Starting phenix.real_space_refine
on Mon Jul 28 10:03:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ptv_13641/07_2025/7ptv_13641.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ptv_13641/07_2025/7ptv_13641.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2025/7ptv_13641.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2025/7ptv_13641.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2025/7ptv_13641.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2025/7ptv_13641.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      30      5.16       5
     C    6374      2.51       5
     N    1678      2.21       5
     O    1910      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9996
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 645, 4945
          Classifications: {'peptide': 645}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 603}
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.27, per 1000 atoms: 0.93
  Number of scatterers: 9996
  At special positions: 0
  Unit cell: (88.29, 98.1, 110.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       4     15.00
     O    1910      8.00
     N    1678      7.00
     C    6374      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: 2.37
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2344

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 16 sheets defined
      38.4% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 3.707A  pdb=" N   PHE A  80 " --> pdb=" O   TYR A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 102
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 112 through 116
      removed outlier: 4.295A  pdb=" N   ASN A 116 " --> pdb=" O   PRO A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 122
    Processing helix  chain 'A' and resid 151 through 156
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 4.442A  pdb=" N   PHE A 169 " --> pdb=" O   GLY A 165 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TRP A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 181
    Processing helix  chain 'A' and resid 182 through 194
    Processing helix  chain 'A' and resid 202 through 221
      removed outlier: 3.764A  pdb=" N   ASN A 206 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLN A 218 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 288
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 354 through 363
    Processing helix  chain 'A' and resid 366 through 374
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.929A  pdb=" N   GLY A 442 " --> pdb=" O   SER A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 468
    Processing helix  chain 'A' and resid 520 through 523
    Processing helix  chain 'A' and resid 524 through 558
      removed outlier: 3.725A  pdb=" N   ALA A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   LYS A 530 " --> pdb=" O   PRO A 526 " (cutoff:3.500A)
      Proline residue:  A 534  - end of helix
      removed outlier: 3.914A  pdb=" N   ILE A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL A 549 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   GLN A 550 " --> pdb=" O   TYR A 546 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   GLN A 551 " --> pdb=" O   GLN A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 586
      removed outlier: 3.652A  pdb=" N   LEU A 578 " --> pdb=" O   LEU A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 593
      removed outlier: 4.677A  pdb=" N   TRP A 590 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
      removed outlier: 3.970A  pdb=" N   VAL A 598 " --> pdb=" O   VAL A 594 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   ASN A 599 " --> pdb=" O   PRO A 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 594 through 599'
    Processing helix  chain 'A' and resid 602 through 616
    Processing helix  chain 'A' and resid 616 through 622
      removed outlier: 4.237A  pdb=" N   ARG A 620 " --> pdb=" O   SER A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 659
    Processing helix  chain 'A' and resid 668 through 684
      removed outlier: 3.650A  pdb=" N   ASP A 680 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 691
      removed outlier: 3.524A  pdb=" N   ASN A 690 " --> pdb=" O   LEU A 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 80
      removed outlier: 3.707A  pdb=" N   PHE B  80 " --> pdb=" O   TYR B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 102
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 112 through 116
      removed outlier: 4.295A  pdb=" N   ASN B 116 " --> pdb=" O   PRO B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 122
    Processing helix  chain 'B' and resid 151 through 156
    Processing helix  chain 'B' and resid 165 through 173
      removed outlier: 4.442A  pdb=" N   PHE B 169 " --> pdb=" O   GLY B 165 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TRP B 173 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 181
    Processing helix  chain 'B' and resid 182 through 194
    Processing helix  chain 'B' and resid 202 through 221
      removed outlier: 3.764A  pdb=" N   ASN B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLN B 218 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 288
    Processing helix  chain 'B' and resid 301 through 305
    Processing helix  chain 'B' and resid 354 through 363
    Processing helix  chain 'B' and resid 366 through 374
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.930A  pdb=" N   GLY B 442 " --> pdb=" O   SER B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 468
    Processing helix  chain 'B' and resid 520 through 523
    Processing helix  chain 'B' and resid 524 through 558
      removed outlier: 3.723A  pdb=" N   ALA B 528 " --> pdb=" O   GLN B 524 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   LYS B 530 " --> pdb=" O   PRO B 526 " (cutoff:3.500A)
      Proline residue:  B 534  - end of helix
      removed outlier: 3.915A  pdb=" N   ILE B 548 " --> pdb=" O   ALA B 544 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL B 549 " --> pdb=" O   ILE B 545 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   GLN B 550 " --> pdb=" O   TYR B 546 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   GLN B 551 " --> pdb=" O   GLN B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 586
