Starting phenix.real_space_refine
on Thu Mar  5 02:25:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7syd_25522/03_2026/7syd_25522.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7syd_25522/03_2026/7syd_25522.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7syd_25522/03_2026/7syd_25522.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7syd_25522/03_2026/7syd_25522.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7syd_25522/03_2026/7syd_25522.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7syd_25522/03_2026/7syd_25522.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.038
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 10192 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     134      5.16       5
     C    6316      2.51       5
     N    1810      2.21       5
     O    1956      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10216
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4723
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 614, 4723
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 30, 'TRANS': 583}
    Chain: "C"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 385
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "B"
      Number of atoms: 4723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4723
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 30, 'TRANS': 583}
    Chain: "D"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 385
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
  Time building chain proxies: 2.53, per 1000 atoms: 0.25
  Number of scatterers: 10216
  At special positions: 0
  Unit cell: (82.0344, 141.401, 126.29, 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     134     16.00
     O    1956      8.00
     N    1810      7.00
     C    6316      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=56, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 170 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 199 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 195 " - 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 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 227 " - pdb=" SG  CYS A 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 271 " - pdb=" SG  CYS A 283 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 287 " - pdb=" SG  CYS A 302 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 305 " - pdb=" SG  CYS A 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 446 " - pdb=" SG  CYS A 475 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 482 " - pdb=" SG  CYS A 491 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 486 " - pdb=" SG  CYS A 499 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 502 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 534 " - pdb=" SG  CYS A 547 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 555 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 558 " - pdb=" SG  CYS A 567 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 571 " - pdb=" SG  CYS A 593 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 604 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 600 " - pdb=" SG  CYS A 612 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  20 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  14 " - pdb=" SG  CYS C  31 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C  42 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B   7 " - pdb=" SG  CYS B  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 166 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 170 " - pdb=" SG  CYS B 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 191 " - pdb=" SG  CYS B 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 195 " - 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 224 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 227 " - pdb=" SG  CYS B 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 240 " - pdb=" SG  CYS B 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 271 " - pdb=" SG  CYS B 283 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 287 " - pdb=" SG  CYS B 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 305 " - pdb=" SG  CYS B 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 446 " - pdb=" SG  CYS B 475 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 482 " - pdb=" SG  CYS B 491 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 499 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 502 " - pdb=" SG  CYS B 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 534 " - pdb=" SG  CYS B 547 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 555 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 558 " - pdb=" SG  CYS B 567 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 571 " - pdb=" SG  CYS B 593 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 604 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 600 " - pdb=" SG  CYS B 612 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D   6 " - pdb=" SG  CYS D  20 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  14 " - pdb=" SG  CYS D  31 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  33 " - pdb=" SG  CYS D  42 " distance=2.02

  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: 0.80
  Conformation dependent library (CDL) restraints added in 400.3 milliseconds
  

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2428

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 29 sheets defined
      13.2% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 31
      removed outlier: 3.513A  pdb=" N   LEU A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 91
      removed outlier: 4.140A  pdb=" N   ASN A  91 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 88 through 91'
    Processing helix  chain 'A' and resid 145 through 149
      removed outlier: 3.526A  pdb=" N   LEU A 149 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 174
    Processing helix  chain 'A' and resid 220 through 224
      removed outlier: 4.106A  pdb=" N   CYS A 224 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 322
      removed outlier: 3.527A  pdb=" N   LYS A 322 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 336
      removed outlier: 3.619A  pdb=" N   LYS A 336 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 3.523A  pdb=" N   ASP A 369 " --> pdb=" O   GLN A 366 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 370 " --> pdb=" O   GLU A 367 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   THR A 373 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 410
      removed outlier: 3.773A  pdb=" N   GLY A 410 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 407 through 410'
    Processing helix  chain 'A' and resid 471 through 477
      removed outlier: 3.787A  pdb=" N   LYS A 476 " --> pdb=" O   GLU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 499
