Starting phenix.real_space_refine
on Wed Feb  4 08:17:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vzb_32224/02_2026/7vzb_32224_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vzb_32224/02_2026/7vzb_32224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vzb_32224/02_2026/7vzb_32224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vzb_32224/02_2026/7vzb_32224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vzb_32224/02_2026/7vzb_32224_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vzb_32224/02_2026/7vzb_32224_neut.cif"
  }
  resolution = 3.59
  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=   0.006 sd=   0.087
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      44      5.16       5
     C    6124      2.51       5
     N    1638      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9524
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4656
          Classifications: {'peptide': 585}
          Link IDs: {'PTRANS': 20, 'TRANS': 564}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4656
          Classifications: {'peptide': 585}
          Link IDs: {'PTRANS': 20, 'TRANS': 564}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 106
          Unusual residues: {'FFI': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 106
          Unusual residues: {'FFI': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.30, per 1000 atoms: 0.24
  Number of scatterers: 9524
  At special positions: 0
  Unit cell: (88.81, 95.23, 145.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       6     15.00
     O    1712      8.00
     N    1638      7.00
     C    6124      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.87
  Conformation dependent library (CDL) restraints added in 453.9 milliseconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2188

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 8 sheets defined
      65.8% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 80
      removed outlier: 4.067A  pdb=" N   TRP A  77 " --> pdb=" O   GLN A  73 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU A  78 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 108
      removed outlier: 3.730A  pdb=" N   SER A 108 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 124
      removed outlier: 3.657A  pdb=" N   VAL A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 140
      removed outlier: 3.581A  pdb=" N   GLY A 131 " --> pdb=" O   PRO A 127 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TRP A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 175
      removed outlier: 4.187A  pdb=" N   ASN A 148 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ARG A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ARG A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 192 through 200
      removed outlier: 3.573A  pdb=" N   SER A 196 " --> pdb=" O   ASN A 192 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP A 200 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 217
      removed outlier: 3.623A  pdb=" N   ALA A 205 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 206 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   SER A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ASN A 214 " --> pdb=" O   HIS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 236
      removed outlier: 4.171A  pdb=" N   ALA A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   LEU A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 261
      removed outlier: 4.199A  pdb=" N   THR A 254 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 289
      removed outlier: 3.566A  pdb=" N   ALA A 270 " --> pdb=" O   GLY A 266 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 275 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ASN A 289 " --> pdb=" O   ARG A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 296
      removed outlier: 3.670A  pdb=" N   ILE A 293 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   TYR A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 314
    Processing helix  chain 'A' and resid 319 through 332
      removed outlier: 4.249A  pdb=" N   LEU A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   TRP A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   MET A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU A 330 " --> pdb=" O   TRP A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 347
      removed outlier: 4.321A  pdb=" N   LEU A 345 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 353
      removed outlier: 3.733A  pdb=" N   ILE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 426
      removed outlier: 3.907A  pdb=" N   SER A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA A 394 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ALA A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER A 405 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LYS A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLU A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   THR A 410 " --> pdb=" O   TYR A 406 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU A 411 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   GLY A 414 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A 415 " --> pdb=" O   GLU A 411 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A 426 " --> pdb=" O   MET A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 521
      removed outlier: 3.621A  pdb=" N   LEU A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A 517 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 558
    Processing helix  chain 'A' and resid 562 through 569
      removed outlier: 3.503A  pdb=" N   ARG A 568 " --> pdb=" O   GLU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 583
      removed outlier: 3.911A  pdb=" N   GLU A 577 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 590
      removed outlier: 4.279A  pdb=" N   LEU A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLN A 590 " --> pdb=" O   HIS A 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 585 through 590'
    Processing helix  chain 'A' and resid 606 through 622
    Processing helix  chain 'A' and resid 636 through 650
      removed outlier: 3.518A  pdb=" N   GLU A 640 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY A 641 " --> pdb=" O   ILE A 637 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.816A  pdb=" N   LEU A 663 " --> pdb=" O   ARG A 660 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TRP A 664 " --> pdb=" O   PRO A 661 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS A 665 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   HIS A 667 " --> pdb=" O   TRP A 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 80
