Starting phenix.real_space_refine
on Fri Jan 17 00:25:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r8u_19011/01_2025/8r8u_19011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r8u_19011/01_2025/8r8u_19011.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r8u_19011/01_2025/8r8u_19011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r8u_19011/01_2025/8r8u_19011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r8u_19011/01_2025/8r8u_19011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r8u_19011/01_2025/8r8u_19011.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.059
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
     Ca     10      9.91       5
     S      74      5.16       5
     C    6462      2.51       5
     N    1706      2.21       5
     O    1888      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10140
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 628, 4944
          Classifications: {'peptide': 628}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 42, 'TRANS': 585}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 121
          Classifications: {'peptide': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'UNK:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 121
          Classifications: {'peptide': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'UNK:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 4944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 628, 4944
          Classifications: {'peptide': 628}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 42, 'TRANS': 585}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' CA': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' CA': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 6.45, per 1000 atoms: 0.64
  Number of scatterers: 10140
  At special positions: 0
  Unit cell: (99.75, 141.55, 73.15, 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)
     Ca     10     19.99
     S      74     16.00
     O    1888      8.00
     N    1706      7.00
     C    6462      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: 2.39
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2404

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 26 sheets defined
      22.5% alpha, 31.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 164 through 168
      removed outlier: 4.128A  pdb=" N   ASP A 168 " --> pdb=" O   ASP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 180
      removed outlier: 3.642A  pdb=" N   ASP A 179 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   MET A 180 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 209
      No H-bonds generated for 'chain 'A' and resid 207 through 209'
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 347 through 351
      removed outlier: 3.837A  pdb=" N   GLU A 351 " --> pdb=" O   TRP A 347 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 347 through 351'
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 402 through 406
      removed outlier: 3.536A  pdb=" N   ASP A 405 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER A 406 " --> pdb=" O   GLY A 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 402 through 406'
    Processing helix  chain 'A' and resid 444 through 454
    Processing helix  chain 'A' and resid 471 through 474
    Processing helix  chain 'A' and resid 494 through 507
    Processing helix  chain 'A' and resid 526 through 531
    Processing helix  chain 'A' and resid 532 through 558
    Processing helix  chain 'A' and resid 560 through 562
      No H-bonds generated for 'chain 'A' and resid 560 through 562'
    Processing helix  chain 'A' and resid 575 through 577
      No H-bonds generated for 'chain 'A' and resid 575 through 577'
    Processing helix  chain 'A' and resid 611 through 621
    Processing helix  chain 'A' and resid 622 through 624
      No H-bonds generated for 'chain 'A' and resid 622 through 624'
    Processing helix  chain 'A' and resid 643 through 647
    Processing helix  chain 'A' and resid 657 through 661
    Processing helix  chain 'B' and resid 164 through 168
      removed outlier: 4.127A  pdb=" N   ASP B 168 " --> pdb=" O   ASP B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 180
      removed outlier: 3.642A  pdb=" N   ASP B 179 " --> pdb=" O   ASP B 176 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   MET B 180 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 209
      No H-bonds generated for 'chain 'B' and resid 207 through 209'
    Processing helix  chain 'B' and resid 317 through 331
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 347 through 351
      removed outlier: 3.837A  pdb=" N   GLU B 351 " --> pdb=" O   TRP B 347 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 347 through 351'
    Processing helix  chain 'B' and resid 378 through 383
    Processing helix  chain 'B' and resid 402 through 406
      removed outlier: 3.536A  pdb=" N   ASP B 405 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER B 406 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 402 through 406'
    Processing helix  chain 'B' and resid 444 through 454
    Processing helix  chain 'B' and resid 471 through 474
    Processing helix  chain 'B' and resid 494 through 507
    Processing helix  chain 'B' and resid 526 through 531
    Processing helix  chain 'B' and resid 532 through 558
    Processing helix  chain 'B' and resid 560 through 562
      No H-bonds generated for 'chain 'B' and resid 560 through 562'
    Processing helix  chain 'B' and resid 575 through 577
      No H-bonds generated for 'chain 'B' and resid 575 through 577'
    Processing helix  chain 'B' and resid 611 through 621
    Processing helix  chain 'B' and resid 622 through 624
      No H-bonds generated for 'chain 'B' and resid 622 through 624'
    Processing helix  chain 'B' and resid 643 through 647
    Processing helix  chain 'B' and resid 657 through 661
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 5.851A  pdb=" N   THR A   5 " --> pdb=" O   GLN A  26 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASP A  28 " --> pdb=" O   THR A   5 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   ILE A   7 " --> pdb=" O   ASP A  28 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   THR A  25 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL A  76 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20
      removed outlier: 5.969A  pdb=" N   THR A  15 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   THR A 111 " --> pdb=" O   THR A  15 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA A  17 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   VAL A 113 " --> pdb=" O   ALA A  17 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   CYS A  19 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ILE A 115 " --> pdb=" O   CYS A  19 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER A  39 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TRP A  68 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20
