Starting phenix.real_space_refine
on Fri Jun 20 19:24:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sl1_25188/06_2025/7sl1_25188_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sl1_25188/06_2025/7sl1_25188.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sl1_25188/06_2025/7sl1_25188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sl1_25188/06_2025/7sl1_25188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sl1_25188/06_2025/7sl1_25188_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sl1_25188/06_2025/7sl1_25188_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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 12534 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     110      5.16       5
     C    8774      2.51       5
     N    2374      2.21       5
     O    2572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13830
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 813, 6566
          Classifications: {'peptide': 813}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 769}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 6566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 813, 6566
          Classifications: {'peptide': 813}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 769}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 185
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "D"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 185
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "E"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 164
          Classifications: {'peptide': 21}
          Link IDs: {'TRANS': 20}
    Chain: "F"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 164
          Classifications: {'peptide': 21}
          Link IDs: {'TRANS': 20}
  Time building chain proxies: 7.71, per 1000 atoms: 0.56
  Number of scatterers: 13830
  At special positions: 0
  Unit cell: (155.21, 108.73, 141.93, 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     110     16.00
     O    2572      8.00
     N    2374      7.00
     C    8774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=42, 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 159 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 188 " distance=2.04
    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 304 " - pdb=" SG  CYS A 308 " 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 649 " - pdb=" SG  CYS A 862 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 788 " - pdb=" SG  CYS A 797 " distance=2.04
    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 159 " - pdb=" SG  CYS B 182 " 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=2.04
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 304 " - pdb=" SG  CYS B 308 " 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 649 " - pdb=" SG  CYS B 862 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 788 " - pdb=" SG  CYS B 797 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS E   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  19 " - pdb=" SG  CYS E  20 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS F   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS F  20 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   6 " - pdb=" SG  CYS E  11 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   6 " - pdb=" SG  CYS F  11 " 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: 3.09
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3228

