 (  329)
  hydrogen bonds       : angle       5.38711 (  843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2346.38 seconds
wall clock time: 41 minutes 22.21 seconds (2482.21 seconds total)