      removed outlier: 5.969A  pdb=" N   THR A  15 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   THR A 111 " --> pdb=" O   THR A  15 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA A  17 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   VAL A 113 " --> pdb=" O   ALA A  17 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   CYS A  19 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ILE A 115 " --> pdb=" O   CYS A  19 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   ASP A 248 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL A 213 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150
      removed outlier: 3.531A  pdb=" N   ALA A 148 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU A 271 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLN A 286 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ILE A 269 " --> pdb=" O   GLN A 286 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   SER A 288 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU A 267 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   VAL A 290 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE A 265 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   LEU A 199 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 337
      removed outlier: 3.574A  pdb=" N   LYS A 333 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 359
    Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412
      removed outlier: 6.442A  pdb=" N   ILE A 428 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU A 462 " --> pdb=" O   ILE A 428 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE A 430 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418
    Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480
      removed outlier: 8.149A  pdb=" N   ILE A 565 " --> pdb=" O   PHE A 487 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   LEU A 489 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ILE A 567 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   LEU A 491 " --> pdb=" O   ILE A 567 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 514
    Processing sheet with id=AB2, first strand: chain 'A' and resid 571 through 573
    Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 592
      removed outlier: 5.842A  pdb=" N   LEU A 596 " --> pdb=" O   THR A 628 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ILE A 630 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE A 598 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 605 through 606
    Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8
      removed outlier: 5.851A  pdb=" N   THR B   5 " --> pdb=" O   GLN B  26 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASP B  28 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   ILE B   7 " --> pdb=" O   ASP B  28 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   THR B  25 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL B  76 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 20
      removed outlier: 5.970A  pdb=" N   THR B  15 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   THR B 111 " --> pdb=" O   THR B  15 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA B  17 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   VAL B 113 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   CYS B  19 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ILE B 115 " --> pdb=" O   CYS B  19 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER B  39 " --> pdb=" O   TYR B  97 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TRP B  68 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 15 through 20
      removed outlier: 5.970A  pdb=" N   THR B  15 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   THR B 111 " --> pdb=" O   THR B  15 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA B  17 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   VAL B 113 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   CYS B  19 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ILE B 115 " --> pdb=" O   CYS B  19 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   ASP B 248 " --> pdb=" O   ALA B 216 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL B 213 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 150
      removed outlier: 3.532A  pdb=" N   ALA B 148 " --> pdb=" O   VAL B 290 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU B 271 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLN B 286 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ILE B 269 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   SER B 288 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 267 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   VAL B 290 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 265 " --> pdb=" O   VAL B 290 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   LEU B 199 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 333 through 337
      removed outlier: 3.574A  pdb=" N   LYS B 333 " --> pdb=" O   GLN B 306 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 359
    Processing sheet with id=AC2, first strand: chain 'B' and resid 410 through 412
      removed outlier: 6.442A  pdb=" N   ILE B 428 " --> pdb=" O   VAL B 460 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU B 462 " --> pdb=" O   ILE B 428 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   PHE B 430 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 418
    Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 480
      removed outlier: 8.148A  pdb=" N   ILE B 565 " --> pdb=" O   PHE B 487 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   LEU B 489 " --> pdb=" O   ILE B 565 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ILE B 567 " --> pdb=" O   LEU B 489 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   LEU B 491 " --> pdb=" O   ILE B 567 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 513 through 514
    Processing sheet with id=AC6, first strand: chain 'B' and resid 571 through 573
    Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592
      removed outlier: 5.841A  pdb=" N   LEU B 596 " --> pdb=" O   THR B 628 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ILE B 630 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE B 598 " --> pdb=" O   ILE B 630 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 605 through 606

    344 hydrogen bonds defined for protein.