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 32 sheets defined
      13.9% alpha, 25.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 24
      removed outlier: 4.195A  pdb=" N   ARG A  19 " --> pdb=" O   ASN A  16 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   HIS A  21 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 47
      removed outlier: 3.520A  pdb=" N   ARG A  47 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
      removed outlier: 4.182A  pdb=" N   ASN A 268 " --> pdb=" O   PHE A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 330
      removed outlier: 3.574A  pdb=" N   ALA A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LEU A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 359
    Processing helix  chain 'A' and resid 435 through 446
      removed outlier: 3.833A  pdb=" N   ILE A 439 " --> pdb=" O   CYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 640 through 644
    Processing helix  chain 'A' and resid 692 through 711
    Processing helix  chain 'A' and resid 865 through 872
    Processing helix  chain 'B' and resid 16 through 24
      removed outlier: 4.183A  pdb=" N   ARG B  19 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   HIS B  21 " --> pdb=" O   THR B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 47
      removed outlier: 3.523A  pdb=" N   ARG B  47 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 268
      removed outlier: 4.217A  pdb=" N   ASN B 268 " --> pdb=" O   PHE B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 318
    Processing helix  chain 'B' and resid 323 through 330
      removed outlier: 3.595A  pdb=" N   ALA B 327 " --> pdb=" O   SER B 323 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU B 329 " --> pdb=" O   THR B 325 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LEU B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 359
    Processing helix  chain 'B' and resid 435 through 446
      removed outlier: 3.813A  pdb=" N   ILE B 439 " --> pdb=" O   CYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 640 through 644
    Processing helix  chain 'B' and resid 692 through 711
    Processing helix  chain 'B' and resid 865 through 872
    Processing helix  chain 'C' and resid 8 through 19
    Processing helix  chain 'D' and resid 8 through 19
    Processing helix  chain 'E' and resid 2 through 7
      removed outlier: 3.549A  pdb=" N   CYS E   7 " --> pdb=" O   GLU E   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 12 through 18
    Processing helix  chain 'F' and resid 2 through 7
      removed outlier: 3.563A  pdb=" N   CYS F   7 " --> pdb=" O   GLU F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 18
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 14
      removed outlier: 7.007A  pdb=" N   CYS A   8 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   HIS A  32 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLY A  10 " --> pdb=" O   HIS A  32 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   GLN A  34 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ASP A  12 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   LEU A  36 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ARG A  14 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   MET A  38 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 14
      removed outlier: 7.007A  pdb=" N   CYS A   8 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   HIS A  32 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLY A  10 " --> pdb=" O   HIS A  32 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   GLN A  34 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ASP A  12 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   LEU A  36 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ARG A  14 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   MET A  38 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
      removed outlier: 8.716A  pdb=" N   LEU A  62 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LEU A  33 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   PHE A  64 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE A  35 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   VAL A  66 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   LEU A  37 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   PHE A  96 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   LEU A  63 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ARG A 118 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   VAL A  94 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   GLU A 120 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   PHE A  96 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ASN A 122 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ASN A 148 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172
      removed outlier: 3.538A  pdb=" N   THR A 172 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233
    Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 248
    Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280
    Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321
      removed outlier: 6.764A  pdb=" N   VAL A 335 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLN A 313 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ASN A 337 " --> pdb=" O   GLN A 313 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   LEU A 315 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   SER A 339 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLY A 317 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ILE A 341 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   LYS A 319 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 321
      removed outlier: 6.764A  pdb=" N   VAL A 335 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLN A 313 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ASN A 337 " --> pdb=" O   GLN A 313 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   LEU A 315 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   SER A 339 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLY A 317 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ILE A 341 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   LYS A 319 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   LYS A 369 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   LEU A 340 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG A 371 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ILE A 342 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   LYS A 425 " --> pdb=" O   TYR A 398 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE A 400 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 473
      removed outlier: 6.329A  pdb=" N   GLU A 471 " --> pdb=" O   LYS A 584 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480
      removed outlier: 3.797A  pdb=" N   PHE A 477 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A 479 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534
      removed outlier: 3.567A  pdb=" N   GLY A 502 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 607
      removed outlier: 3.805A  pdb=" N   ILE A 613 " --> pdb=" O   ILE A 772 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 765
    Processing sheet with id=AB6, first strand: chain 'A' and resid 830 through 832
    Processing sheet with id=AB7, first strand: chain 'A' and resid 858 through 864
      removed outlier: 3.790A  pdb=" N   LEU A 846 " --> pdb=" O   THR A 891 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU A 848 " --> pdb=" O   ARG A 889 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG A 889 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE A 905 " --> pdb=" O   TYR A 884 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 7 through 14
      removed outlier: 7.010A  pdb=" N   CYS B   8 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   HIS B  32 " --> pdb=" O   CYS B   8 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLY B  10 " --> pdb=" O   HIS B  32 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   GLN B  34 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   ASP B  12 " --> pdb=" O   GLN B  34 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU B  36 " --> pdb=" O   ASP B  12 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ARG B  14 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   MET B  38 " --> pdb=" O   ARG B  14 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 7 through 14
      removed outlier: 7.010A  pdb=" N   CYS B   8 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   HIS B  32 " --> pdb=" O   CYS B   8 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLY B  10 " --> pdb=" O   HIS B  32 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   GLN B  34 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   ASP B  12 " --> pdb=" O   GLN B  34 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU B  36 " --> pdb=" O   ASP B  12 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ARG B  14 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   MET B  38 " --> pdb=" O   ARG B  14 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   LEU B  62 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   LEU B  33 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   PHE B  64 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ILE B  35 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL B  66 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   LEU B  37 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   PHE B  96 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B  63 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   ARG B 118 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL B  94 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   GLU B 120 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   PHE B  96 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ASN B 122 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ASN B 148 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.537A  pdb=" N   THR B 172 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 231 through 233
    Processing sheet with id=AC3, first strand: chain 'B' and resid 245 through 248
    Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 280
    Processing sheet with id=AC5, first strand: chain 'B' and resid 292 through 294
    Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 313
      removed outlier: 6.925A  pdb=" N   CYS B 312 " --> pdb=" O   ASN B 337 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 319 through 321
      removed outlier: 6.176A  pdb=" N   LYS B 319 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LEU B 340 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   ARG B 371 " --> pdb=" O   LEU B 340 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   ILE B 342 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   LYS B 425 " --> pdb=" O   TYR B 398 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   PHE B 400 " --> pdb=" O   LYS B 425 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 473
      removed outlier: 6.329A  pdb=" N   GLU B 471 " --> pdb=" O   LYS B 584 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'B' and resid 475 through 480
      removed outlier: 6.612A  pdb=" N   ARG B 488 " --> pdb=" O   SER B 476 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   ILE B 478 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   LEU B 486 " --> pdb=" O   ILE B 478 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 530 through 534
      removed outlier: 3.586A  pdb=" N   GLY B 502 " --> pdb=" O   LEU B 571 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 604 through 607
      removed outlier: 3.636A  pdb=" N   ILE B 613 " --> pdb=" O   ILE B 772 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 761 through 765
    Processing sheet with id=AD4, first strand: chain 'B' and resid 830 through 832
    Processing sheet with id=AD5, first strand: chain 'B' and resid 858 through 864
      removed outlier: 3.787A  pdb=" N   LEU B 846 " --> pdb=" O   THR B 891 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU B 848 " --> pdb=" O   ARG B 889 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG B 889 " --> pdb=" O   GLU B 848 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B 852 " --> pdb=" O   SER B 885 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE B 905 " --> pdb=" O   TYR B 884 " (cutoff:3.500A)