      removed outlier: 4.066A  pdb=" N   TRP B  77 " --> pdb=" O   GLN B  73 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU B  78 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 108
      removed outlier: 3.730A  pdb=" N   SER B 108 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 124
      removed outlier: 3.657A  pdb=" N   VAL B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 124 " --> pdb=" O   ARG B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 140
      removed outlier: 3.582A  pdb=" N   GLY B 131 " --> pdb=" O   PRO B 127 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TRP B 132 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN B 133 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 175
      removed outlier: 4.187A  pdb=" N   ASN B 148 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ARG B 152 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA B 159 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ARG B 172 " --> pdb=" O   ALA B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 192 through 200
      removed outlier: 3.572A  pdb=" N   SER B 196 " --> pdb=" O   ASN B 192 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP B 200 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 217
      removed outlier: 3.622A  pdb=" N   ALA B 205 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   SER B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN B 214 " --> pdb=" O   HIS B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 236
      removed outlier: 4.171A  pdb=" N   ALA B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   LEU B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 261
      removed outlier: 4.200A  pdb=" N   THR B 254 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ARG B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 289
      removed outlier: 3.565A  pdb=" N   ALA B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG B 275 " --> pdb=" O   GLU B 271 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ASN B 289 " --> pdb=" O   ARG B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 296
      removed outlier: 3.670A  pdb=" N   ILE B 293 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   TYR B 296 " --> pdb=" O   GLU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 314
    Processing helix  chain 'B' and resid 319 through 332
      removed outlier: 4.250A  pdb=" N   LEU B 325 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   TRP B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   MET B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU B 330 " --> pdb=" O   TRP B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 347
      removed outlier: 4.321A  pdb=" N   LEU B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 3.732A  pdb=" N   ILE B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 426
      removed outlier: 3.907A  pdb=" N   SER B 379 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU B 392 " --> pdb=" O   ALA B 388 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA B 394 " --> pdb=" O   ASN B 390 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ALA B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LYS B 407 " --> pdb=" O   MET B 403 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLU B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR B 410 " --> pdb=" O   TYR B 406 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU B 411 " --> pdb=" O   LYS B 407 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY B 414 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR B 415 " --> pdb=" O   GLU B 411 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE B 426 " --> pdb=" O   MET B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 521
      removed outlier: 3.622A  pdb=" N   LEU B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   PHE B 517 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 558
    Processing helix  chain 'B' and resid 562 through 569
      removed outlier: 3.504A  pdb=" N   ARG B 568 " --> pdb=" O   GLU B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 583
      removed outlier: 3.910A  pdb=" N   GLU B 577 " --> pdb=" O   GLU B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 590
      removed outlier: 4.279A  pdb=" N   LEU B 589 " --> pdb=" O   LEU B 585 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLN B 590 " --> pdb=" O   HIS B 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 585 through 590'
    Processing helix  chain 'B' and resid 606 through 622
    Processing helix  chain 'B' and resid 636 through 650
      removed outlier: 3.517A  pdb=" N   GLU B 640 " --> pdb=" O   SER B 636 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY B 641 " --> pdb=" O   ILE B 637 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 3.817A  pdb=" N   LEU B 663 " --> pdb=" O   ARG B 660 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TRP B 664 " --> pdb=" O   PRO B 661 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS B 665 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   HIS B 667 " --> pdb=" O   TRP B 664 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469
      removed outlier: 3.855A  pdb=" N   VAL A 530 " --> pdb=" O   GLU A 477 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE A 474 " --> pdb=" O   VAL A 497 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 482
      removed outlier: 7.623A  pdb=" N   ILE A 481 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 489 " --> pdb=" O   ILE A 481 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 506
    Processing sheet with id=AA4, first strand: chain 'A' and resid 625 through 628
    Processing sheet with id=AA5, first strand: chain 'B' and resid 466 through 469
      removed outlier: 3.854A  pdb=" N   VAL B 530 " --> pdb=" O   GLU B 477 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE B 474 " --> pdb=" O   VAL B 497 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 481 through 482
      removed outlier: 7.623A  pdb=" N   ILE B 481 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL B 489 " --> pdb=" O   ILE B 481 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 505 through 506
    Processing sheet with id=AA8, first strand: chain 'B' and resid 625 through 628

    491 hydrogen bonds defined for protein.