    888 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: 3.94

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3292
        1.34 -     1.46: 2108
        1.46 -     1.58: 4868
        1.58 -     1.69: 0
        1.69 -     1.81: 108
  Bond restraints: 10376
  Sorted by residual:
  bond pdb=" N   ARG B 650 "
       pdb=" CA  ARG B 650 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 1.23e-02 6.61e+03 5.37e+00
  bond pdb=" N   ARG A 650 "
       pdb=" CA  ARG A 650 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 1.23e-02 6.61e+03 5.37e+00
  bond pdb=" N   ARG B 495 "
       pdb=" CA  ARG B 495 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 5.05e+00
  bond pdb=" N   ARG A 495 "
       pdb=" CA  ARG A 495 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 5.05e+00
  bond pdb=" N   ARG B 488 "
       pdb=" CA  ARG B 488 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.26e-02 6.30e+03 4.40e+00
  ... (remaining 10371 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 13445
        0.98 -     1.95: 469
        1.95 -     2.93: 125
        2.93 -     3.90: 27
        3.90 -     4.88: 8
  Bond angle restraints: 14074
  Sorted by residual:
  angle pdb=" CA  ARG A 123 "
        pdb=" C   ARG A 123 "
        pdb=" O   ARG A 123 "
      ideal   model   delta    sigma   weight residual
     121.28  118.04    3.24 1.19e+00 7.06e-01 7.41e+00
  angle pdb=" CA  ARG B 123 "
        pdb=" C   ARG B 123 "
        pdb=" O   ARG B 123 "
      ideal   model   delta    sigma   weight residual
     121.28  118.04    3.24 1.19e+00 7.06e-01 7.41e+00
  angle pdb=" CA  ARG A 650 "
        pdb=" C   ARG A 650 "
        pdb=" O   ARG A 650 "
      ideal   model   delta    sigma   weight residual
     120.43  117.61    2.82 1.09e+00 8.42e-01 6.69e+00
  angle pdb=" CA  ARG B 495 "
        pdb=" C   ARG B 495 "
        pdb=" O   ARG B 495 "
      ideal   model   delta    sigma   weight residual
     120.82  118.12    2.70 1.05e+00 9.07e-01 6.59e+00
  angle pdb=" CA  ARG B 650 "
        pdb=" C   ARG B 650 "
        pdb=" O   ARG B 650 "
      ideal   model   delta    sigma   weight residual
     120.43  117.63    2.80 1.09e+00 8.42e-01 6.58e+00
  ... (remaining 14069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.11: 5372
       16.11 -    32.21: 598
       32.21 -    48.32: 192
       48.32 -    64.43: 86
       64.43 -    80.53: 10
  Dihedral angle restraints: 6258
    sinusoidal: 2552
      harmonic: 3706
  Sorted by residual:
  dihedral pdb=" CA  PHE B 407 "
           pdb=" C   PHE B 407 "
           pdb=" N   GLY B 408 "
           pdb=" CA  GLY B 408 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.38   18.62     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  PHE A 407 "
           pdb=" C   PHE A 407 "
           pdb=" N   GLY A 408 "
           pdb=" CA  GLY A 408 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.38   18.62     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  ASP B 405 "
           pdb=" CB  ASP B 405 "
           pdb=" CG  ASP B 405 "
           pdb=" OD1 ASP B 405 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.39   56.39     1      2.00e+01 2.50e-03 1.07e+01
  ... (remaining 6255 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 912
       0.028 -    0.057: 382
       0.057 -    0.085: 118
       0.085 -    0.113: 115
       0.113 -    0.141: 35
  Chirality restraints: 1562
  Sorted by residual:
  chirality pdb=" CA  ILE B  94 "
            pdb=" N   ILE B  94 "
            pdb=" C   ILE B  94 "
            pdb=" CB  ILE B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  ILE A  94 "
            pdb=" N   ILE A  94 "
            pdb=" C   ILE A  94 "
            pdb=" CB  ILE A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  VAL B 203 "
            pdb=" N   VAL B 203 "
            pdb=" C   VAL B 203 "
            pdb=" CB  VAL B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.79e-01
  ... (remaining 1559 not shown)

  Planarity restraints: 1818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 449 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.13e+00
        pdb=" CG  ASP B 449 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 449 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 449 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 449 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" CG  ASP A 449 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 449 "    0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 449 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 488 "    0.147 9.50e-02 1.11e+02   6.60e-02 2.70e+00
        pdb=" NE  ARG B 488 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 488 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 488 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 488 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1815 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 32