      removed outlier: 3.860A  pdb=" N   CYS A 499 " --> pdb=" O   PRO A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 555
      removed outlier: 4.257A  pdb=" N   ASN A 554 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   CYS A 555 " --> pdb=" O   PRO A 552 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 551 through 555'
    Processing helix  chain 'C' and resid 7 through 11
    Processing helix  chain 'B' and resid 19 through 32
    Processing helix  chain 'B' and resid 52 through 57
      removed outlier: 3.544A  pdb=" N   LYS B  56 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   THR B  57 " --> pdb=" O   PHE B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 91
      removed outlier: 4.204A  pdb=" N   ASN B  91 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 91'
    Processing helix  chain 'B' and resid 170 through 174
      removed outlier: 3.512A  pdb=" N   GLY B 173 " --> pdb=" O   CYS B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 336
    Processing helix  chain 'B' and resid 348 through 354
      removed outlier: 4.261A  pdb=" N   PHE B 352 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 374
      removed outlier: 3.823A  pdb=" N   ASP B 369 " --> pdb=" O   GLN B 366 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   THR B 373 " --> pdb=" O   ILE B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 397
      removed outlier: 3.637A  pdb=" N   GLU B 397 " --> pdb=" O   HIS B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 410
    Processing helix  chain 'B' and resid 452 through 457
      removed outlier: 4.121A  pdb=" N   LEU B 456 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 478
      removed outlier: 3.729A  pdb=" N   THR B 478 " --> pdb=" O   SER B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 555
      removed outlier: 3.802A  pdb=" N   CYS B 555 " --> pdb=" O   PRO B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 581
      removed outlier: 3.947A  pdb=" N   ASN B 580 " --> pdb=" O   GLY B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 612
      removed outlier: 3.656A  pdb=" N   GLY B 611 " --> pdb=" O   PRO B 607 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   CYS B 612 " --> pdb=" O   GLY B 608 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 607 through 612'
    Processing helix  chain 'D' and resid 7 through 11
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44
      removed outlier: 5.627A  pdb=" N   ALA A 123 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A  95 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL A 124 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83
    Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 247
      removed outlier: 3.734A  pdb=" N   GLN A 252 " --> pdb=" O   ASN A 247 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 263
    Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277
    Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 296
    Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.730A  pdb=" N   CYS A 313 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 347
      removed outlier: 6.120A  pdb=" N   LEU A 345 " --> pdb=" O   LEU A 382 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   PHE A 412 " --> pdb=" O   ASP A 436 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   ILE A 438 " --> pdb=" O   PHE A 412 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   LEU A 414 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   SER A 440 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   VAL A 416 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 377
    Processing sheet with id=AB2, first strand: chain 'A' and resid 505 through 507
    Processing sheet with id=AB3, first strand: chain 'A' and resid 524 through 527
      removed outlier: 3.651A  pdb=" N   GLU A 527 " --> pdb=" O   GLU A 530 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AB5, first strand: chain 'C' and resid 19 through 23
      removed outlier: 3.571A  pdb=" N   VAL C  19 " --> pdb=" O   ASN C  32 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 37 through 38
    Processing sheet with id=AB7, first strand: chain 'B' and resid 6 through 7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 16 through 17
      removed outlier: 3.504A  pdb=" N   LYS D  28 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL D  19 " --> pdb=" O   ASN D  32 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 41 through 44
      removed outlier: 6.381A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   ALA B  68 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ILE B  43 " --> pdb=" O   ALA B  68 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   ALA B 123 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU B  95 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL B 124 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 230 through 231
    Processing sheet with id=AC2, first strand: chain 'B' and resid 244 through 247
      removed outlier: 3.653A  pdb=" N   GLN B 252 " --> pdb=" O   ASN B 247 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 261 through 263
    Processing sheet with id=AC4, first strand: chain 'B' and resid 283 through 284
      removed outlier: 3.534A  pdb=" N   VAL B 277 " --> pdb=" O   ARG B 300 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   CYS B 302 " --> pdb=" O   VAL B 277 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS B 301 " --> pdb=" O   MET B 294 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 347
      removed outlier: 6.204A  pdb=" N   LEU B 345 " --> pdb=" O   LEU B 382 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   PHE B 412 " --> pdb=" O   ASP B 436 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   ILE B 438 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   LEU B 414 " --> pdb=" O   ILE B 438 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   SER B 440 " --> pdb=" O   LEU B 414 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL B 416 " --> pdb=" O   SER B 440 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL B 437 " --> pdb=" O   LYS B 465 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 376 through 377
    Processing sheet with id=AC7, first strand: chain 'B' and resid 505 through 506
      removed outlier: 3.573A  pdb=" N   VAL B 505 " --> pdb=" O   VAL B 512 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 524 through 527
      removed outlier: 3.530A  pdb=" N   GLU B 527 " --> pdb=" O   GLU B 530 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 561 through 563
    Processing sheet with id=AD1, first strand: chain 'B' and resid 585 through 587
    Processing sheet with id=AD2, first strand: chain 'D' and resid 37 through 38

    155 hydrogen bonds defined for protein.