      removed outlier: 3.651A  pdb=" N   LEU B 578 " --> pdb=" O   LEU B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 593
      removed outlier: 4.677A  pdb=" N   TRP B 590 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 599
      removed outlier: 3.969A  pdb=" N   VAL B 598 " --> pdb=" O   VAL B 594 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ASN B 599 " --> pdb=" O   PRO B 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 594 through 599'
    Processing helix  chain 'B' and resid 602 through 616
    Processing helix  chain 'B' and resid 616 through 622
      removed outlier: 4.237A  pdb=" N   ARG B 620 " --> pdb=" O   SER B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 659
    Processing helix  chain 'B' and resid 668 through 684
      removed outlier: 3.650A  pdb=" N   ASP B 680 " --> pdb=" O   ALA B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 691
      removed outlier: 3.524A  pdb=" N   ASN B 690 " --> pdb=" O   LEU B 687 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310
      removed outlier: 6.304A  pdb=" N   ILE A  85 " --> pdb=" O   ARG A 308 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ILE A 310 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A  87 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ASP A  60 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   GLU A 347 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL A  62 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL A 326 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 9.968A  pdb=" N   LYS A 344 " --> pdb=" O   ARG A 324 " (cutoff:3.500A)
      removed outlier: 9.713A  pdb=" N   ARG A 324 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   ALA A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   GLU A 321 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR A 329 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ARG A 317 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE A 331 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   VAL A 315 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 310
      removed outlier: 6.304A  pdb=" N   ILE A  85 " --> pdb=" O   ARG A 308 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ILE A 310 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A  87 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ASP A  60 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   GLU A 347 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL A  62 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   ARG A 652 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   VAL A 346 " --> pdb=" O   ARG A 652 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263
      removed outlier: 3.623A  pdb=" N   GLY A 426 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA A 481 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TYR A 393 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   GLN A 398 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263
      removed outlier: 3.623A  pdb=" N   GLY A 426 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA A 481 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TYR A 393 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273
    Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 365
    Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 493
    Processing sheet with id=AA9, first strand: chain 'B' and resid 307 through 310
      removed outlier: 6.304A  pdb=" N   ILE B  85 " --> pdb=" O   ARG B 308 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ILE B 310 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU B  87 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ASP B  60 " --> pdb=" O   GLU B 345 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   GLU B 347 " --> pdb=" O   ASP B  60 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL B  62 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL B 326 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 9.967A  pdb=" N   LYS B 344 " --> pdb=" O   ARG B 324 " (cutoff:3.500A)
      removed outlier: 9.714A  pdb=" N   ARG B 324 " --> pdb=" O   LYS B 344 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   ALA B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   GLU B 321 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR B 329 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ARG B 317 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE B 331 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   VAL B 315 " --> pdb=" O   ILE B 331 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310
      removed outlier: 6.304A  pdb=" N   ILE B  85 " --> pdb=" O   ARG B 308 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ILE B 310 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU B  87 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ASP B  60 " --> pdb=" O   GLU B 345 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   GLU B 347 " --> pdb=" O   ASP B  60 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL B  62 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   ARG B 652 " --> pdb=" O   LYS B 344 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   VAL B 346 " --> pdb=" O   ARG B 652 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 126 through 127
    Processing sheet with id=AB3, first strand: chain 'B' and resid 262 through 263
      removed outlier: 3.623A  pdb=" N   GLY B 426 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA B 481 " --> pdb=" O   PRO B 395 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TYR B 393 " --> pdb=" O   ASP B 483 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   GLN B 398 " --> pdb=" O   ALA B 568 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 262 through 263
      removed outlier: 3.623A  pdb=" N   GLY B 426 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA B 481 " --> pdb=" O   PRO B 395 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TYR B 393 " --> pdb=" O   ASP B 483 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 271 through 273
    Processing sheet with id=AB6, first strand: chain 'B' and resid 364 through 365
    Processing sheet with id=AB7, first strand: chain 'B' and resid 491 through 493

    386 hydrogen bonds defined for protein.