        2.41 -     3.04: 5637
        3.04 -     3.66: 14068
        3.66 -     4.28: 22381
        4.28 -     4.90: 39446
  Nonbonded interactions: 81564
  Sorted by model distance:
  nonbonded pdb=" CA  UNK C   0 "
            pdb=" SG  CYS C  12 "
     model   vdw
     1.792 3.830
  nonbonded pdb=" CA  UNK D   0 "
            pdb=" SG  CYS D  12 "
     model   vdw
     1.792 3.830
  nonbonded pdb=" OH  TYR A 435 "
            pdb=" OE2 GLU B 281 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OE2 GLU A 281 "
            pdb=" OH  TYR B 435 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG  SER B  84 "
            pdb=" OG1 THR B 111 "
     model   vdw
     2.254 3.040
  ... (remaining 81559 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  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:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.210
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10376  Z= 0.152
  Angle     :  0.481   4.875  14074  Z= 0.267
  Chirality :  0.044   0.141   1562
  Planarity :  0.005   0.066   1818
  Dihedral  : 16.319  80.534   3854
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.37 %
    Favored  : 78.63 %
  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:  0.37 (0.24), residues: 1256
  helix:  0.82 (0.36), residues: 218
  sheet:  1.06 (0.26), residues: 402
  loop : -0.47 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 347 
 HIS   0.002   0.001   HIS A 236 
 PHE   0.011   0.001   PHE B 583 
 TYR   0.010   0.001   TYR B 391 
 ARG   0.003   0.000   ARG B 488 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.188 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2605
  time to fit residues: 54.8558
Evaluate side-chains
  143 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    0.2980
   chunk 51 optimal weight:    0.5980
   chunk 98 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
B 215 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.130640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.098239 restraints weight = 11207.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.81
r_work: 0.2779 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.0606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10376  Z= 0.215
  Angle     :  0.497   4.881  14074  Z= 0.261
  Chirality :  0.045   0.135   1562
  Planarity :  0.004   0.037   1818
  Dihedral  :  4.037  19.928   1358
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.53 %
    Favored  : 78.63 %
  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:  0.50 (0.24), residues: 1256
  helix:  1.23 (0.37), residues: 206
  sheet:  0.97 (0.26), residues: 410
  loop : -0.36 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 659 
 HIS   0.004   0.001   HIS B 202 
 PHE   0.013   0.001   PHE B 583 
 TYR   0.010   0.001   TYR A 391 
 ARG   0.004   0.000   ARG A 372 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7925 (m)
REVERT: B   19 CYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7935 (m)
  outliers start: 21
  outliers final: 15
  residues processed: 170
  average time/residue: 0.2477
  time to fit residues: 60.4739
Evaluate side-chains
  170 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  534 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.126518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.095250 restraints weight = 11504.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 1.75
r_work: 0.2772 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  10376  Z= 0.354
  Angle     :  0.579   6.731  14074  Z= 0.301
  Chirality :  0.048   0.143   1562
  Planarity :  0.005   0.040   1818
  Dihedral  :  4.489  21.755   1358
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.56 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.25 (0.24), residues: 1256
  helix:  0.91 (0.37), residues: 206
  sheet:  0.85 (0.26), residues: 410
  loop : -0.51 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 347 
 HIS   0.006   0.001   HIS A 202 
 PHE   0.014   0.002   PHE B 583 
 TYR   0.012   0.001   TYR A 391 
 ARG   0.005   0.001   ARG A 372 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 158
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8007 (m)
REVERT: B   19 CYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8005 (m)
  outliers start: 41
  outliers final: 32
  residues processed: 182
  average time/residue: 0.2272
  time to fit residues: 59.2242
Evaluate side-chains
  187 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  570 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0570
   chunk 12 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.132174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.099564 restraints weight = 11214.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.86