    317 hydrogen bonds defined for protein.
    798 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: 5.33

  Time building geometry restraints manager: 3.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4533
        1.35 -     1.47: 3389
        1.47 -     1.59: 6108
        1.59 -     1.71: 0
        1.71 -     1.83: 134
  Bond restraints: 14164
  Sorted by residual:
  bond pdb=" N   ASP B 234 "
       pdb=" CA  ASP B 234 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.016 1.29e-02 6.01e+03 1.62e+00
  bond pdb=" CA  GLN B 538 "
       pdb=" CB  GLN B 538 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.21e-02 6.83e+03 1.28e+00
  bond pdb=" N   TYR A 144 "
       pdb=" CA  TYR A 144 "
    ideal  model  delta    sigma   weight residual
    1.465  1.451  0.014 1.31e-02 5.83e+03 1.13e+00
  bond pdb=" CA  ASP B 464 "
       pdb=" C   ASP B 464 "
    ideal  model  delta    sigma   weight residual
    1.520  1.515  0.005 4.80e-03 4.34e+04 9.56e-01
  bond pdb=" CG  GLU B 391 "
       pdb=" CD  GLU B 391 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.78e-01
  ... (remaining 14159 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 18839
        2.01 -     4.02: 310
        4.02 -     6.02: 29
        6.02 -     8.03: 6
        8.03 -    10.04: 2
  Bond angle restraints: 19186
  Sorted by residual:
  angle pdb=" C   THR A 167 "
        pdb=" N   ASN A 168 "
        pdb=" CA  ASN A 168 "
      ideal   model   delta    sigma   weight residual
     121.54  129.44   -7.90 1.91e+00 2.74e-01 1.71e+01
  angle pdb=" C   THR B 167 "
        pdb=" N   ASN B 168 "
        pdb=" CA  ASN B 168 "
      ideal   model   delta    sigma   weight residual
     121.54  129.43   -7.89 1.91e+00 2.74e-01 1.71e+01
  angle pdb=" C   ARG A 454 "
        pdb=" N   ASN A 455 "
        pdb=" CA  ASN A 455 "
      ideal   model   delta    sigma   weight residual
     121.54  127.38   -5.84 1.91e+00 2.74e-01 9.35e+00
  angle pdb=" C   ARG B 454 "
        pdb=" N   ASN B 455 "
        pdb=" CA  ASN B 455 "
      ideal   model   delta    sigma   weight residual
     121.54  127.33   -5.79 1.91e+00 2.74e-01 9.20e+00
  angle pdb=" C   PRO B 837 "
        pdb=" N   LYS B 838 "
        pdb=" CA  LYS B 838 "
      ideal   model   delta    sigma   weight residual
     120.38  124.71   -4.33 1.46e+00 4.69e-01 8.82e+00
  ... (remaining 19181 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 7633
       17.12 -    34.25: 782
       34.25 -    51.37: 156
       51.37 -    68.49: 23
       68.49 -    85.61: 8
  Dihedral angle restraints: 8602
    sinusoidal: 3600
      harmonic: 5002
  Sorted by residual:
  dihedral pdb=" CB  CYS A 169 "
           pdb=" SG  CYS A 169 "
           pdb=" SG  CYS A 188 "
           pdb=" CB  CYS A 188 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.08   73.08     1      1.00e+01 1.00e-02 6.81e+01
  dihedral pdb=" CB  CYS B 169 "
           pdb=" SG  CYS B 169 "
           pdb=" SG  CYS B 188 "
           pdb=" CB  CYS B 188 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.95   72.95     1      1.00e+01 1.00e-02 6.79e+01
  dihedral pdb=" CB  CYS A 435 "
           pdb=" SG  CYS A 435 "
           pdb=" SG  CYS A 468 "
           pdb=" CB  CYS A 468 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.28  -70.28     1      1.00e+01 1.00e-02 6.36e+01
  ... (remaining 8599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1198
       0.028 -    0.056: 506
       0.056 -    0.083: 191
       0.083 -    0.111: 128
       0.111 -    0.139: 53
  Chirality restraints: 2076
  Sorted by residual:
  chirality pdb=" CA  ILE A 388 "
            pdb=" N   ILE A 388 "
            pdb=" C   ILE A 388 "
            pdb=" CB  ILE A 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  chirality pdb=" CA  ILE A 341 "
            pdb=" N   ILE A 341 "
            pdb=" C   ILE A 341 "
            pdb=" CB  ILE A 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE B 341 "
            pdb=" N   ILE B 341 "
            pdb=" C   ILE B 341 "
            pdb=" CB  ILE B 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  ... (remaining 2073 not shown)

