Starting phenix.real_space_refine
on Sun Jul 27 20:38:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vzb_32224/07_2025/7vzb_32224_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vzb_32224/07_2025/7vzb_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_32224/07_2025/7vzb_32224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vzb_32224/07_2025/7vzb_32224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vzb_32224/07_2025/7vzb_32224_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vzb_32224/07_2025/7vzb_32224_neut.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.22, per 1000 atoms: 0.65
  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: 2.35
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.10
  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: 2.83

  Time building geometry restraints manager: 2.83 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: 0.04
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:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.300
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.740
-------------------------------------------------------------------------------
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 : 14.30
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (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
 TRP   0.014   0.001   TRP A 524 
 HIS   0.006   0.001   HIS A 669 
 PHE   0.051   0.002   PHE B 295 
 TYR   0.033   0.002   TYR B 181 
 ARG   0.009   0.001   ARG A 401 

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

*********************** 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  : 1.036 
Fit side-chains
REVERT: A  186 MET cc_start: 0.6216 (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: 0.5850 (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: 0.2200
  time to fit residues: 31.8155
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  : 1.043 
-------------------------------------------------------------------------------
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 97 optimal weight:   40.0000
   chunk 87 optimal weight:   10.0000
   chunk 48 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:   40.0000
   chunk 67 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.4330 r_free = 0.4330 target = 0.200763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.131812 restraints weight = 12578.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.124274 restraints weight = 15946.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.126538 restraints weight = 14692.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9736  Z= 0.201
  Angle     :  0.741   8.608  13202  Z= 0.365
  Chirality :  0.046   0.325   1470
  Planarity :  0.004   0.059   1648
  Dihedral  : 14.445 128.757   1622
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  9.98 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.25), residues: 1162
  helix: -0.58 (0.20), residues: 742
  sheet: -1.29 (0.55), residues: 82
  loop : -1.54 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 242 
 HIS   0.006   0.001   HIS B 667 
 PHE   0.029   0.002   PHE B 295 
 TYR   0.021   0.002   TYR A 181 
 ARG   0.003   0.000   ARG A 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05853 (  491)
  hydrogen bonds       : angle       5.06200 ( 1449)
  covalent geometry    : bond        0.00473 ( 9736)
  covalent geometry    : angle       0.74082 (13202)

*********************** 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
  105 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 1.053 
Fit side-chains
REVERT: A  138 LEU cc_start: 0.8968 (pt) cc_final: 0.8657 (pt)
REVERT: A  186 MET cc_start: 0.6088 (tmm) cc_final: 0.5471 (tmm)
REVERT: A  191 ARG cc_start: 0.7928 (mmp-170) cc_final: 0.7570 (mmp-170)
REVERT: A  406 TYR cc_start: 0.8427 (t80) cc_final: 0.7789 (t80)
REVERT: A  586 HIS cc_start: 0.7893 (t70) cc_final: 0.7614 (t-90)
REVERT: B  186 MET cc_start: 0.6052 (tmm) cc_final: 0.5461 (tmm)
REVERT: B  406 TYR cc_start: 0.8457 (t80) cc_final: 0.7817 (t80)
REVERT: B  586 HIS cc_start: 0.7899 (t70) cc_final: 0.7619 (t-90)
  outliers start: 9
  outliers final: 5
  residues processed: 100
  average time/residue: 0.2088
  time to fit residues: 29.9621
Evaluate side-chains
  98 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
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 115 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 54 optimal weight:   20.0000
   chunk 63 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.9180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.203442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.134648 restraints weight = 12735.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.126750 restraints weight = 15960.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.129441 restraints weight = 13927.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1707

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= 0.134
  Angle     :  0.638   8.018  13202  Z= 0.313
  Chirality :  0.042   0.320   1470
  Planarity :  0.004   0.055   1648
  Dihedral  : 13.328 129.629   1614
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.95 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.25), residues: 1162
  helix: -0.23 (0.20), residues: 740
  sheet: -1.23 (0.55), residues: 82
  loop : -1.42 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.008   0.001   HIS A 587 
 PHE   0.015   0.001   PHE A 295 
 TYR   0.018   0.002   TYR A 181 
 ARG   0.002   0.000   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04878 (  491)
  hydrogen bonds       : angle       4.48639 ( 1449)
  covalent geometry    : bond        0.00298 ( 9736)
  covalent geometry    : angle       0.63781 (13202)