    984 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: 3.17

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3225
        1.34 -     1.45: 1512
        1.45 -     1.57: 5465
        1.57 -     1.68: 10
        1.68 -     1.80: 48
  Bond restraints: 10260
  Sorted by residual:
  bond pdb=" O3P FAD B 901 "
       pdb=" P   FAD B 901 "
    ideal  model  delta    sigma   weight residual
    1.660  1.571  0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" O3P FAD A 901 "
       pdb=" P   FAD A 901 "
    ideal  model  delta    sigma   weight residual
    1.660  1.572  0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" O5B FAD A 901 "
       pdb=" PA  FAD A 901 "
    ideal  model  delta    sigma   weight residual
    1.634  1.559  0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" O5B FAD B 901 "
       pdb=" PA  FAD B 901 "
    ideal  model  delta    sigma   weight residual
    1.634  1.559  0.075 2.00e-02 2.50e+03 1.40e+01
  bond pdb=" O5' FAD A 901 "
       pdb=" P   FAD A 901 "
    ideal  model  delta    sigma   weight residual
    1.637  1.572  0.065 2.00e-02 2.50e+03 1.05e+01
  ... (remaining 10255 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 13514
        1.85 -     3.71: 440
        3.71 -     5.56: 52
        5.56 -     7.41: 14
        7.41 -     9.27: 12
  Bond angle restraints: 14032
  Sorted by residual:
  angle pdb=" CA  GLN A 551 "
        pdb=" CB  GLN A 551 "
        pdb=" CG  GLN A 551 "
      ideal   model   delta    sigma   weight residual
     114.10  121.61   -7.51 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" CA  GLN B 551 "
        pdb=" CB  GLN B 551 "
        pdb=" CG  GLN B 551 "
      ideal   model   delta    sigma   weight residual
     114.10  121.61   -7.51 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" CB  GLN B 551 "
        pdb=" CG  GLN B 551 "
        pdb=" CD  GLN B 551 "
      ideal   model   delta    sigma   weight residual
     112.60  118.43   -5.83 1.70e+00 3.46e-01 1.17e+01
  angle pdb=" CB  GLN A 551 "
        pdb=" CG  GLN A 551 "
        pdb=" CD  GLN A 551 "
      ideal   model   delta    sigma   weight residual
     112.60  118.41   -5.81 1.70e+00 3.46e-01 1.17e+01
  angle pdb=" CA  LYS A 303 "
        pdb=" CB  LYS A 303 "
        pdb=" CG  LYS A 303 "
      ideal   model   delta    sigma   weight residual
     114.10  120.45   -6.35 2.00e+00 2.50e-01 1.01e+01
  ... (remaining 14027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 5436
       16.71 -    33.42: 455
       33.42 -    50.13: 105
       50.13 -    66.84: 40
       66.84 -    83.55: 8
  Dihedral angle restraints: 6044
    sinusoidal: 2342
      harmonic: 3702
  Sorted by residual:
  dihedral pdb=" CA  HIS B 319 "
           pdb=" C   HIS B 319 "
           pdb=" N   PHE B 320 "
           pdb=" CA  PHE B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.51  -36.49     0      5.00e+00 4.00e-02 5.33e+01
  dihedral pdb=" CA  HIS A 319 "
           pdb=" C   HIS A 319 "
           pdb=" N   PHE A 320 "
           pdb=" CA  PHE A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.52  -36.48     0      5.00e+00 4.00e-02 5.32e+01
  dihedral pdb=" CA  VAL B 144 "
           pdb=" C   VAL B 144 "
           pdb=" N   ALA B 145 "
           pdb=" CA  ALA B 145 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.30  -20.70     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 6041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 874
       0.041 -    0.082: 471
       0.082 -    0.122: 177
       0.122 -    0.163: 38
       0.163 -    0.204: 4
  Chirality restraints: 1564
  Sorted by residual:
  chirality pdb=" CA  TYR A 161 "
            pdb=" N   TYR A 161 "
            pdb=" C   TYR A 161 "
            pdb=" CB  TYR A 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  TYR B 161 "
            pdb=" N   TYR B 161 "
            pdb=" C   TYR B 161 "
            pdb=" CB  TYR B 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C2B FAD A 901 "
            pdb=" C1B FAD A 901 "
            pdb=" C3B FAD A 901 "
            pdb=" O2B FAD A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.72    0.18 2.00e-01 2.50e+01 8.12e-01
  ... (remaining 1561 not shown)

  Planarity restraints: 1812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 128 "    0.042 5.00e-02 4.00e+02   6.29e-02 6.32e+00
        pdb=" N   PRO A 129 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 129 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 129 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 128 "    0.041 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO B 129 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 525 "    0.033 5.00e-02 4.00e+02   5.01e-02 4.01e+00