  Planarity restraints: 2480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 169 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.61e+00
        pdb=" N   PRO A 170 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 170 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 170 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 169 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.59e+00
        pdb=" N   PRO B 170 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 170 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 170 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  16 "   -0.009 2.00e-02 2.50e+03   1.23e-02 3.00e+00
        pdb=" CG  TYR C  16 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  16 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  16 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  16 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  16 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  16 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C  16 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2477 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 677
        2.73 -     3.27: 13737
        3.27 -     3.81: 22587
        3.81 -     4.36: 28015
        4.36 -     4.90: 46799
  Nonbonded interactions: 111815
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 295 "
            pdb=" OG  SER B 297 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OE1 GLN A 406 "
            pdb=" NE2 GLN B 406 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" OD1 ASN A 295 "
            pdb=" OG  SER A 297 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OG  SER A 399 "
            pdb=" O   GLN A 423 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG  SER B 399 "
            pdb=" O   GLN B 423 "
     model   vdw
     2.200 3.040
  ... (remaining 111810 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             109.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.170
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     34.480
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  148.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
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      :  0.002   0.045  14206  Z= 0.108
  Angle     :  0.599  10.038  19270  Z= 0.317
  Chirality :  0.044   0.139   2076
  Planarity :  0.003   0.048   2480
  Dihedral  : 13.617  85.613   5248
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.79 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.21), residues: 1682
  helix:  0.30 (0.41), residues: 180
  sheet: -0.83 (0.27), residues: 384
  loop : -0.80 (0.20), residues: 1118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 834 
 HIS   0.003   0.001   HIS A 831 
 PHE   0.011   0.001   PHE A 178 
 TYR   0.030   0.001   TYR C  16 
 ARG   0.004   0.000   ARG B 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25490 (  317)
  hydrogen bonds       : angle       9.04431 (  798)
  SS BOND              : bond        0.00210 (   42)
  SS BOND              : angle       1.05348 (   84)
  covalent geometry    : bond        0.00232 (14164)
  covalent geometry    : angle       0.59670 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8262 (mmt) cc_final: 0.8057 (mmp)
REVERT: A  863 VAL cc_start: 0.8018 (t) cc_final: 0.7709 (t)
REVERT: B  794 ASP cc_start: 0.7362 (t70) cc_final: 0.7081 (t70)
REVERT: B  863 VAL cc_start: 0.8082 (t) cc_final: 0.7770 (t)
REVERT: D   22 ARG cc_start: 0.6801 (ptt90) cc_final: 0.6585 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.2587
  time to fit residues: 43.7133
Evaluate side-chains
  84 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    5.9990
   chunk 128 optimal weight:    0.0980
   chunk 71 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 133 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 99 optimal weight:    9.9990
   chunk 154 optimal weight:    5.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 357 ASN
A 455 ASN
A 867 HIS
** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 455 ASN
** B 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.087507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.063621 restraints weight = 41803.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 3.69
r_work: 0.3042 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099  14206  Z= 0.254
  Angle     :  0.689  11.222  19270  Z= 0.355
  Chirality :  0.048   0.163   2076
  Planarity :  0.004   0.048   2480
  Dihedral  :  5.153  24.058   1870
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.65 %
    Favored  : 91.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.21), residues: 1682
  helix: -0.07 (0.38), residues: 192
  sheet: -0.70 (0.26), residues: 406
  loop : -1.07 (0.19), residues: 1084