    1449 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: 1.30

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.12 -     1.27: 1510
        1.27 -     1.42: 2545
        1.42 -     1.56: 5579
        1.56 -     1.71: 26
        1.71 -     1.85: 76
  Bond restraints: 9736
  Sorted by residual:
  bond pdb=" C29 FFI A 802 "
       pdb=" C30 FFI A 802 "
    ideal  model  delta    sigma   weight residual
    1.548  1.246  0.302 2.00e-02 2.50e+03 2.28e+02
  bond pdb=" C29 FFI B 802 "
       pdb=" C30 FFI B 802 "
    ideal  model  delta    sigma   weight residual
    1.548  1.246  0.302 2.00e-02 2.50e+03 2.28e+02
  bond pdb=" C   LYS A 217 "
       pdb=" N   PRO A 218 "
    ideal  model  delta    sigma   weight residual
    1.334  1.489 -0.155 1.51e-02 4.39e+03 1.05e+02
  bond pdb=" C   LYS B 217 "
       pdb=" N   PRO B 218 "
    ideal  model  delta    sigma   weight residual
    1.334  1.489 -0.155 1.51e-02 4.39e+03 1.05e+02
  bond pdb=" C   LYS B 217 "
       pdb=" O   LYS B 217 "
    ideal  model  delta    sigma   weight residual
    1.244  1.155  0.089 1.00e-02 1.00e+04 7.87e+01
  ... (remaining 9731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.70: 12982
        3.70 -     7.40: 192
        7.40 -    11.09: 21
       11.09 -    14.79: 6
       14.79 -    18.49: 1
  Bond angle restraints: 13202
  Sorted by residual:
  angle pdb=" CA  LYS B 217 "
        pdb=" C   LYS B 217 "
        pdb=" N   PRO B 218 "
      ideal   model   delta    sigma   weight residual
     120.81  128.37   -7.56 8.60e-01 1.35e+00 7.73e+01
  angle pdb=" CG  ARG A 401 "
        pdb=" CD  ARG A 401 "
        pdb=" NE  ARG A 401 "
      ideal   model   delta    sigma   weight residual
     112.00   93.51   18.49 2.20e+00 2.07e-01 7.06e+01
  angle pdb=" C   LYS A 217 "
        pdb=" N   PRO A 218 "
        pdb=" CA  PRO A 218 "
      ideal   model   delta    sigma   weight residual
     119.32  128.78   -9.46 1.14e+00 7.69e-01 6.88e+01
  angle pdb=" C   LYS B 217 "
        pdb=" N   PRO B 218 "
        pdb=" CA  PRO B 218 "
      ideal   model   delta    sigma   weight residual
     119.32  128.77   -9.45 1.14e+00 7.69e-01 6.88e+01
  angle pdb=" N   LYS B 217 "
        pdb=" CA  LYS B 217 "
        pdb=" C   LYS B 217 "
      ideal   model   delta    sigma   weight residual
     112.35  102.42    9.93 1.34e+00 5.57e-01 5.49e+01
  ... (remaining 13197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.44: 5470
       24.44 -    48.87: 438
       48.87 -    73.31: 61
       73.31 -    97.74: 16
       97.74 -   122.18: 7
  Dihedral angle restraints: 5992
    sinusoidal: 2588
      harmonic: 3404
  Sorted by residual:
  dihedral pdb=" CA  CYS A 599 "
           pdb=" C   CYS A 599 "
           pdb=" N   ASP A 600 "
           pdb=" CA  ASP A 600 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.21   24.79     0      5.00e+00 4.00e-02 2.46e+01
  dihedral pdb=" CA  CYS B 599 "
           pdb=" C   CYS B 599 "
           pdb=" N   ASP B 600 "
           pdb=" CA  ASP B 600 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.26   24.74     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  ASN B 148 "
           pdb=" C   ASN B 148 "
           pdb=" N   SER B 149 "
           pdb=" CA  SER B 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.73   24.27     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 5989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1040
       0.053 -    0.106: 343
       0.106 -    0.159: 75
       0.159 -    0.212: 10
       0.212 -    0.265: 2
  Chirality restraints: 1470
  Sorted by residual:
  chirality pdb=" C30 FFI B 802 "
            pdb=" C29 FFI B 802 "
            pdb=" C32 FFI B 802 "
            pdb=" O7  FFI B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    2.44    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" C30 FFI A 802 "
            pdb=" C29 FFI A 802 "
            pdb=" C32 FFI A 802 "
            pdb=" O7  FFI A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    2.44    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CG  LEU B 523 "
            pdb=" CB  LEU B 523 "
            pdb=" CD1 LEU B 523 "
            pdb=" CD2 LEU B 523 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1467 not shown)

  Planarity restraints: 1648
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 401 "    0.019 2.00e-02 2.50e+03   4.09e-02 1.68e+01
        pdb=" C   ARG A 401 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   ARG A 401 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ILE A 402 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 400 "    0.018 2.00e-02 2.50e+03   3.62e-02 1.31e+01
        pdb=" C   GLU A 400 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   GLU A 400 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ARG A 401 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 295 "   -0.028 2.00e-02 2.50e+03   2.24e-02 8.78e+00
        pdb=" CG  PHE B 295 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 295 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 295 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 295 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 295 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 295 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1645 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 811
        2.72 -     3.26: 10037