        pdb=" N   PRO B 526 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B 526 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 526 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1809 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2574
        2.79 -     3.32: 9064
        3.32 -     3.84: 16491
        3.84 -     4.37: 20057
        4.37 -     4.90: 33931
  Nonbonded interactions: 82117
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 157 "
            pdb=" NH2 ARG A 281 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   ASN B 157 "
            pdb=" NH2 ARG B 281 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" NH2 ARG A 213 "
            pdb=" O   GLU A 241 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" NH2 ARG B 213 "
            pdb=" O   GLU B 241 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" OD2 ASP B 192 "
            pdb=" OH  TYR B 288 "
     model   vdw
     2.312 3.040
  ... (remaining 82112 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     28.290
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
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      :  0.008   0.089  10260  Z= 0.321
  Angle     :  0.803   9.268  14032  Z= 0.422
  Chirality :  0.055   0.204   1564
  Planarity :  0.005   0.063   1812
  Dihedral  : 14.239  83.554   3700
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  1.12 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.22), residues: 1286
  helix: -0.54 (0.24), residues: 420
  sheet: -0.23 (0.37), residues: 172
  loop : -1.52 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 668 
 HIS   0.008   0.001   HIS A 343 
 PHE   0.019   0.002   PHE A 367 
 TYR   0.034   0.002   TYR B 161 
 ARG   0.003   0.001   ARG B 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17016 (  348)
  hydrogen bonds       : angle       6.15883 (  984)
  covalent geometry    : bond        0.00758 (10260)
  covalent geometry    : angle       0.80259 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A  343 HIS cc_start: 0.8284 (m-70) cc_final: 0.8078 (m170)
REVERT: A  398 GLN cc_start: 0.6857 (pp30) cc_final: 0.6620 (pp30)
REVERT: A  551 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7384 (mp10)
REVERT: A  641 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8638 (p)
REVERT: B  518 THR cc_start: 0.8851 (p) cc_final: 0.8585 (t)
  outliers start: 22
  outliers final: 1
  residues processed: 145
  average time/residue: 0.2112
  time to fit residues: 44.7239
Evaluate side-chains
  112 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  551 GLN
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  641 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 116 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
A 551 GLN
B 142 ASN
B 206 ASN
B 387 GLN
B 440 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.074623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.065211 restraints weight = 20131.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2658 rms_B_bonded: 1.98
r_work: 0.2566 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2453 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10260  Z= 0.132
  Angle     :  0.615   7.349  14032  Z= 0.320
  Chirality :  0.048   0.145   1564
  Planarity :  0.005   0.049   1812
  Dihedral  :  9.039  85.987   1498
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  7.64 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.23), residues: 1286
  helix: -0.09 (0.26), residues: 400
  sheet: -0.41 (0.37), residues: 160
  loop : -1.39 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 127 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.014   0.001   PHE A 228 
 TYR   0.017   0.001   TYR B  75 
 ARG   0.003   0.000   ARG B 677 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05115 (  348)
  hydrogen bonds       : angle       4.94660 (  984)
  covalent geometry    : bond        0.00294 (10260)
  covalent geometry    : angle       0.61451 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  161 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.8009 (m-10)
REVERT: A  398 GLN cc_start: 0.7702 (pp30) cc_final: 0.7464 (pp30)
REVERT: A  523 GLN cc_start: 0.8756 (pt0) cc_final: 0.8188 (pp30)
REVERT: A  641 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9035 (p)
REVERT: B  329 THR cc_start: 0.8972 (p) cc_final: 0.8757 (p)
REVERT: B  387 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8142 (mm110)
REVERT: B  518 THR cc_start: 0.8862 (p) cc_final: 0.8525 (t)
  outliers start: 18
  outliers final: 10
  residues processed: 121
  average time/residue: 0.2020
  time to fit residues: 36.3383
Evaluate side-chains
  115 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0670
   chunk 59 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 78 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 127 optimal weight:    9.9990
   overall best weight:    0.9718

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