    300 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.67

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3094
        1.33 -     1.45: 1748
        1.45 -     1.58: 5424
        1.58 -     1.70: 0
        1.70 -     1.82: 156
  Bond restraints: 10422
  Sorted by residual:
  bond pdb=" N   CYS B 571 "
       pdb=" CA  CYS B 571 "
    ideal  model  delta    sigma   weight residual
    1.454  1.497 -0.043 1.14e-02 7.69e+03 1.43e+01
  bond pdb=" N   LEU B 595 "
       pdb=" CA  LEU B 595 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.25e-02 6.40e+03 9.88e+00
  bond pdb=" N   THR A 601 "
       pdb=" CA  THR A 601 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.26e-02 6.30e+03 9.32e+00
  bond pdb=" N   CYS B 183 "
       pdb=" CA  CYS B 183 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 1.29e-02 6.01e+03 8.96e+00
  bond pdb=" N   CYS B 558 "
       pdb=" CA  CYS B 558 "
    ideal  model  delta    sigma   weight residual
    1.453  1.492 -0.039 1.31e-02 5.83e+03 8.90e+00
  ... (remaining 10417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 13635
        1.97 -     3.95: 417
        3.95 -     5.92: 41
        5.92 -     7.90: 6
        7.90 -     9.87: 1
  Bond angle restraints: 14100
  Sorted by residual:
  angle pdb=" N   ILE B 556 "
        pdb=" CA  ILE B 556 "
        pdb=" C   ILE B 556 "
      ideal   model   delta    sigma   weight residual
     110.53  106.22    4.31 9.40e-01 1.13e+00 2.10e+01
  angle pdb=" C   ASN B 182 "
        pdb=" N   CYS B 183 "
        pdb=" CA  CYS B 183 "
      ideal   model   delta    sigma   weight residual
     122.59  115.47    7.12 1.57e+00 4.06e-01 2.06e+01
  angle pdb=" N   PRO A 613 "
        pdb=" CA  PRO A 613 "
        pdb=" CB  PRO A 613 "
      ideal   model   delta    sigma   weight residual
     103.25   98.49    4.76 1.05e+00 9.07e-01 2.06e+01
  angle pdb=" C   CYS B 596 "
        pdb=" CA  CYS B 596 "
        pdb=" CB  CYS B 596 "
      ideal   model   delta    sigma   weight residual
     111.71  101.84    9.87 2.23e+00 2.01e-01 1.96e+01
  angle pdb=" N   VAL B 526 "
        pdb=" CA  VAL B 526 "
        pdb=" C   VAL B 526 "
      ideal   model   delta    sigma   weight residual
     107.75  114.15   -6.40 1.46e+00 4.69e-01 1.92e+01
  ... (remaining 14095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 5761
       17.82 -    35.64: 575
       35.64 -    53.46: 99
       53.46 -    71.28: 31
       71.28 -    89.09: 14
  Dihedral angle restraints: 6480
    sinusoidal: 2692
      harmonic: 3788
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 163 "
           pdb=" CB  CYS A 163 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.68  -81.68     1      1.00e+01 1.00e-02 8.21e+01
  dihedral pdb=" CB  CYS C   6 "
           pdb=" SG  CYS C   6 "
           pdb=" SG  CYS C  20 "
           pdb=" CB  CYS C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.16  -75.16     1      1.00e+01 1.00e-02 7.14e+01
  dihedral pdb=" CB  CYS A 558 "
           pdb=" SG  CYS A 558 "
           pdb=" SG  CYS A 567 "
           pdb=" CB  CYS A 567 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.51   67.51     1      1.00e+01 1.00e-02 5.93e+01
  ... (remaining 6477 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1206
       0.063 -    0.127: 296
       0.127 -    0.190: 24
       0.190 -    0.253: 6
       0.253 -    0.316: 2
  Chirality restraints: 1534
  Sorted by residual:
  chirality pdb=" CA  CYS B 596 "
            pdb=" N   CYS B 596 "
            pdb=" C   CYS B 596 "
            pdb=" CB  CYS B 596 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CA  THR B 614 "
            pdb=" N   THR B 614 "
            pdb=" C   THR B 614 "
            pdb=" CB  THR B 614 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.83   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  CYS B 555 "
            pdb=" N   CYS B 555 "
            pdb=" C   CYS B 555 "
            pdb=" CB  CYS B 555 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 1531 not shown)

  Planarity restraints: 1864
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 169 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   SER B 169 "    0.053 2.00e-02 2.50e+03
        pdb=" O   SER B 169 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   CYS B 170 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 515 "   -0.011 2.00e-02 2.50e+03   2.34e-02 5.46e+00
        pdb=" C   CYS A 515 "    0.040 2.00e-02 2.50e+03
        pdb=" O   CYS A 515 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN A 516 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 521 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.83e+00
        pdb=" N   PRO B 522 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 522 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 522 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1861 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 110
        2.63 -     3.20: 9182
        3.20 -     3.77: 14227
        3.77 -     4.33: 21466
        4.33 -     4.90: 35992
  Nonbonded interactions: 80977
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  10 "