        3.26 -     3.81: 15271
        3.81 -     4.35: 17897
        4.35 -     4.90: 29750
  Nonbonded interactions: 73766
  Sorted by model distance:
  nonbonded pdb=" O6  FFI B 802 "
            pdb=" O7  FFI B 802 "
     model   vdw
     2.175 2.432
  nonbonded pdb=" O6  FFI A 802 "
            pdb=" O7  FFI A 802 "
     model   vdw
     2.175 2.432
  nonbonded pdb=" O   TYR A 174 "
            pdb=" OG1 THR A 179 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   TYR B 174 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" NH1 ARG B 152 "
            pdb=" O10 FFI A 802 "
     model   vdw
     2.214 3.120
  ... (remaining 73761 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.980
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
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      :  0.013   0.302   9736  Z= 0.626
  Angle     :  1.104  18.489  13202  Z= 0.549
  Chirality :  0.054   0.265   1470
  Planarity :  0.005   0.059   1648
  Dihedral  : 17.822 122.179   3804
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.92 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.09 %
  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: -1.94 (0.24), residues: 1162
  helix: -1.09 (0.19), residues: 718
  sheet: -1.20 (0.65), residues: 64
  loop : -1.34 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 401 
 TYR   0.033   0.002   TYR B 181 
 PHE   0.051   0.002   PHE B 295 
 TRP   0.014   0.001   TRP A 524 
 HIS   0.006   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.01305 ( 9736)
  covalent geometry    : angle       1.10372 (13202)
  hydrogen bonds       : bond        0.19998 (  491)
  hydrogen bonds       : angle       6.70096 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  186 MET cc_start: 0.6215 (tmm) cc_final: 0.5871 (tmm)
REVERT: A  406 TYR cc_start: 0.8484 (t80) cc_final: 0.7743 (t80)
REVERT: B  186 MET cc_start: 0.6177 (tmm) cc_final: 0.5849 (tmm)
REVERT: B  406 TYR cc_start: 0.8494 (t80) cc_final: 0.7736 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 101
  average time/residue: 0.0949
  time to fit residues: 13.8700
Evaluate side-chains
  95 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 LYS
Chi-restraints excluded: chain B residue  217 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   40.0000
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:   40.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 587 HIS
A 611 GLN
A 621 HIS
B 587 HIS
B 611 GLN
B 621 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.201376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.132405 restraints weight = 12630.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.124932 restraints weight = 14910.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.127416 restraints weight = 14782.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.126641 restraints weight = 8570.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.128694 restraints weight = 7556.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9736  Z= 0.191
  Angle     :  0.732   8.772  13202  Z= 0.361
  Chirality :  0.046   0.303   1470
  Planarity :  0.004   0.058   1648
  Dihedral  : 14.214 130.411   1622
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.18 %
    Favored  : 88.90 %
  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: -1.46 (0.25), residues: 1162
  helix: -0.55 (0.20), residues: 740
  sheet: -1.28 (0.55), residues: 82
  loop : -1.50 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 554 
 TYR   0.022   0.002   TYR A 181 
 PHE   0.028   0.002   PHE A 295 
 TRP   0.009   0.001   TRP A 132 
 HIS   0.006   0.001   HIS B 667 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 9736)
  covalent geometry    : angle       0.73247 (13202)
  hydrogen bonds       : bond        0.05606 (  491)
  hydrogen bonds       : angle       4.97763 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  138 LEU cc_start: 0.8982 (pt) cc_final: 0.8666 (pt)
REVERT: A  199 GLU cc_start: 0.7953 (tp30) cc_final: 0.7746 (tp30)
REVERT: A  406 TYR cc_start: 0.8478 (t80) cc_final: 0.7870 (t80)
REVERT: A  586 HIS cc_start: 0.8028 (t70) cc_final: 0.7719 (t-90)
REVERT: B  138 LEU cc_start: 0.8969 (pt) cc_final: 0.8655 (pt)
REVERT: B  186 MET cc_start: 0.6093 (tmm) cc_final: 0.5503 (tmm)
REVERT: B  199 GLU cc_start: 0.7950 (tp30) cc_final: 0.7740 (tp30)
REVERT: B  406 TYR cc_start: 0.8494 (t80) cc_final: 0.7909 (t80)
REVERT: B  586 HIS cc_start: 0.7885 (t70) cc_final: 0.7596 (t-90)
  outliers start: 9
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0954
  time to fit residues: 13.8307
Evaluate side-chains
  97 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  587 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 621 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.202524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.133135 restraints weight = 12671.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.127783 restraints weight = 13656.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.129369 restraints weight = 14625.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.129520 restraints weight = 8582.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.130227 restraints weight = 7634.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9736  Z= 0.152
  Angle     :  0.655   8.027  13202  Z= 0.321
  Chirality :  0.043   0.317   1470