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 529 
 HIS   0.011   0.001   HIS B 831 
 PHE   0.018   0.002   PHE A 178 
 TYR   0.028   0.002   TYR B 633 
 ARG   0.004   0.001   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04903 (  317)
  hydrogen bonds       : angle       6.92028 (  798)
  SS BOND              : bond        0.00343 (   42)
  SS BOND              : angle       1.46214 (   84)
  covalent geometry    : bond        0.00598 (14164)
  covalent geometry    : angle       0.68333 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 1.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 ARG cc_start: 0.7835 (tpt-90) cc_final: 0.7191 (ptt90)
REVERT: B  318 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7664 (mp0)
REVERT: B  454 ARG cc_start: 0.7814 (tpt-90) cc_final: 0.7172 (ptt90)
REVERT: B  794 ASP cc_start: 0.7868 (t70) cc_final: 0.7501 (t70)
REVERT: E   14 TYR cc_start: 0.7897 (m-80) cc_final: 0.7520 (m-80)
REVERT: E   18 ASN cc_start: 0.8797 (m110) cc_final: 0.8580 (m110)
  outliers start: 9
  outliers final: 7
  residues processed: 107
  average time/residue: 0.3277
  time to fit residues: 54.0533
Evaluate side-chains
  94 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  867 HIS
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain E residue   17 GLU
Chi-restraints excluded: chain F residue   17 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 114 optimal weight:    0.8980
   chunk 135 optimal weight:    1.9990
   chunk 155 optimal weight:    0.0060
   chunk 58 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 126 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 118 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 127 optimal weight:    0.0570
   overall best weight:    0.7516

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

Flipped N/Q/H residues before XYZ refinement:
A 455 ASN
B 455 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.089581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.065574 restraints weight = 42779.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 3.72
r_work: 0.3096 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14206  Z= 0.120
  Angle     :  0.597  10.994  19270  Z= 0.305
  Chirality :  0.045   0.153   2076
  Planarity :  0.004   0.048   2480
  Dihedral  :  4.850  21.165   1870
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 10.35 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.21), residues: 1682
  helix:  0.56 (0.39), residues: 180
  sheet: -0.76 (0.26), residues: 406
  loop : -0.98 (0.20), residues: 1096

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 251 
 HIS   0.005   0.001   HIS A 867 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.016   0.001   TYR B 507 
 ARG   0.004   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  317)
  hydrogen bonds       : angle       6.51222 (  798)
  SS BOND              : bond        0.00254 (   42)
  SS BOND              : angle       1.06894 (   84)
  covalent geometry    : bond        0.00280 (14164)
  covalent geometry    : angle       0.59418 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.564 
Fit side-chains
REVERT: A  110 MET cc_start: 0.9042 (mmm) cc_final: 0.8763 (mmt)
REVERT: A  454 ARG cc_start: 0.7779 (tpt-90) cc_final: 0.7075 (ptt90)
REVERT: A  901 GLU cc_start: 0.8073 (pp20) cc_final: 0.7792 (pp20)
REVERT: B  110 MET cc_start: 0.9098 (mmt) cc_final: 0.8862 (mmt)
REVERT: B  318 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7550 (mp0)
REVERT: B  454 ARG cc_start: 0.7769 (tpt-90) cc_final: 0.7052 (ptt90)
REVERT: B  794 ASP cc_start: 0.7804 (t70) cc_final: 0.7418 (t70)
REVERT: E   14 TYR cc_start: 0.7880 (m-80) cc_final: 0.7401 (m-80)
REVERT: F   14 TYR cc_start: 0.7903 (m-80) cc_final: 0.7663 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 98
  average time/residue: 0.2544
  time to fit residues: 37.7973
Evaluate side-chains
  88 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue  867 HIS
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 136 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 88 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 125 optimal weight:    0.0010
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 135 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    2.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 GLN
E  21 ASN
F  18 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.087489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.064783 restraints weight = 41402.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.43
r_work: 0.3091 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  14206  Z= 0.228
  Angle     :  0.639  10.939  19270  Z= 0.326
  Chirality :  0.046   0.152   2076
  Planarity :  0.004   0.046   2480
  Dihedral  :  5.077  22.486   1870
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.44 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.21), residues: 1682
  helix:  0.10 (0.38), residues: 194
  sheet: -0.83 (0.26), residues: 408
  loop : -1.08 (0.19), residues: 1080

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 529 
 HIS   0.005   0.001   HIS B 550 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.018   0.002   TYR A 633 
 ARG   0.003   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04136 (  317)
  hydrogen bonds       : angle       6.35326 (  798)
  SS BOND              : bond        0.00310 (   42)
  SS BOND              : angle       1.36691 (   84)
  covalent geometry    : bond        0.00537 (14164)
  covalent geometry    : angle       0.63376 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 1.465 
Fit side-chains
REVERT: A  454 ARG cc_start: 0.7816 (tpt-90) cc_final: 0.7210 (ptt90)
REVERT: B  454 ARG cc_start: 0.7825 (tpt-90) cc_final: 0.7218 (ptt90)
REVERT: B  794 ASP cc_start: 0.7763 (t70) cc_final: 0.7378 (t70)
REVERT: E   12 SER cc_start: 0.8636 (t) cc_final: 0.8242 (p)
  outliers start: 25
  outliers final: 14
  residues processed: 107
  average time/residue: 0.2085
  time to fit residues: 36.6441
Evaluate side-chains
  94 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASN
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  710 TYR
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  562 THR
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue  845 VAL
Chi-restraints excluded: chain B residue  867 HIS
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 157 optimal weight:    9.9990
   chunk 72 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 101 optimal weight:   10.0000
   chunk 149 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 79 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.087766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.063810 restraints weight = 42529.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 3.62
r_work: 0.3071 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084  14206  Z= 0.220
  Angle     :  0.639  11.207  19270  Z= 0.325
  Chirality :  0.046   0.191   2076
  Planarity :  0.004   0.041   2480
  Dihedral  :  5.145  22.368   1870
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 13.24 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.21), residues: 1682
  helix:  0.13 (0.39), residues: 192
  sheet: -0.86 (0.26), residues: 406
  loop : -1.13 (0.19), residues: 1084