*********************** 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
  131 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.8656 (tt) cc_final: 0.8349 (tp)
REVERT: A  138 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8621 (pt)
REVERT: A  191 ARG cc_start: 0.7943 (mmp-170) cc_final: 0.7693 (mmp-170)
REVERT: A  295 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7810 (m-10)
REVERT: A  406 TYR cc_start: 0.8484 (t80) cc_final: 0.7939 (t80)
REVERT: B   76 LEU cc_start: 0.8701 (tt) cc_final: 0.8403 (tp)
REVERT: B  138 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8642 (pt)
REVERT: B  295 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7773 (m-10)
REVERT: B  406 TYR cc_start: 0.8397 (t80) cc_final: 0.7853 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 115
  average time/residue: 0.2045
  time to fit residues: 34.0763
Evaluate side-chains
  117 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  284 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  587 HIS
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  284 SER
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 69 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 113 optimal weight:   30.0000
   chunk 109 optimal weight:   20.0000
   chunk 2 optimal weight:    0.7980
   chunk 52 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 584 HIS
B 586 HIS
B 621 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.203747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.135865 restraints weight = 12608.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.131372 restraints weight = 14160.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.132772 restraints weight = 15023.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1910

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= 0.137
  Angle     :  0.633   7.668  13202  Z= 0.309
  Chirality :  0.042   0.306   1470
  Planarity :  0.004   0.050   1648
  Dihedral  : 12.909 129.415   1614
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.50 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.25), residues: 1162
  helix: -0.10 (0.20), residues: 738
  sheet: -1.10 (0.57), residues: 82
  loop : -1.37 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.006   0.001   HIS A 299 
 PHE   0.013   0.001   PHE A 295 
 TYR   0.024   0.001   TYR A 181 
 ARG   0.002   0.000   ARG B 612 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04612 (  491)
  hydrogen bonds       : angle       4.32220 ( 1449)
  covalent geometry    : bond        0.00313 ( 9736)
  covalent geometry    : angle       0.63327 (13202)

*********************** 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
  128 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A  138 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8499 (pt)
REVERT: A  191 ARG cc_start: 0.7964 (mmp-170) cc_final: 0.7731 (mmp-170)
REVERT: A  295 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7829 (m-10)
REVERT: A  321 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8305 (mp)
REVERT: A  346 MET cc_start: 0.8260 (mtp) cc_final: 0.8052 (mtm)
REVERT: A  406 TYR cc_start: 0.8386 (t80) cc_final: 0.7925 (t80)
REVERT: B  138 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8518 (pt)
REVERT: B  186 MET cc_start: 0.6106 (tmm) cc_final: 0.5461 (tmm)
REVERT: B  295 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7828 (m-10)
REVERT: B  321 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8316 (mp)
REVERT: B  406 TYR cc_start: 0.8368 (t80) cc_final: 0.7902 (t80)
  outliers start: 25
  outliers final: 14
  residues processed: 115
  average time/residue: 0.2058
  time to fit residues: 34.8009
Evaluate side-chains
  123 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
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  138 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  321 LEU
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  138 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  321 LEU
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 109 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0030
   chunk 69 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 587 HIS
A 621 HIS
B 584 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 587 HIS
B 621 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.205791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.137806 restraints weight = 12681.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.130086 restraints weight = 14391.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.132037 restraints weight = 14997.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9736  Z= 0.114
  Angle     :  0.602   8.882  13202  Z= 0.290
  Chirality :  0.041   0.271   1470
  Planarity :  0.003   0.046   1648
  Dihedral  : 12.223 129.946   1614
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.72 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.26), residues: 1162
  helix:  0.05 (0.20), residues: 738
  sheet: -0.91 (0.58), residues: 82
  loop : -1.29 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 326 
 HIS   0.007   0.001   HIS B 299 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.028   0.001   TYR B 181 
 ARG   0.001   0.000   ARG A 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  491)
  hydrogen bonds       : angle       4.03675 ( 1449)
  covalent geometry    : bond        0.00248 ( 9736)
  covalent geometry    : angle       0.60188 (13202)