  Planarity :  0.004   0.057   1648
  Dihedral  : 13.432 129.271   1614
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.36 %
    Favored  : 84.01 %
  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: -1.12 (0.25), residues: 1162
  helix: -0.25 (0.20), residues: 740
  sheet: -1.21 (0.55), residues: 82
  loop : -1.45 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  69 
 TYR   0.018   0.002   TYR A 296 
 PHE   0.014   0.001   PHE A 295 
 TRP   0.008   0.001   TRP A 132 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9736)
  covalent geometry    : angle       0.65519 (13202)
  hydrogen bonds       : bond        0.05034 (  491)
  hydrogen bonds       : angle       4.54406 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.8692 (tt) cc_final: 0.8393 (tp)
REVERT: A  138 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8644 (pt)
REVERT: A  191 ARG cc_start: 0.7823 (mmp-170) cc_final: 0.7572 (mmp-170)
REVERT: A  295 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7791 (m-10)
REVERT: A  406 TYR cc_start: 0.8512 (t80) cc_final: 0.7981 (t80)
REVERT: A  586 HIS cc_start: 0.7938 (t70) cc_final: 0.7719 (t-90)
REVERT: B   76 LEU cc_start: 0.8732 (tt) cc_final: 0.8438 (tp)
REVERT: B  138 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (pt)
REVERT: B  191 ARG cc_start: 0.7866 (mmp-170) cc_final: 0.7589 (mmp-170)
REVERT: B  295 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7781 (m-10)
REVERT: B  406 TYR cc_start: 0.8434 (t80) cc_final: 0.7892 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0900
  time to fit residues: 14.2502
Evaluate side-chains
  110 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  587 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:   30.0000
   chunk 12 optimal weight:    0.6980
   chunk 108 optimal weight:    9.9990
   chunk 67 optimal weight:    0.7980
   chunk 113 optimal weight:   50.0000
   chunk 47 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
A 587 HIS
A 621 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 587 HIS
B 621 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.202471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132366 restraints weight = 12775.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.125230 restraints weight = 14393.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127140 restraints weight = 13351.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.126760 restraints weight = 8611.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.127082 restraints weight = 7087.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9736  Z= 0.156
  Angle     :  0.649   8.530  13202  Z= 0.317
  Chirality :  0.042   0.308   1470
  Planarity :  0.004   0.052   1648
  Dihedral  : 13.072 129.340   1614
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.60 %
    Favored  : 80.65 %
  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: -1.01 (0.25), residues: 1162
  helix: -0.15 (0.20), residues: 740
  sheet: -1.19 (0.56), residues: 82
  loop : -1.41 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  69 
 TYR   0.024   0.001   TYR A 181 
 PHE   0.013   0.001   PHE A 295 
 TRP   0.008   0.001   TRP A 132 
 HIS   0.006   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9736)
  covalent geometry    : angle       0.64943 (13202)
  hydrogen bonds       : bond        0.04797 (  491)
  hydrogen bonds       : angle       4.39737 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  138 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8627 (pt)
REVERT: A  158 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8445 (tp)
REVERT: A  191 ARG cc_start: 0.7892 (mmp-170) cc_final: 0.7627 (mmp-170)
REVERT: A  295 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7828 (m-10)
REVERT: A  406 TYR cc_start: 0.8486 (t80) cc_final: 0.7997 (t80)
REVERT: B  138 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8632 (pt)
REVERT: B  158 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8443 (tp)
REVERT: B  186 MET cc_start: 0.6097 (tmm) cc_final: 0.5476 (tmm)
REVERT: B  191 ARG cc_start: 0.7901 (mmp-170) cc_final: 0.7629 (mmp-170)
REVERT: B  295 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7816 (m-10)
REVERT: B  406 TYR cc_start: 0.8433 (t80) cc_final: 0.7950 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 113
  average time/residue: 0.0937
  time to fit residues: 15.4020
Evaluate side-chains
  120 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  587 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 621 HIS
B 586 HIS
B 621 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.201610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132017 restraints weight = 12739.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.125565 restraints weight = 14687.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.127577 restraints weight = 14521.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.127122 restraints weight = 8885.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.128797 restraints weight = 7772.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9736  Z= 0.202
  Angle     :  0.674   8.148  13202  Z= 0.329
  Chirality :  0.044   0.294   1470
  Planarity :  0.004   0.051   1648
  Dihedral  : 12.972 128.639   1614
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.23 %
    Favored  : 78.41 %