            pdb=" OE1 GLU A  42 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" OG1 THR B  10 "
            pdb=" OE1 GLU B  42 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" OD2 ASP B 167 "
            pdb=" OG  SER B 169 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   CYS B  34 "
            pdb=" OG1 THR B  57 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OE2 GLU A 376 "
            pdb=" NH1 ARG A 403 "
     model   vdw
     2.231 3.120
  ... (remaining 80972 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 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:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.370
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
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      :  0.007   0.046  10478  Z= 0.359
  Angle     :  0.812  11.340  14212  Z= 0.499
  Chirality :  0.054   0.316   1534
  Planarity :  0.004   0.042   1864
  Dihedral  : 14.223  89.095   3884
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.43 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  7.45 %
    Favored  : 90.55 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.66 (0.20), residues: 1314
  helix: -4.33 (0.32), residues: 67
  sheet: -3.00 (0.34), residues: 168
  loop : -2.43 (0.16), residues: 1079

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  29 
 TYR   0.013   0.002   TYR B  64 
 PHE   0.015   0.002   PHE B 380 
 TRP   0.013   0.002   TRP C  50 
 HIS   0.005   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00724 (10422)
  covalent geometry    : angle       0.78678 (14100)
  SS BOND              : bond        0.00782 (   56)
  SS BOND              : angle       2.41255 (  112)
  hydrogen bonds       : bond        0.29774 (  155)
  hydrogen bonds       : angle       9.43728 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
  outliers start: 23
  outliers final: 7
  residues processed: 93
  average time/residue: 0.1148
  time to fit residues: 14.7226
Evaluate side-chains
  52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  502 CYS
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  600 CYS
Chi-restraints excluded: chain A residue  601 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain B residue  596 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 129 optimal weight:    0.2980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A 232 ASN
A 384 GLN
A 480 GLN
A 544 ASN
A 557 GLN
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 ASN
B 134 ASN
B 398 ASN
B 480 GLN
B 594 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.060737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.041151 restraints weight = 38275.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 4.01
r_work: 0.2580 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10478  Z= 0.116
  Angle     :  0.577   8.109  14212  Z= 0.302
  Chirality :  0.046   0.191   1534
  Planarity :  0.004   0.040   1864
  Dihedral  :  5.215  49.325   1429
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.97 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.21), residues: 1314
  helix: -3.18 (0.47), residues: 74
  sheet: -2.38 (0.37), residues: 161
  loop : -1.66 (0.18), residues: 1079

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 273 
 TYR   0.024   0.001   TYR B 561 
 PHE   0.007   0.001   PHE B 380 
 TRP   0.022   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 594 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10422)
  covalent geometry    : angle       0.57411 (14100)
  SS BOND              : bond        0.00322 (   56)
  SS BOND              : angle       0.90117 (  112)
  hydrogen bonds       : bond        0.03973 (  155)
  hydrogen bonds       : angle       6.11138 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9601 (tpt) cc_final: 0.9202 (tpp)
REVERT: A  253 MET cc_start: 0.9472 (mmm) cc_final: 0.9005 (mmm)
REVERT: A  376 GLU cc_start: 0.9139 (pt0) cc_final: 0.8832 (pt0)
REVERT: A  528 ASN cc_start: 0.9027 (t0) cc_final: 0.8813 (t0)
REVERT: A  561 TYR cc_start: 0.9188 (m-80) cc_final: 0.8730 (t80)
REVERT: C   46 ASP cc_start: 0.9162 (t0) cc_final: 0.8910 (t0)
REVERT: B  244 MET cc_start: 0.9451 (mtp) cc_final: 0.8642 (mmm)
REVERT: B  523 ARG cc_start: 0.8976 (mmt-90) cc_final: 0.8396 (mmm160)
REVERT: B  543 MET cc_start: 0.8404 (ttt) cc_final: 0.8186 (ttp)
  outliers start: 13
  outliers final: 4
  residues processed: 65
  average time/residue: 0.0749
  time to fit residues: 7.9082
Evaluate side-chains
  53 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  502 CYS
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue  562 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 110 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 106 optimal weight:    0.2980
   chunk 75 optimal weight:    5.9990
   chunk 114 optimal weight:    4.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
A 452 ASN
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 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 = 0.3287 r_free = 0.3287 target = 0.058621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.039447 restraints weight = 38887.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2678 rms_B_bonded: 3.92