*********************** 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
  135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 1.063 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.8711 (tt) cc_final: 0.8445 (tp)
REVERT: A  138 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8493 (pt)
REVERT: A  191 ARG cc_start: 0.8065 (mmp-170) cc_final: 0.7863 (mmp-170)
REVERT: A  199 GLU cc_start: 0.7895 (tp30) cc_final: 0.7510 (tp30)
REVERT: A  295 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7844 (m-10)
REVERT: A  321 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8184 (mp)
REVERT: A  406 TYR cc_start: 0.8179 (t80) cc_final: 0.7807 (t80)
REVERT: B   76 LEU cc_start: 0.8702 (tt) cc_final: 0.8437 (tp)
REVERT: B  138 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8511 (pt)
REVERT: B  186 MET cc_start: 0.5920 (tmm) cc_final: 0.5307 (tmm)
REVERT: B  295 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7841 (m-10)
REVERT: B  321 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8186 (mp)
REVERT: B  392 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8162 (tt)
REVERT: B  406 TYR cc_start: 0.8152 (t80) cc_final: 0.7437 (t80)
  outliers start: 30
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1951
  time to fit residues: 33.8381
Evaluate side-chains
  126 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
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  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  305 LEU
Chi-restraints excluded: chain A residue  321 LEU
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  114 LEU
Chi-restraints excluded: chain B residue  138 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  305 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  587 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 28 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0040
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   chunk 6 optimal weight:    4.9990
   chunk 55 optimal weight:   30.0000
   chunk 87 optimal weight:    0.0770
   chunk 89 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.6552

-------------------------------------------------------------------------------
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
B 584 HIS
B 586 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.205886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138709 restraints weight = 12695.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.130095 restraints weight = 14903.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.132562 restraints weight = 14603.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9736  Z= 0.114
  Angle     :  0.592   8.545  13202  Z= 0.285
  Chirality :  0.040   0.249   1470
  Planarity :  0.003   0.043   1648
  Dihedral  : 11.880 130.142   1614
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.14 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.26), residues: 1162
  helix:  0.12 (0.20), residues: 740
  sheet: -0.87 (0.58), residues: 82
  loop : -1.19 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 326 
 HIS   0.007   0.001   HIS A 299 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.015   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  491)
  hydrogen bonds       : angle       3.93412 ( 1449)
  covalent geometry    : bond        0.00253 ( 9736)
  covalent geometry    : angle       0.59227 (13202)

*********************** 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
  135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.8716 (tt) cc_final: 0.8470 (tp)
REVERT: A  114 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8283 (tp)
REVERT: A  138 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (pt)
REVERT: A  191 ARG cc_start: 0.8048 (mmp-170) cc_final: 0.7848 (mmp-170)
REVERT: A  199 GLU cc_start: 0.7941 (tp30) cc_final: 0.7484 (tp30)
REVERT: A  295 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7947 (m-10)
REVERT: A  321 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8191 (mp)
REVERT: A  392 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8027 (tt)
REVERT: A  406 TYR cc_start: 0.8103 (t80) cc_final: 0.7762 (t80)
REVERT: A  625 TYR cc_start: 0.7035 (m-80) cc_final: 0.6827 (t80)
REVERT: B   76 LEU cc_start: 0.8709 (tt) cc_final: 0.8464 (tp)
REVERT: B  114 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8260 (tp)
REVERT: B  138 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8505 (pt)
REVERT: B  186 MET cc_start: 0.5938 (tmm) cc_final: 0.5378 (tmm)
REVERT: B  199 GLU cc_start: 0.8022 (tp30) cc_final: 0.7573 (tp30)
REVERT: B  295 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7944 (m-10)
REVERT: B  321 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: B  392 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8119 (tt)
REVERT: B  406 TYR cc_start: 0.8065 (t80) cc_final: 0.7664 (t80)
  outliers start: 26
  outliers final: 14
  residues processed: 124
  average time/residue: 0.1956
  time to fit residues: 35.6066
Evaluate side-chains
  128 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
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  183 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  392 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  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  305 LEU
Chi-restraints excluded: chain B residue  321 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 60 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 114 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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
B 584 HIS
B 586 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.203545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.134032 restraints weight = 12781.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.126011 restraints weight = 14816.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.128338 restraints weight = 14738.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9736  Z= 0.165
  Angle     :  0.640  10.623  13202  Z= 0.309
  Chirality :  0.043   0.231   1470
  Planarity :  0.003   0.042   1648
  Dihedral  : 12.025 129.449   1614
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.57 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.26), residues: 1162
  helix:  0.10 (0.20), residues: 740
  sheet: -0.89 (0.52), residues: 94
  loop : -1.14 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 HIS   0.007   0.001   HIS A 299 
 PHE   0.010   0.001   PHE B 295 
 TYR   0.018   0.001   TYR A 181 
 ARG   0.002   0.000   ARG A 612 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04496 (  491)
  hydrogen bonds       : angle       4.12219 ( 1449)
  covalent geometry    : bond        0.00396 ( 9736)
  covalent geometry    : angle       0.63983 (13202)