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 529 
 HIS   0.005   0.001   HIS B 831 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.019   0.002   TYR A 507 
 ARG   0.004   0.000   ARG B 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03989 (  317)
  hydrogen bonds       : angle       6.21907 (  798)
  SS BOND              : bond        0.00297 (   42)
  SS BOND              : angle       1.30695 (   84)
  covalent geometry    : bond        0.00518 (14164)
  covalent geometry    : angle       0.63475 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.597 
Fit side-chains
REVERT: A  454 ARG cc_start: 0.7814 (tpt-90) cc_final: 0.7234 (ptt90)
REVERT: B  454 ARG cc_start: 0.7812 (tpt-90) cc_final: 0.7224 (ptt90)
REVERT: B  794 ASP cc_start: 0.7835 (t70) cc_final: 0.7435 (t70)
REVERT: E   14 TYR cc_start: 0.7961 (m-80) cc_final: 0.7635 (m-80)
REVERT: F   12 SER cc_start: 0.8647 (t) cc_final: 0.8251 (p)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.2181
  time to fit residues: 35.2500
Evaluate side-chains
  92 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  710 TYR
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue  867 HIS
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 76 optimal weight:   20.0000
   chunk 91 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 151 optimal weight:    0.8980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 410 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.088964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.065336 restraints weight = 42579.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 3.63
r_work: 0.3103 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14206  Z= 0.139
  Angle     :  0.593  11.305  19270  Z= 0.302
  Chirality :  0.045   0.182   2076
  Planarity :  0.003   0.042   2480
  Dihedral  :  4.939  20.416   1870
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.07 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.21), residues: 1682
  helix:  0.67 (0.41), residues: 180
  sheet: -0.73 (0.26), residues: 396
  loop : -1.06 (0.20), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 834 
 HIS   0.003   0.001   HIS A 440 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.022   0.001   TYR A 507 
 ARG   0.003   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  317)
  hydrogen bonds       : angle       5.97437 (  798)
  SS BOND              : bond        0.00218 (   42)
  SS BOND              : angle       1.06065 (   84)
  covalent geometry    : bond        0.00330 (14164)
  covalent geometry    : angle       0.58970 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 2.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 ARG cc_start: 0.7817 (tpt-90) cc_final: 0.7202 (ptt90)
REVERT: A  893 LEU cc_start: 0.9534 (mt) cc_final: 0.9309 (mp)
REVERT: B   56 MET cc_start: 0.8580 (tpt) cc_final: 0.8314 (tpt)
REVERT: B  454 ARG cc_start: 0.7885 (tpt-90) cc_final: 0.7246 (ptt90)
REVERT: B  794 ASP cc_start: 0.7781 (t70) cc_final: 0.7374 (t70)
REVERT: B  893 LEU cc_start: 0.9524 (mt) cc_final: 0.9281 (mp)
  outliers start: 20
  outliers final: 15
  residues processed: 103
  average time/residue: 0.2548
  time to fit residues: 43.2177
Evaluate side-chains
  95 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 1.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  710 TYR
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  562 THR
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue  845 VAL
Chi-restraints excluded: chain B residue  867 HIS
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain E residue    6 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 141 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 139 optimal weight:    0.0070
   chunk 122 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 145 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 133 optimal weight:    2.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A 410 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.089582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.065927 restraints weight = 42503.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 3.61
r_work: 0.3125 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14206  Z= 0.112
  Angle     :  0.583  11.483  19270  Z= 0.297
  Chirality :  0.045   0.178   2076
  Planarity :  0.003   0.044   2480
  Dihedral  :  4.864  19.974   1870
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 14.27 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.21), residues: 1682
  helix:  0.47 (0.40), residues: 192
  sheet: -0.69 (0.26), residues: 396
  loop : -1.08 (0.19), residues: 1094