r_work: 0.2521 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2522 r_free = 0.2522    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2522 r_free = 0.2522    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10478  Z= 0.232
  Angle     :  0.588   7.065  14212  Z= 0.306
  Chirality :  0.046   0.151   1534
  Planarity :  0.004   0.040   1864
  Dihedral  :  4.945  23.362   1425
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.27 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.22), residues: 1314
  helix: -2.71 (0.51), residues: 80
  sheet: -2.15 (0.39), residues: 167
  loop : -1.28 (0.19), residues: 1067

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 273 
 TYR   0.014   0.001   TYR B 561 
 PHE   0.008   0.001   PHE A 380 
 TRP   0.019   0.002   TRP A 584 
 HIS   0.006   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (10422)
  covalent geometry    : angle       0.58301 (14100)
  SS BOND              : bond        0.00373 (   56)
  SS BOND              : angle       1.00853 (  112)
  hydrogen bonds       : bond        0.03866 (  155)
  hydrogen bonds       : angle       5.57189 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 MET cc_start: 0.9465 (mmm) cc_final: 0.8758 (mmm)
REVERT: A  528 ASN cc_start: 0.9126 (t0) cc_final: 0.8906 (t0)
REVERT: A  561 TYR cc_start: 0.9190 (m-80) cc_final: 0.8688 (t80)
REVERT: C   46 ASP cc_start: 0.9327 (t0) cc_final: 0.9075 (t0)
REVERT: B  244 MET cc_start: 0.9602 (mtp) cc_final: 0.8915 (mmm)
REVERT: B  253 MET cc_start: 0.9129 (mmm) cc_final: 0.8691 (mmm)
  outliers start: 14
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0781
  time to fit residues: 7.6143
Evaluate side-chains
  53 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  562 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 110 optimal weight:    0.0870
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 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 = 0.3282 r_free = 0.3282 target = 0.058345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.039116 restraints weight = 39055.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.2678 rms_B_bonded: 3.96
r_work: 0.2516 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2514
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2514 r_free = 0.2514    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2514 r_free = 0.2514    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2514
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10478  Z= 0.206
  Angle     :  0.560   6.344  14212  Z= 0.293
  Chirality :  0.046   0.149   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.778  23.133   1424
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.65 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.22), residues: 1314
  helix: -2.35 (0.53), residues: 81
  sheet: -2.10 (0.38), residues: 171
  loop : -1.05 (0.19), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 273 
 TYR   0.012   0.001   TYR B 447 
 PHE   0.007   0.001   PHE B 380 
 TRP   0.015   0.002   TRP A 584 
 HIS   0.005   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (10422)
  covalent geometry    : angle       0.55679 (14100)
  SS BOND              : bond        0.00341 (   56)
  SS BOND              : angle       0.91321 (  112)
  hydrogen bonds       : bond        0.03397 (  155)
  hydrogen bonds       : angle       5.30517 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9756 (tpp) cc_final: 0.9419 (tpp)
REVERT: A  253 MET cc_start: 0.9442 (mmm) cc_final: 0.8642 (mmm)
REVERT: A  376 GLU cc_start: 0.9196 (pt0) cc_final: 0.8983 (pt0)
REVERT: A  528 ASN cc_start: 0.9197 (t0) cc_final: 0.8961 (t0)
REVERT: A  561 TYR cc_start: 0.9211 (m-80) cc_final: 0.8713 (t80)
REVERT: C   46 ASP cc_start: 0.9392 (t0) cc_final: 0.9088 (t0)
REVERT: B  160 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8570 (mt)
REVERT: B  244 MET cc_start: 0.9656 (mtp) cc_final: 0.9053 (mmm)
REVERT: B  253 MET cc_start: 0.9244 (mmm) cc_final: 0.8593 (mmm)
REVERT: B  523 ARG cc_start: 0.8954 (mmt-90) cc_final: 0.8600 (mmt-90)
  outliers start: 18
  outliers final: 11
  residues processed: 64
  average time/residue: 0.0815
  time to fit residues: 8.5150
Evaluate side-chains
  56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  601 THR
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  562 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 90 optimal weight:    0.0980
   chunk 18 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 120 optimal weight:    0.0770
   chunk 24 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 124 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0040
   chunk 44 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.3550

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 232 ASN
A 252 GLN
A 384 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.059632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.040361 restraints weight = 38857.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 4.02
r_work: 0.2568 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10478  Z= 0.081