  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: -0.96 (0.25), residues: 1162
  helix: -0.11 (0.20), residues: 740
  sheet: -1.08 (0.57), residues: 82
  loop : -1.42 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.027   0.002   TYR A 181 
 PHE   0.013   0.001   PHE A 295 
 TRP   0.007   0.001   TRP B 132 
 HIS   0.013   0.002   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 9736)
  covalent geometry    : angle       0.67433 (13202)
  hydrogen bonds       : bond        0.04984 (  491)
  hydrogen bonds       : angle       4.39555 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  138 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8609 (pt)
REVERT: A  158 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8442 (tp)
REVERT: A  191 ARG cc_start: 0.7895 (mmp-170) cc_final: 0.7660 (mmp-170)
REVERT: A  295 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7806 (m-10)
REVERT: A  392 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8469 (tt)
REVERT: A  406 TYR cc_start: 0.8467 (t80) cc_final: 0.7987 (t80)
REVERT: A  615 MET cc_start: 0.9068 (mpp) cc_final: 0.8599 (mpp)
REVERT: B  138 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8644 (pt)
REVERT: B  158 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8440 (tp)
REVERT: B  191 ARG cc_start: 0.7880 (mmp-170) cc_final: 0.7636 (mmp-170)
REVERT: B  295 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7803 (m-10)
REVERT: B  392 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8408 (tt)
REVERT: B  406 TYR cc_start: 0.8445 (t80) cc_final: 0.7638 (t80)
REVERT: B  615 MET cc_start: 0.9068 (mpp) cc_final: 0.8593 (mpp)
  outliers start: 33
  outliers final: 18
  residues processed: 128
  average time/residue: 0.0812
  time to fit residues: 15.4279
Evaluate side-chains
  134 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS
B 586 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.204340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.136882 restraints weight = 12675.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.131255 restraints weight = 14912.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.132953 restraints weight = 14749.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132757 restraints weight = 8194.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.133562 restraints weight = 7381.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9736  Z= 0.121
  Angle     :  0.604   8.089  13202  Z= 0.293
  Chirality :  0.041   0.262   1470
  Planarity :  0.004   0.076   1648
  Dihedral  : 12.193 129.824   1614
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.65 %
    Favored  : 77.39 %
  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: -0.69 (0.26), residues: 1162
  helix:  0.09 (0.20), residues: 740
  sheet: -0.99 (0.57), residues: 82
  loop : -1.31 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  69 
 TYR   0.018   0.001   TYR B 181 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 326 
 HIS   0.007   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9736)
  covalent geometry    : angle       0.60362 (13202)
  hydrogen bonds       : bond        0.04296 (  491)
  hydrogen bonds       : angle       4.09349 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8548 (pt)
REVERT: A  295 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7861 (m-10)
REVERT: A  406 TYR cc_start: 0.8228 (t80) cc_final: 0.7846 (t80)
REVERT: B  138 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8545 (pt)
REVERT: B  295 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7855 (m-10)
REVERT: B  392 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (tt)
REVERT: B  406 TYR cc_start: 0.8206 (t80) cc_final: 0.7828 (t80)
  outliers start: 29
  outliers final: 21
  residues processed: 124
  average time/residue: 0.0895
  time to fit residues: 16.0989
Evaluate side-chains
  130 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  609 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 110 optimal weight:   30.0000
   chunk 99 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 61 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS
B 586 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.204139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134837 restraints weight = 12736.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.128660 restraints weight = 14475.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.129987 restraints weight = 14387.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130986 restraints weight = 8486.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.131313 restraints weight = 7437.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9736  Z= 0.145
  Angle     :  0.652  12.311  13202  Z= 0.311
  Chirality :  0.042   0.245   1470
  Planarity :  0.004   0.065   1648
  Dihedral  : 12.058 129.403   1614
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.57 %
    Favored  : 75.97 %
  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: -0.70 (0.26), residues: 1162
  helix:  0.07 (0.20), residues: 742
  sheet: -0.97 (0.56), residues: 82
  loop : -1.27 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  69 
 TYR   0.019   0.001   TYR A 181 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 132 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9736)
  covalent geometry    : angle       0.65210 (13202)
  hydrogen bonds       : bond        0.04438 (  491)