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 834 
 HIS   0.003   0.001   HIS B 831 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.020   0.001   TYR B 507 
 ARG   0.002   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03512 (  317)
  hydrogen bonds       : angle       5.82052 (  798)
  SS BOND              : bond        0.00271 (   42)
  SS BOND              : angle       1.03810 (   84)
  covalent geometry    : bond        0.00268 (14164)
  covalent geometry    : angle       0.58064 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 1.564 
Fit side-chains
REVERT: A  454 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7196 (ptt90)
REVERT: A  893 LEU cc_start: 0.9529 (mt) cc_final: 0.9291 (mp)
REVERT: B  454 ARG cc_start: 0.7871 (tpt-90) cc_final: 0.7238 (ptt90)
REVERT: B  794 ASP cc_start: 0.7755 (t70) cc_final: 0.7341 (t70)
REVERT: B  893 LEU cc_start: 0.9516 (mt) cc_final: 0.9269 (mp)
REVERT: E   14 TYR cc_start: 0.7839 (m-80) cc_final: 0.7515 (m-80)
  outliers start: 19
  outliers final: 16
  residues processed: 102
  average time/residue: 0.2056
  time to fit residues: 34.5755
Evaluate side-chains
  96 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 1.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  710 TYR
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  562 THR
Chi-restraints excluded: chain B residue  845 VAL
Chi-restraints excluded: chain B residue  867 HIS
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain E residue    6 CYS
Chi-restraints excluded: chain E residue   18 ASN
Chi-restraints excluded: chain F residue    6 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 160 optimal weight:   10.0000
   chunk 156 optimal weight:   10.0000
   chunk 138 optimal weight:    2.9990
   chunk 104 optimal weight:    0.4980
   chunk 141 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 151 optimal weight:    6.9990
   chunk 83 optimal weight:    2.9990
   chunk 119 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0270
   chunk 150 optimal weight:    4.9990
   overall best weight:    1.4642

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.089075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.065110 restraints weight = 42550.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 3.64
r_work: 0.3099 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  14206  Z= 0.148
  Angle     :  0.596  11.351  19270  Z= 0.304
  Chirality :  0.045   0.210   2076
  Planarity :  0.003   0.044   2480
  Dihedral  :  4.934  20.211   1870
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 15.30 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.21), residues: 1682
  helix:  0.50 (0.39), residues: 194
  sheet: -0.76 (0.26), residues: 406
  loop : -1.09 (0.20), residues: 1082

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 553 
 HIS   0.002   0.001   HIS B 209 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.020   0.001   TYR D  16 
 ARG   0.002   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  317)
  hydrogen bonds       : angle       5.76229 (  798)
  SS BOND              : bond        0.00226 (   42)
  SS BOND              : angle       1.14479 (   84)
  covalent geometry    : bond        0.00356 (14164)
  covalent geometry    : angle       0.59202 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 1.717 
Fit side-chains
REVERT: A  454 ARG cc_start: 0.7804 (tpt-90) cc_final: 0.7198 (ptt180)
REVERT: B  454 ARG cc_start: 0.7883 (tpt-90) cc_final: 0.7239 (ptt180)
REVERT: B  794 ASP cc_start: 0.7800 (t70) cc_final: 0.7389 (t70)
REVERT: E   14 TYR cc_start: 0.7797 (m-80) cc_final: 0.7580 (m-80)
REVERT: F   14 TYR cc_start: 0.7966 (m-80) cc_final: 0.7641 (m-80)
  outliers start: 19
  outliers final: 15
  residues processed: 100
  average time/residue: 0.2152
  time to fit residues: 35.2278
Evaluate side-chains
  94 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 1.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  710 TYR
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  562 THR
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue  845 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain E residue    6 CYS
Chi-restraints excluded: chain F residue    6 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 137 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 GLN
** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.087828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.063899 restraints weight = 42569.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 3.60
r_work: 0.3067 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  14206  Z= 0.226
  Angle     :  0.656  11.328  19270  Z= 0.335
  Chirality :  0.047   0.188   2076
  Planarity :  0.004   0.065   2480
  Dihedral  :  5.212  21.298   1870
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.94 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.21), residues: 1682
  helix:  0.44 (0.39), residues: 194
  sheet: -0.90 (0.26), residues: 410
  loop : -1.12 (0.20), residues: 1078