  Angle     :  0.494   6.740  14212  Z= 0.259
  Chirality :  0.044   0.149   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.326  20.786   1424
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 13.60 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.23), residues: 1314
  helix: -2.03 (0.56), residues: 82
  sheet: -1.89 (0.40), residues: 166
  loop : -0.82 (0.19), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 550 
 TYR   0.009   0.001   TYR B 447 
 PHE   0.007   0.001   PHE A 525 
 TRP   0.015   0.001   TRP B 584 
 HIS   0.003   0.001   HIS B 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 (10422)
  covalent geometry    : angle       0.49224 (14100)
  SS BOND              : bond        0.00186 (   56)
  SS BOND              : angle       0.68367 (  112)
  hydrogen bonds       : bond        0.02545 (  155)
  hydrogen bonds       : angle       4.95299 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9764 (tpp) cc_final: 0.9404 (tpp)
REVERT: A  253 MET cc_start: 0.9469 (mmm) cc_final: 0.8661 (mmm)
REVERT: A  376 GLU cc_start: 0.9206 (pt0) cc_final: 0.8947 (pt0)
REVERT: A  528 ASN cc_start: 0.9233 (t0) cc_final: 0.8997 (t0)
REVERT: A  561 TYR cc_start: 0.9245 (m-80) cc_final: 0.8718 (t80)
REVERT: C   46 ASP cc_start: 0.9350 (t0) cc_final: 0.8955 (t0)
REVERT: B  160 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8496 (mt)
REVERT: B  244 MET cc_start: 0.9552 (mtp) cc_final: 0.9009 (mmm)
REVERT: B  253 MET cc_start: 0.9265 (mmm) cc_final: 0.8615 (mmm)
REVERT: D   21 MET cc_start: 0.8774 (ptp) cc_final: 0.8486 (ptp)
  outliers start: 16
  outliers final: 8
  residues processed: 67
  average time/residue: 0.0795
  time to fit residues: 8.5457
Evaluate side-chains
  58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  601 THR
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  562 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 113 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 ASN
** B 535 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 = 0.3292 r_free = 0.3292 target = 0.058706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.039512 restraints weight = 39249.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.2695 rms_B_bonded: 3.99
r_work: 0.2541 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2540 r_free = 0.2540    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2540 r_free = 0.2540    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10478  Z= 0.161
  Angle     :  0.522   7.496  14212  Z= 0.272
  Chirality :  0.045   0.146   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.407  21.828   1424
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 14.30 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.23), residues: 1314
  helix: -1.84 (0.56), residues: 82
  sheet: -1.81 (0.40), residues: 166
  loop : -0.72 (0.19), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 523 
 TYR   0.009   0.001   TYR B 447 
 PHE   0.007   0.001   PHE A 380 
 TRP   0.020   0.001   TRP A 584 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (10422)
  covalent geometry    : angle       0.51921 (14100)
  SS BOND              : bond        0.00281 (   56)
  SS BOND              : angle       0.82049 (  112)
  hydrogen bonds       : bond        0.02955 (  155)
  hydrogen bonds       : angle       4.97225 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9777 (tpp) cc_final: 0.9411 (tpp)
REVERT: A  253 MET cc_start: 0.9454 (mmm) cc_final: 0.8584 (mmm)
REVERT: A  376 GLU cc_start: 0.9217 (pt0) cc_final: 0.8995 (pt0)
REVERT: A  528 ASN cc_start: 0.9239 (t0) cc_final: 0.9002 (t0)
REVERT: A  561 TYR cc_start: 0.9253 (m-80) cc_final: 0.8738 (t80)
REVERT: C   46 ASP cc_start: 0.9365 (t0) cc_final: 0.8954 (t0)
REVERT: B  160 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8502 (mt)
REVERT: B  244 MET cc_start: 0.9620 (mtp) cc_final: 0.9057 (mmm)
REVERT: B  253 MET cc_start: 0.9303 (mmm) cc_final: 0.8635 (mmm)
REVERT: D   21 MET cc_start: 0.8806 (ptp) cc_final: 0.8538 (ptp)
  outliers start: 14
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0782
  time to fit residues: 7.6348
Evaluate side-chains
  58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  523 ARG
Chi-restraints excluded: chain B residue  562 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 114 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0670
   chunk 49 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.8920

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 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 = 0.3310 r_free = 0.3310 target = 0.059269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.040233 restraints weight = 38898.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 3.95
r_work: 0.2558 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10478  Z= 0.107
  Angle     :  0.501   7.991  14212  Z= 0.261
  Chirality :  0.044   0.149   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.276  20.502   1424
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.90 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.23), residues: 1314