r_work: 0.2797 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.0830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10376  Z= 0.134
  Angle     :  0.455   5.193  14074  Z= 0.240
  Chirality :  0.043   0.133   1562
  Planarity :  0.004   0.037   1818
  Dihedral  :  3.993  19.947   1358
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.88 %
    Favored  : 77.23 %
  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:  0.50 (0.24), residues: 1256
  helix:  1.20 (0.37), residues: 206
  sheet:  1.00 (0.26), residues: 410
  loop : -0.36 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 659 
 HIS   0.002   0.000   HIS B 236 
 PHE   0.010   0.001   PHE B 475 
 TYR   0.010   0.001   TYR A 391 
 ARG   0.005   0.000   ARG A 383 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 158
  time to evaluate  : 1.231 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7960 (m)
REVERT: A  274 THR cc_start: 0.8799 (m) cc_final: 0.8458 (p)
REVERT: A  626 GLN cc_start: 0.8585 (mt0) cc_final: 0.8179 (mt0)
REVERT: B   19 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7975 (m)
REVERT: B  274 THR cc_start: 0.8799 (m) cc_final: 0.8462 (p)
REVERT: B  626 GLN cc_start: 0.8590 (mt0) cc_final: 0.8188 (mt0)
  outliers start: 33
  outliers final: 15
  residues processed: 178
  average time/residue: 0.2342
  time to fit residues: 58.9771
Evaluate side-chains
  161 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  434 CYS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  534 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.125716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.094129 restraints weight = 11473.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 1.81
r_work: 0.2716 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2577 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  10376  Z= 0.407
  Angle     :  0.607   8.493  14074  Z= 0.312
  Chirality :  0.049   0.142   1562
  Planarity :  0.005   0.040   1818
  Dihedral  :  4.540  21.871   1358
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.09 %
    Favored  : 77.15 %
  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:  0.20 (0.24), residues: 1256
  helix:  0.81 (0.37), residues: 206
  sheet:  0.86 (0.26), residues: 410
  loop : -0.55 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 347 
 HIS   0.007   0.001   HIS B 202 
 PHE   0.015   0.002   PHE B 475 
 TYR   0.012   0.002   TYR B 391 
 ARG   0.004   0.001   ARG B 383 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8043 (m)
REVERT: A  626 GLN cc_start: 0.8661 (mt0) cc_final: 0.8265 (mt0)
REVERT: B   19 CYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8039 (m)
REVERT: B  626 GLN cc_start: 0.8655 (mt0) cc_final: 0.8255 (mt0)
  outliers start: 43
  outliers final: 36
  residues processed: 176
  average time/residue: 0.2269
  time to fit residues: 56.5991
Evaluate side-chains
  179 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 141
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  413 SER
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  434 CYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  570 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 115 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 111 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 102 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 116 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.128184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.096533 restraints weight = 11457.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.81
r_work: 0.2758 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10376  Z= 0.210
  Angle     :  0.506   7.481  14074  Z= 0.263
  Chirality :  0.045   0.135   1562
  Planarity :  0.005   0.039   1818
  Dihedral  :  4.255  20.962   1358
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.88 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.30 (0.24), residues: 1256
  helix:  0.99 (0.37), residues: 206
  sheet:  0.91 (0.26), residues: 410
  loop : -0.51 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 347 
 HIS   0.004   0.001   HIS B 202 
 PHE   0.012   0.001   PHE B 475 
 TYR   0.011   0.001   TYR A 391 
 ARG   0.004   0.000   ARG A 383 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 148
  time to evaluate  : 1.234 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7971 (m)
REVERT: A   80 MET cc_start: 0.8161 (mtp) cc_final: 0.7917 (mtp)
REVERT: A  626 GLN cc_start: 0.8651 (mt0) cc_final: 0.8268 (mt0)
REVERT: B   19 CYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7978 (m)
REVERT: B  626 GLN cc_start: 0.8648 (mt0) cc_final: 0.8262 (mt0)
  outliers start: 36
  outliers final: 31
  residues processed: 170
  average time/residue: 0.2247
  time to fit residues: 54.5357
Evaluate side-chains