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 553 
 HIS   0.009   0.001   HIS A 831 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.018   0.002   TYR B 507 
 ARG   0.003   0.000   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  317)
  hydrogen bonds       : angle       5.90443 (  798)
  SS BOND              : bond        0.00291 (   42)
  SS BOND              : angle       1.58106 (   84)
  covalent geometry    : bond        0.00536 (14164)
  covalent geometry    : angle       0.64883 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 1.875 
Fit side-chains
REVERT: A   56 MET cc_start: 0.8616 (tpt) cc_final: 0.8320 (tpt)
REVERT: A  454 ARG cc_start: 0.7812 (tpt-90) cc_final: 0.7207 (ptt90)
REVERT: B  454 ARG cc_start: 0.7891 (tpt-90) cc_final: 0.7255 (ptt90)
REVERT: B  794 ASP cc_start: 0.7864 (t70) cc_final: 0.7450 (t70)
REVERT: B  893 LEU cc_start: 0.9529 (mt) cc_final: 0.9316 (mp)
REVERT: F   14 TYR cc_start: 0.8011 (m-80) cc_final: 0.7744 (m-80)
  outliers start: 17
  outliers final: 15
  residues processed: 90
  average time/residue: 0.2240
  time to fit residues: 33.5505
Evaluate side-chains
  92 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  710 TYR
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  562 THR
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue  845 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain E residue    6 CYS
Chi-restraints excluded: chain F residue    6 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 118 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 142 optimal weight:    5.9990
   chunk 150 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 GLN
** B 247 HIS ** 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 = 0.3745 r_free = 0.3745 target = 0.089230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.065376 restraints weight = 42575.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 3.64
r_work: 0.3109 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14206  Z= 0.121
  Angle     :  0.608  11.470  19270  Z= 0.309
  Chirality :  0.045   0.171   2076
  Planarity :  0.004   0.058   2480
  Dihedral  :  4.979  20.123   1870
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.00 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.21), residues: 1682
  helix:  0.50 (0.39), residues: 194
  sheet: -0.71 (0.26), residues: 396
  loop : -1.12 (0.19), residues: 1092

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 834 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.018   0.001   PHE B 703 
 TYR   0.023   0.001   TYR C  16 
 ARG   0.002   0.000   ARG B 759 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  317)
  hydrogen bonds       : angle       5.76653 (  798)
  SS BOND              : bond        0.00227 (   42)
  SS BOND              : angle       1.40759 (   84)
  covalent geometry    : bond        0.00291 (14164)
  covalent geometry    : angle       0.60183 (19186)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 3.525 
Fit side-chains
REVERT: A  454 ARG cc_start: 0.7760 (tpt-90) cc_final: 0.7086 (ptt90)
REVERT: B  454 ARG cc_start: 0.7854 (tpt-90) cc_final: 0.7131 (ptt90)
REVERT: B  794 ASP cc_start: 0.7779 (t70) cc_final: 0.7358 (t70)
REVERT: B  893 LEU cc_start: 0.9528 (mt) cc_final: 0.9306 (mp)
REVERT: E   14 TYR cc_start: 0.7936 (m-80) cc_final: 0.7670 (m-80)
REVERT: F   14 TYR cc_start: 0.7957 (m-80) cc_final: 0.7666 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 98
  average time/residue: 0.3008
  time to fit residues: 48.4038
Evaluate side-chains
  95 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 1.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  710 TYR
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  867 HIS
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  562 THR
Chi-restraints excluded: chain B residue  845 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain E residue    6 CYS
Chi-restraints excluded: chain F residue    6 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 154 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 122 optimal weight:    1.9990
   chunk 158 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 HIS ** 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 = 0.3751 r_free = 0.3751 target = 0.089503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.065729 restraints weight = 42739.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 3.64
r_work: 0.3120 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14206  Z= 0.119
  Angle     :  0.597  11.483  19270  Z= 0.303
  Chirality :  0.045   0.164   2076
  Planarity :  0.004   0.060   2480
  Dihedral  :  4.887  19.607   1870
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 16.26 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.21), residues: 1682
  helix:  0.57 (0.39), residues: 194
  sheet: -0.68 (0.26), residues: 396
  loop : -1.10 (0.20), residues: 1092

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 834 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.019   0.001   PHE B 703 
 TYR   0.016   0.001   TYR B 507 
 ARG   0.004   0.000   ARG B  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  317)
  hydrogen bonds       : angle       5.67434 (  798)
  SS BOND              : bond        0.00217 (   42)
  SS BOND              : angle       1.27026 (   84)
  covalent geometry    : bond        0.00287 (14164)
  covalent geometry    : angle       0.59264 (19186)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7708.10 seconds
wall clock time: 137 minutes 17.82 seconds (8237.82 seconds total)