  helix: -1.71 (0.57), residues: 82
  sheet: -1.74 (0.40), residues: 166
  loop : -0.61 (0.19), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.010   0.001   TYR B 447 
 PHE   0.007   0.001   PHE A 380 
 TRP   0.020   0.001   TRP A 584 
 HIS   0.003   0.000   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10422)
  covalent geometry    : angle       0.49912 (14100)
  SS BOND              : bond        0.00202 (   56)
  SS BOND              : angle       0.68119 (  112)
  hydrogen bonds       : bond        0.02696 (  155)
  hydrogen bonds       : angle       4.87198 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9769 (tpp) cc_final: 0.9397 (tpp)
REVERT: A  253 MET cc_start: 0.9449 (mmm) cc_final: 0.8528 (mmm)
REVERT: A  376 GLU cc_start: 0.9229 (pt0) cc_final: 0.8920 (pt0)
REVERT: A  528 ASN cc_start: 0.9260 (t0) cc_final: 0.9019 (t0)
REVERT: A  561 TYR cc_start: 0.9239 (m-80) cc_final: 0.8701 (t80)
REVERT: C   46 ASP cc_start: 0.9346 (t0) cc_final: 0.8889 (t0)
REVERT: B  244 MET cc_start: 0.9614 (mtp) cc_final: 0.9051 (mmm)
REVERT: B  253 MET cc_start: 0.9319 (mmm) cc_final: 0.8616 (mmm)
REVERT: D   21 MET cc_start: 0.8789 (ptp) cc_final: 0.8537 (ptp)
  outliers start: 16
  outliers final: 13
  residues processed: 61
  average time/residue: 0.0777
  time to fit residues: 7.7728
Evaluate side-chains
  61 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  152 MET
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  523 ARG
Chi-restraints excluded: chain B residue  562 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 56 optimal weight:    9.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 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 = 0.3304 r_free = 0.3304 target = 0.059025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.039856 restraints weight = 39070.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.2707 rms_B_bonded: 4.00
r_work: 0.2547 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10478  Z= 0.135
  Angle     :  0.515   9.015  14212  Z= 0.267
  Chirality :  0.044   0.148   1534
  Planarity :  0.003   0.042   1864
  Dihedral  :  4.294  20.655   1424
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.47 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.23), residues: 1314
  helix: -1.63 (0.58), residues: 82
  sheet: -1.69 (0.40), residues: 166
  loop : -0.55 (0.19), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 550 
 TYR   0.009   0.001   TYR B 447 
 PHE   0.007   0.001   PHE A 380 
 TRP   0.022   0.001   TRP A 584 
 HIS   0.003   0.000   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10422)
  covalent geometry    : angle       0.51291 (14100)
  SS BOND              : bond        0.00241 (   56)
  SS BOND              : angle       0.72976 (  112)
  hydrogen bonds       : bond        0.02821 (  155)
  hydrogen bonds       : angle       4.85984 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9767 (tpp) cc_final: 0.9382 (tpp)
REVERT: A  253 MET cc_start: 0.9418 (mmm) cc_final: 0.8428 (mmm)
REVERT: A  376 GLU cc_start: 0.9258 (pt0) cc_final: 0.9022 (pt0)
REVERT: A  528 ASN cc_start: 0.9289 (t0) cc_final: 0.9049 (t0)
REVERT: A  561 TYR cc_start: 0.9251 (m-80) cc_final: 0.8728 (t80)
REVERT: C   46 ASP cc_start: 0.9358 (t0) cc_final: 0.8894 (t0)
REVERT: B  244 MET cc_start: 0.9648 (mtp) cc_final: 0.9042 (mmm)
REVERT: B  253 MET cc_start: 0.9317 (mmm) cc_final: 0.8623 (mmm)
REVERT: D   21 MET cc_start: 0.8758 (ptp) cc_final: 0.8519 (ptp)
  outliers start: 21
  outliers final: 15
  residues processed: 64
  average time/residue: 0.0768
  time to fit residues: 8.0308
Evaluate side-chains
  63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  152 MET
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  523 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 112 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 120 optimal weight:    5.9990
   chunk 114 optimal weight:    0.4980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 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 = 0.3306 r_free = 0.3306 target = 0.059139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.039894 restraints weight = 38967.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 3.97
r_work: 0.2557 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10478  Z= 0.116
  Angle     :  0.514   9.349  14212  Z= 0.265
  Chirality :  0.044   0.148   1534
  Planarity :  0.003   0.045   1864
  Dihedral  :  4.210  20.317   1422
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 15.25 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.23), residues: 1314
  helix: -1.57 (0.58), residues: 82
  sheet: -1.64 (0.40), residues: 166
  loop : -0.51 (0.19), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 300 
 TYR   0.009   0.001   TYR B 447 
 PHE   0.007   0.001   PHE A 380 
 TRP   0.023   0.001   TRP A 584 
 HIS   0.003   0.000   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10422)
  covalent geometry    : angle       0.51205 (14100)
  SS BOND              : bond        0.00213 (   56)
  SS BOND              : angle       0.67734 (  112)
  hydrogen bonds       : bond        0.02672 (  155)