  175 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  413 SER
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  434 CYS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  570 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 100 optimal weight:    0.0000
   chunk 48 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.5790

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

Flipped N/Q/H residues before XYZ refinement:
B  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.125793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.094202 restraints weight = 11589.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 1.81
r_work: 0.2722 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2582 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  10376  Z= 0.370
  Angle     :  0.590   8.081  14074  Z= 0.305
  Chirality :  0.048   0.143   1562
  Planarity :  0.005   0.042   1818
  Dihedral  :  4.542  21.997   1358
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 18.39 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.06 (0.24), residues: 1256
  helix:  0.46 (0.36), residues: 218
  sheet:  0.91 (0.26), residues: 406
  loop : -0.67 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 347 
 HIS   0.006   0.001   HIS B 202 
 PHE   0.015   0.002   PHE A 583 
 TYR   0.012   0.001   TYR B 391 
 ARG   0.005   0.000   ARG A 383 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 140
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7996 (m)
REVERT: A   80 MET cc_start: 0.8201 (mtp) cc_final: 0.7923 (mtp)
REVERT: A  626 GLN cc_start: 0.8678 (mt0) cc_final: 0.8294 (mt0)
REVERT: B   19 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8034 (m)
REVERT: B  626 GLN cc_start: 0.8669 (mt0) cc_final: 0.8282 (mt0)
  outliers start: 53
  outliers final: 46
  residues processed: 178
  average time/residue: 0.2213
  time to fit residues: 56.2537
Evaluate side-chains
  186 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 138
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  328 MET
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  413 SER
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  434 CYS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  611 CYS
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  611 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 120 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 124 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.127830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.096350 restraints weight = 11442.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.79
r_work: 0.2756 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2618 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10376  Z= 0.227
  Angle     :  0.516   7.308  14074  Z= 0.269
  Chirality :  0.046   0.136   1562
  Planarity :  0.005   0.045   1818
  Dihedral  :  4.313  21.117   1358
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.61 %
    Favored  : 76.62 %
  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:  0.25 (0.24), residues: 1256
  helix:  0.91 (0.37), residues: 206
  sheet:  0.89 (0.26), residues: 410
  loop : -0.55 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 347 
 HIS   0.004   0.001   HIS A 202 
 PHE   0.012   0.001   PHE B 475 
 TYR   0.012   0.001   TYR A 391 
 ARG   0.005   0.000   ARG A 383 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 146
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7991 (m)
REVERT: A  237 TYR cc_start: 0.9062 (m-80) cc_final: 0.8834 (m-80)
REVERT: A  626 GLN cc_start: 0.8655 (mt0) cc_final: 0.8273 (mt0)
REVERT: B   19 CYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7974 (m)
REVERT: B  237 TYR cc_start: 0.9061 (m-80) cc_final: 0.8833 (m-80)
REVERT: B  626 GLN cc_start: 0.8651 (mt0) cc_final: 0.8266 (mt0)
  outliers start: 43
  outliers final: 40
  residues processed: 177
  average time/residue: 0.2262
  time to fit residues: 57.6714
Evaluate side-chains
  185 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 143
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  413 SER
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  434 CYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  611 CYS
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  611 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 99 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.128819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.097278 restraints weight = 11463.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.81
r_work: 0.2771 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2629 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10376  Z= 0.197
  Angle     :  0.503   7.070  14074  Z= 0.263
  Chirality :  0.045   0.136   1562
  Planarity :  0.005   0.046   1818
  Dihedral  :  4.201  20.779   1358