  hydrogen bonds       : angle       4.14953 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8498 (pt)
REVERT: A  295 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7871 (m-10)
REVERT: A  406 TYR cc_start: 0.8240 (t80) cc_final: 0.7876 (t80)
REVERT: B  138 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8491 (pt)
REVERT: B  199 GLU cc_start: 0.7792 (tp30) cc_final: 0.7427 (tp30)
REVERT: B  295 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7858 (m-10)
REVERT: B  392 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (tt)
REVERT: B  406 TYR cc_start: 0.8216 (t80) cc_final: 0.7495 (t80)
  outliers start: 34
  outliers final: 26
  residues processed: 126
  average time/residue: 0.0854
  time to fit residues: 15.6868
Evaluate side-chains
  140 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  609 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 30 optimal weight:    0.1980
   chunk 53 optimal weight:    8.9990
   chunk 109 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 115 optimal weight:    0.8980
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.205788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.136260 restraints weight = 12724.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.130168 restraints weight = 14751.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.132185 restraints weight = 15062.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.131792 restraints weight = 8675.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.133015 restraints weight = 7571.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9736  Z= 0.124
  Angle     :  0.628  10.140  13202  Z= 0.301
  Chirality :  0.041   0.210   1470
  Planarity :  0.004   0.078   1648
  Dihedral  : 11.911 129.859   1614
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.69 %
    Favored  : 75.36 %
  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: -0.61 (0.26), residues: 1162
  helix:  0.13 (0.20), residues: 742
  sheet: -0.89 (0.52), residues: 94
  loop : -1.25 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 496 
 TYR   0.022   0.001   TYR A 181 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.006   0.001   TRP B 326 
 HIS   0.007   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9736)
  covalent geometry    : angle       0.62787 (13202)
  hydrogen bonds       : bond        0.04187 (  491)
  hydrogen bonds       : angle       4.04486 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8315 (tp)
REVERT: A  138 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8548 (pt)
REVERT: A  186 MET cc_start: 0.6054 (tmm) cc_final: 0.5512 (tmm)
REVERT: A  406 TYR cc_start: 0.8149 (t80) cc_final: 0.7432 (t80)
REVERT: B  114 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8335 (tp)
REVERT: B  138 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8549 (pt)
REVERT: B  186 MET cc_start: 0.6008 (tmm) cc_final: 0.5529 (tmm)
REVERT: B  295 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7868 (m-10)
REVERT: B  392 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8268 (tt)
REVERT: B  406 TYR cc_start: 0.8104 (t80) cc_final: 0.7696 (t80)
  outliers start: 29
  outliers final: 21
  residues processed: 120
  average time/residue: 0.0834
  time to fit residues: 14.7104
Evaluate side-chains
  133 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  609 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 98 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0870
   chunk 7 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 56 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.205744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.134642 restraints weight = 12691.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.128427 restraints weight = 14855.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.130017 restraints weight = 12659.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.130063 restraints weight = 7724.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130178 restraints weight = 6831.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9736  Z= 0.130
  Angle     :  0.644   9.689  13202  Z= 0.307
  Chirality :  0.041   0.185   1470
  Planarity :  0.004   0.071   1648
  Dihedral  : 11.851 129.782   1614
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.40 %
    Favored  : 74.54 %
  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: -0.56 (0.26), residues: 1162
  helix:  0.14 (0.20), residues: 742
  sheet: -0.73 (0.53), residues: 94
  loop : -1.19 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 496 
 TYR   0.025   0.001   TYR A 181 
 PHE   0.009   0.001   PHE B 295 
 TRP   0.006   0.001   TRP A 132 
 HIS   0.007   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9736)
  covalent geometry    : angle       0.64378 (13202)
  hydrogen bonds       : bond        0.04146 (  491)
  hydrogen bonds       : angle       4.03625 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8238 (tp)
REVERT: A  138 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8515 (pt)
REVERT: A  186 MET cc_start: 0.5935 (tmm) cc_final: 0.5414 (tmm)
REVERT: A  406 TYR cc_start: 0.8117 (t80) cc_final: 0.7725 (t80)
REVERT: B   76 LEU cc_start: 0.8729 (tt) cc_final: 0.8482 (tp)
REVERT: B  114 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8335 (tp)
REVERT: B  138 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (pt)