  hydrogen bonds       : angle       4.77909 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9782 (tpp) cc_final: 0.9414 (tpp)
REVERT: A  253 MET cc_start: 0.9439 (mmm) cc_final: 0.8466 (mmm)
REVERT: A  376 GLU cc_start: 0.9245 (pt0) cc_final: 0.9018 (pt0)
REVERT: A  528 ASN cc_start: 0.9276 (t0) cc_final: 0.9028 (t0)
REVERT: A  561 TYR cc_start: 0.9278 (m-80) cc_final: 0.8757 (t80)
REVERT: C   46 ASP cc_start: 0.9345 (t0) cc_final: 0.8875 (t0)
REVERT: B  244 MET cc_start: 0.9615 (mtp) cc_final: 0.9059 (mmm)
REVERT: B  253 MET cc_start: 0.9335 (mmm) cc_final: 0.8718 (mmm)
REVERT: B  543 MET cc_start: 0.9008 (ttt) cc_final: 0.8557 (tmm)
REVERT: B  584 TRP cc_start: 0.7328 (m-90) cc_final: 0.6414 (m-90)
REVERT: D   21 MET cc_start: 0.8736 (ptp) cc_final: 0.8504 (ptp)
  outliers start: 15
  outliers final: 14
  residues processed: 59
  average time/residue: 0.0824
  time to fit residues: 7.7186
Evaluate side-chains
  62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  152 MET
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  523 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 59 optimal weight:   20.0000
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0170
   chunk 58 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    2.4026

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 GLN
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  16 HIS
B 444 ASN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.058108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.038568 restraints weight = 39322.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2671 rms_B_bonded: 4.04
r_work: 0.2512 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2515
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2515 r_free = 0.2515    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2515 r_free = 0.2515    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2515
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  10478  Z= 0.244
  Angle     :  0.587   9.135  14212  Z= 0.303
  Chirality :  0.046   0.144   1534
  Planarity :  0.003   0.044   1864
  Dihedral  :  4.542  23.277   1422
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 15.16 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.23), residues: 1314
  helix: -1.60 (0.58), residues: 82
  sheet: -1.63 (0.38), residues: 182
  loop : -0.55 (0.19), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 550 
 TYR   0.011   0.001   TYR B 447 
 PHE   0.007   0.001   PHE A 380 
 TRP   0.025   0.002   TRP A 584 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 (10422)
  covalent geometry    : angle       0.58337 (14100)
  SS BOND              : bond        0.00375 (   56)
  SS BOND              : angle       0.96818 (  112)
  hydrogen bonds       : bond        0.03309 (  155)
  hydrogen bonds       : angle       5.03889 (  300)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.9775 (tpp) cc_final: 0.9380 (tpp)
REVERT: A  253 MET cc_start: 0.9439 (mmm) cc_final: 0.8454 (mmm)
REVERT: A  528 ASN cc_start: 0.9311 (t0) cc_final: 0.9071 (t0)
REVERT: A  561 TYR cc_start: 0.9258 (m-80) cc_final: 0.8777 (t80)
REVERT: C   46 ASP cc_start: 0.9444 (t0) cc_final: 0.9034 (t0)
REVERT: B  244 MET cc_start: 0.9679 (mtp) cc_final: 0.9073 (mmm)
REVERT: B  253 MET cc_start: 0.9308 (mmm) cc_final: 0.8555 (mmm)
REVERT: B  584 TRP cc_start: 0.7335 (m-90) cc_final: 0.6463 (m-90)
REVERT: D   21 MET cc_start: 0.8739 (ptp) cc_final: 0.8501 (ptp)
  outliers start: 15
  outliers final: 12
  residues processed: 59
  average time/residue: 0.0759
  time to fit residues: 7.2699
Evaluate side-chains
  58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  523 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 99 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 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 = 0.3289 r_free = 0.3289 target = 0.058578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.039356 restraints weight = 38417.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.2694 rms_B_bonded: 3.96
r_work: 0.2535 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10478  Z= 0.158
  Angle     :  0.539   9.085  14212  Z= 0.279
  Chirality :  0.045   0.147   1534
  Planarity :  0.003   0.044   1864
  Dihedral  :  4.401  21.666   1422
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 15.60 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.23), residues: 1314
  helix: -1.57 (0.58), residues: 82
  sheet: -1.60 (0.39), residues: 180
  loop : -0.51 (0.19), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 550 
 TYR   0.010   0.001   TYR B 447 
 PHE   0.006   0.001   PHE A 380 
 TRP   0.024   0.001   TRP A 584 
 HIS   0.003   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10422)
  covalent geometry    : angle       0.53674 (14100)
  SS BOND              : bond        0.00274 (   56)
  SS BOND              : angle       0.80219 (  112)
  hydrogen bonds       : bond        0.02933 (  155)
  hydrogen bonds       : angle       4.93035 (  300)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2787.80 seconds
wall clock time: 48 minutes 44.65 seconds (2924.65 seconds total)