*********************** 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
  140 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8533 (pt)
REVERT: A  295 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7924 (m-10)
REVERT: A  321 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8391 (mp)
REVERT: A  392 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: A  406 TYR cc_start: 0.8204 (t80) cc_final: 0.7495 (t80)
REVERT: B  138 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8485 (pt)
REVERT: B  186 MET cc_start: 0.5938 (tmm) cc_final: 0.5428 (tmm)
REVERT: B  199 GLU cc_start: 0.7994 (tp30) cc_final: 0.7678 (tp30)
REVERT: B  295 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7927 (m-10)
REVERT: B  321 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8389 (mp)
REVERT: B  392 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8294 (tt)
REVERT: B  406 TYR cc_start: 0.8175 (t80) cc_final: 0.7734 (t80)
  outliers start: 31
  outliers final: 20
  residues processed: 126
  average time/residue: 0.2065
  time to fit residues: 37.9218
Evaluate side-chains
  140 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  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  321 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  392 LEU
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  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  321 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 95 optimal weight:   20.0000
   chunk 111 optimal weight:    6.9990
   chunk 101 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.205214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135553 restraints weight = 12810.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.129994 restraints weight = 14310.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.131633 restraints weight = 14697.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9736  Z= 0.144
  Angle     :  0.636   9.694  13202  Z= 0.305
  Chirality :  0.042   0.204   1470
  Planarity :  0.004   0.086   1648
  Dihedral  : 11.988 129.573   1614
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.08 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.26), residues: 1162
  helix:  0.15 (0.20), residues: 740
  sheet: -0.80 (0.52), residues: 94
  loop : -1.11 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 132 
 HIS   0.008   0.001   HIS B 299 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.022   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04311 (  491)
  hydrogen bonds       : angle       4.04886 ( 1449)
  covalent geometry    : bond        0.00340 ( 9736)
  covalent geometry    : angle       0.63615 (13202)

*********************** 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
  140 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8493 (pt)
REVERT: A  295 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7908 (m-10)
REVERT: A  321 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8387 (mp)
REVERT: A  392 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8137 (tt)
REVERT: A  406 TYR cc_start: 0.8142 (t80) cc_final: 0.7449 (t80)
REVERT: B  138 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8561 (pt)
REVERT: B  186 MET cc_start: 0.6054 (tmm) cc_final: 0.5533 (tmm)
REVERT: B  199 GLU cc_start: 0.7998 (tp30) cc_final: 0.7708 (tp30)
REVERT: B  295 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7897 (m-10)
REVERT: B  321 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8354 (mp)
REVERT: B  392 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8301 (tt)
REVERT: B  406 TYR cc_start: 0.8111 (t80) cc_final: 0.7702 (t80)
REVERT: B  625 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6751 (t80)
  outliers start: 32
  outliers final: 18
  residues processed: 126
  average time/residue: 0.1940
  time to fit residues: 35.8777
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  : 0.996 
-------------------------------------------------------------------------------
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  295 PHE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  392 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  295 PHE
Chi-restraints excluded: chain B residue  321 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
Chi-restraints excluded: chain B residue  625 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 108 optimal weight:   20.0000
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.205235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.136242 restraints weight = 12716.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.129450 restraints weight = 14524.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.131016 restraints weight = 15866.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9736  Z= 0.148
  Angle     :  0.650   9.511  13202  Z= 0.312
  Chirality :  0.041   0.184   1470
  Planarity :  0.004   0.076   1648
  Dihedral  : 11.973 129.435   1614
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.38 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1162
  helix:  0.15 (0.20), residues: 740
  sheet: -0.94 (0.54), residues: 76
  loop : -1.23 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 HIS   0.008   0.001   HIS A 299 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.026   0.002   TYR B 181 
 ARG   0.006   0.000   ARG B 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04310 (  491)
  hydrogen bonds       : angle       4.02585 ( 1449)
  covalent geometry    : bond        0.00347 ( 9736)
  covalent geometry    : angle       0.65050 (13202)