REVERT: B  180 TYR cc_start: 0.8545 (p90) cc_final: 0.7683 (p90)
REVERT: B  186 MET cc_start: 0.5924 (tmm) cc_final: 0.5434 (tmm)
REVERT: B  392 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8202 (tt)
REVERT: B  406 TYR cc_start: 0.8079 (t80) cc_final: 0.7690 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 122
  average time/residue: 0.0733
  time to fit residues: 13.3751
Evaluate side-chains
  135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  609 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 65 optimal weight:    0.0870
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 112 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0970
   chunk 21 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 106 optimal weight:   20.0000
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.8158

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.206195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.136029 restraints weight = 12633.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.129003 restraints weight = 13589.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.130841 restraints weight = 13889.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.130757 restraints weight = 8500.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.131862 restraints weight = 7317.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9736  Z= 0.123
  Angle     :  0.650  10.541  13202  Z= 0.310
  Chirality :  0.040   0.170   1470
  Planarity :  0.004   0.083   1648
  Dihedral  : 11.774 130.028   1614
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.30 %
    Favored  : 74.85 %
  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: -0.41 (0.26), residues: 1162
  helix:  0.28 (0.20), residues: 726
  sheet: -0.95 (0.55), residues: 76
  loop : -1.04 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 612 
 TYR   0.026   0.001   TYR B 181 
 PHE   0.008   0.001   PHE B 295 
 TRP   0.006   0.001   TRP B 326 
 HIS   0.008   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9736)
  covalent geometry    : angle       0.64988 (13202)
  hydrogen bonds       : bond        0.04061 (  491)
  hydrogen bonds       : angle       3.97023 ( 1449)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.8732 (tt) cc_final: 0.8484 (tp)
REVERT: A  114 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8328 (tp)
REVERT: A  138 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8492 (pt)
REVERT: A  180 TYR cc_start: 0.8548 (p90) cc_final: 0.7678 (p90)
REVERT: A  186 MET cc_start: 0.5910 (tmm) cc_final: 0.5381 (tmm)
REVERT: A  406 TYR cc_start: 0.8038 (t80) cc_final: 0.7676 (t80)
REVERT: A  501 MET cc_start: 0.4650 (mpp) cc_final: 0.4101 (mpp)
REVERT: A  609 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7236 (pm20)
REVERT: B   76 LEU cc_start: 0.8720 (tt) cc_final: 0.8473 (tp)
REVERT: B  114 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8316 (tp)
REVERT: B  138 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8529 (pt)
REVERT: B  180 TYR cc_start: 0.8500 (p90) cc_final: 0.7648 (p90)
REVERT: B  186 MET cc_start: 0.5955 (tmm) cc_final: 0.5482 (tmm)
REVERT: B  392 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8228 (tt)
REVERT: B  406 TYR cc_start: 0.8003 (t80) cc_final: 0.7641 (t80)
REVERT: B  501 MET cc_start: 0.4628 (mpp) cc_final: 0.4181 (mpp)
REVERT: B  547 TYR cc_start: 0.7861 (t80) cc_final: 0.7508 (t80)
  outliers start: 28
  outliers final: 17
  residues processed: 126
  average time/residue: 0.0905
  time to fit residues: 16.5734
Evaluate side-chains
  130 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  295 PHE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  609 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0980
   chunk 42 optimal weight:    9.9990
   chunk 110 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 99 optimal weight:    9.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.205745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.137250 restraints weight = 12281.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.128037 restraints weight = 14373.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.130155 restraints weight = 12126.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.130645 restraints weight = 7344.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.131844 restraints weight = 6566.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9736  Z= 0.139
  Angle     :  0.655  10.241  13202  Z= 0.315
  Chirality :  0.041   0.162   1470
  Planarity :  0.004   0.074   1648
  Dihedral  : 11.799 129.415   1614
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.22 %
    Favored  : 74.44 %
  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: -0.35 (0.26), residues: 1162
  helix:  0.31 (0.20), residues: 728
  sheet: -0.82 (0.56), residues: 76
  loop : -0.99 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 189 
 TYR   0.026   0.001   TYR B 181 
 PHE   0.008   0.001   PHE A 295 
 TRP   0.006   0.001   TRP A 132 
 HIS   0.007   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9736)
  covalent geometry    : angle       0.65456 (13202)
  hydrogen bonds       : bond        0.04223 (  491)
  hydrogen bonds       : angle       3.97159 ( 1449)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1355.20 seconds
wall clock time: 24 minutes 9.37 seconds (1449.37 seconds total)