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.61 %
    Favored  : 76.62 %
  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:  0.32 (0.24), residues: 1256
  helix:  0.97 (0.38), residues: 206
  sheet:  0.94 (0.26), residues: 410
  loop : -0.50 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 347 
 HIS   0.003   0.001   HIS B 202 
 PHE   0.012   0.001   PHE B 475 
 TYR   0.011   0.001   TYR A 391 
 ARG   0.005   0.000   ARG B 383 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 150
  time to evaluate  : 1.210 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7963 (m)
REVERT: A  237 TYR cc_start: 0.9069 (m-80) cc_final: 0.8737 (m-80)
REVERT: A  274 THR cc_start: 0.8766 (m) cc_final: 0.8466 (p)
REVERT: A  281 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7675 (pt0)
REVERT: A  626 GLN cc_start: 0.8657 (mt0) cc_final: 0.8278 (mt0)
REVERT: B   19 CYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7963 (m)
REVERT: B  237 TYR cc_start: 0.9071 (m-80) cc_final: 0.8741 (m-80)
REVERT: B  274 THR cc_start: 0.8757 (m) cc_final: 0.8466 (p)
REVERT: B  281 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7671 (pt0)
REVERT: B  626 GLN cc_start: 0.8655 (mt0) cc_final: 0.8272 (mt0)
  outliers start: 43
  outliers final: 35
  residues processed: 181
  average time/residue: 0.2269
  time to fit residues: 57.4728
Evaluate side-chains
  188 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 149
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  434 CYS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  611 CYS
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  611 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 105 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0270
   chunk 108 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.7638

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.128628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.097300 restraints weight = 11349.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.78
r_work: 0.2773 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10376  Z= 0.204
  Angle     :  0.506   7.071  14074  Z= 0.265
  Chirality :  0.045   0.135   1562
  Planarity :  0.005   0.047   1818
  Dihedral  :  4.178  20.424   1358
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.05 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.32 (0.24), residues: 1256
  helix:  0.95 (0.37), residues: 206
  sheet:  0.96 (0.26), residues: 410
  loop : -0.51 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 347 
 HIS   0.004   0.001   HIS B 202 
 PHE   0.012   0.001   PHE B 475 
 TYR   0.011   0.001   TYR B 391 
 ARG   0.005   0.000   ARG A 383 

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 1.261 
Fit side-chains
REVERT: A   19 CYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7966 (m)
REVERT: A  237 TYR cc_start: 0.9054 (m-80) cc_final: 0.8726 (m-80)
REVERT: A  274 THR cc_start: 0.8744 (m) cc_final: 0.8470 (p)
REVERT: A  626 GLN cc_start: 0.8656 (mt0) cc_final: 0.8277 (mt0)
REVERT: B   19 CYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7982 (m)
REVERT: B  237 TYR cc_start: 0.9059 (m-80) cc_final: 0.8729 (m-80)
REVERT: B  274 THR cc_start: 0.8703 (m) cc_final: 0.8444 (p)
REVERT: B  626 GLN cc_start: 0.8656 (mt0) cc_final: 0.8274 (mt0)
  outliers start: 40
  outliers final: 37
  residues processed: 173
  average time/residue: 0.2251
  time to fit residues: 55.4521
Evaluate side-chains
  182 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 143
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  413 SER
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  434 CYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  611 CYS
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   19 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  611 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0010
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.129719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.098437 restraints weight = 11383.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.80
r_work: 0.2793 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10376  Z= 0.171
  Angle     :  0.488   6.835  14074  Z= 0.256
  Chirality :  0.045   0.134   1562
  Planarity :  0.005   0.047   1818
  Dihedral  :  4.080  20.020   1358
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.40 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.37 (0.24), residues: 1256
  helix:  1.00 (0.38), residues: 206
  sheet:  0.98 (0.26), residues: 410
  loop : -0.47 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 347 
 HIS   0.003   0.001   HIS B 202 
 PHE   0.011   0.001   PHE B 475 
 TYR   0.011   0.001   TYR B 391 
 ARG   0.005   0.000   ARG A 383 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5319.97 seconds
wall clock time: 95 minutes 12.11 seconds (5712.11 seconds total)