*********************** 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
  141 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  138 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8550 (pt)
REVERT: A  295 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7957 (m-10)
REVERT: A  321 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (mp)
REVERT: A  392 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8134 (tt)
REVERT: A  406 TYR cc_start: 0.8144 (t80) cc_final: 0.7733 (t80)
REVERT: A  625 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6677 (t80)
REVERT: B   76 LEU cc_start: 0.8739 (tt) cc_final: 0.8497 (tp)
REVERT: B  138 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (pt)
REVERT: B  180 TYR cc_start: 0.8564 (p90) cc_final: 0.7704 (p90)
REVERT: B  186 MET cc_start: 0.5885 (tmm) cc_final: 0.5403 (tmm)
REVERT: B  199 GLU cc_start: 0.8002 (tp30) cc_final: 0.7712 (tp30)
REVERT: B  295 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7874 (m-10)
REVERT: B  321 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: B  392 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8293 (tt)
REVERT: B  406 TYR cc_start: 0.8119 (t80) cc_final: 0.7713 (t80)
  outliers start: 32
  outliers final: 17
  residues processed: 130
  average time/residue: 0.1797
  time to fit residues: 34.9023
Evaluate side-chains
  135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
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  220 LEU
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  321 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  625 TYR
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  295 PHE
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 72 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.205867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.136758 restraints weight = 12443.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.130951 restraints weight = 13808.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.132599 restraints weight = 14200.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9736  Z= 0.131
  Angle     :  0.645   9.521  13202  Z= 0.311
  Chirality :  0.041   0.172   1470
  Planarity :  0.004   0.082   1648
  Dihedral  : 11.924 129.670   1614
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.79 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.26), residues: 1162
  helix:  0.27 (0.20), residues: 726
  sheet: -0.87 (0.55), residues: 76
  loop : -1.04 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 132 
 HIS   0.008   0.001   HIS A 299 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.024   0.001   TYR B 181 
 ARG   0.002   0.000   ARG B 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04220 (  491)
  hydrogen bonds       : angle       3.98987 ( 1449)
  covalent geometry    : bond        0.00305 ( 9736)
  covalent geometry    : angle       0.64540 (13202)

********************** 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: 29
    poor density    : 108
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.8744 (tt) cc_final: 0.8501 (tp)
REVERT: A  138 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (pt)
REVERT: A  180 TYR cc_start: 0.8542 (p90) cc_final: 0.7690 (p90)
REVERT: A  186 MET cc_start: 0.5971 (tmm) cc_final: 0.5438 (tmm)
REVERT: A  295 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7852 (m-10)
REVERT: A  321 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8335 (mp)
REVERT: A  392 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8102 (tt)
REVERT: A  406 TYR cc_start: 0.8085 (t80) cc_final: 0.7697 (t80)
REVERT: A  501 MET cc_start: 0.4423 (OUTLIER) cc_final: 0.4193 (tpt)
REVERT: A  609 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7270 (pm20)
REVERT: B   76 LEU cc_start: 0.8729 (tt) cc_final: 0.8483 (tp)
REVERT: B  138 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8517 (pt)
REVERT: B  180 TYR cc_start: 0.8526 (p90) cc_final: 0.7692 (p90)
REVERT: B  186 MET cc_start: 0.5971 (tmm) cc_final: 0.5506 (tmm)
REVERT: B  199 GLU cc_start: 0.8042 (tp30) cc_final: 0.7735 (tp30)
REVERT: B  295 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7856 (m-10)
REVERT: B  321 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: B  392 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8251 (tt)
REVERT: B  406 TYR cc_start: 0.8056 (t80) cc_final: 0.7670 (t80)
REVERT: B  501 MET cc_start: 0.4367 (mpp) cc_final: 0.3707 (mpp)
REVERT: B  609 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7312 (pm20)
  outliers start: 29
  outliers final: 17
  residues processed: 127
  average time/residue: 0.1920
  time to fit residues: 35.7943
Evaluate side-chains
  135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  295 PHE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  501 MET
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  295 PHE
Chi-restraints excluded: chain B residue  321 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 88 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 41 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 26 optimal weight:    0.6980
   chunk 112 optimal weight:    4.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.4359 r_free = 0.4359 target = 0.203884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.134040 restraints weight = 12608.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.127750 restraints weight = 14623.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.128941 restraints weight = 14461.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9736  Z= 0.170
  Angle     :  0.670  10.146  13202  Z= 0.324
  Chirality :  0.043   0.167   1470
  Planarity :  0.004   0.076   1648
  Dihedral  : 12.053 128.623   1614
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.49 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1162
  helix:  0.21 (0.20), residues: 726
  sheet: -0.81 (0.55), residues: 76
  loop : -1.04 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 132 
 HIS   0.007   0.001   HIS B 299 
 PHE   0.010   0.001   PHE A 130 
 TYR   0.020   0.002   TYR B 181 
 ARG   0.003   0.000   ARG B 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04533 (  491)
  hydrogen bonds       : angle       4.07038 ( 1449)
  covalent geometry    : bond        0.00407 ( 9736)
  covalent geometry    : angle       0.66994 (13202)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2825.26 seconds
wall clock time: 49 minutes 59.92 seconds (2999.92 seconds total)