Flipped N/Q/H residues before XYZ refinement:
A 319 HIS
** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.074121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.064733 restraints weight = 20588.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.2645 rms_B_bonded: 1.94
r_work: 0.2553 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2441 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10260  Z= 0.145
  Angle     :  0.600   7.470  14032  Z= 0.311
  Chirality :  0.049   0.143   1564
  Planarity :  0.005   0.048   1812
  Dihedral  :  8.490  83.388   1495
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.68 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.23), residues: 1286
  helix: -0.01 (0.26), residues: 412
  sheet: -0.15 (0.37), residues: 172
  loop : -1.40 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.014   0.001   PHE A 228 
 TYR   0.017   0.001   TYR B  75 
 ARG   0.005   0.000   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04982 (  348)
  hydrogen bonds       : angle       4.75579 (  984)
  covalent geometry    : bond        0.00342 (10260)
  covalent geometry    : angle       0.59970 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 MET cc_start: 0.9113 (mmm) cc_final: 0.8912 (mmm)
REVERT: A  226 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8485 (t)
REVERT: A  398 GLN cc_start: 0.7834 (pp30) cc_final: 0.7596 (pp30)
REVERT: A  551 GLN cc_start: 0.7826 (mp10) cc_final: 0.7512 (mp10)
REVERT: A  641 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9022 (p)
REVERT: B  161 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7850 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 123
  average time/residue: 0.1949
  time to fit residues: 36.0085
Evaluate side-chains
  120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0070
   chunk 44 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 113 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.074126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.064640 restraints weight = 20121.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 1.97
r_work: 0.2560 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2446 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10260  Z= 0.136
  Angle     :  0.580   6.971  14032  Z= 0.300
  Chirality :  0.048   0.237   1564
  Planarity :  0.004   0.046   1812
  Dihedral  :  8.382  86.731   1495
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 11.36 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.23), residues: 1286
  helix:  0.12 (0.26), residues: 412
  sheet: -0.21 (0.36), residues: 188
  loop : -1.38 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 668 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.012   0.001   PHE A 228 
 TYR   0.018   0.001   TYR B  75 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  348)
  hydrogen bonds       : angle       4.63384 (  984)
  covalent geometry    : bond        0.00322 (10260)
  covalent geometry    : angle       0.57955 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8421 (t)
REVERT: A  398 GLN cc_start: 0.7797 (pp30) cc_final: 0.7558 (pp30)
REVERT: A  641 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9009 (p)
REVERT: B  161 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7837 (m-10)
REVERT: B  227 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8237 (t70)
  outliers start: 27
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1905
  time to fit residues: 34.6486
Evaluate side-chains
  124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  227 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0370
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.075974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.066554 restraints weight = 20224.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.2675 rms_B_bonded: 1.98
r_work: 0.2581 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2468 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10260  Z= 0.109
  Angle     :  0.550   8.332  14032  Z= 0.285
  Chirality :  0.047   0.219   1564
  Planarity :  0.004   0.045   1812
  Dihedral  :  8.301  88.505   1495
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 11.73 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    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: -0.94 (0.23), residues: 1286
  helix:  0.24 (0.27), residues: 412
  sheet: -0.21 (0.36), residues: 188
  loop : -1.28 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 668 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.011   0.001   PHE A 228 
 TYR   0.018   0.001   TYR B  75 
 ARG   0.003   0.000   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04222 (  348)
  hydrogen bonds       : angle       4.48457 (  984)
  covalent geometry    : bond        0.00247 (10260)
  covalent geometry    : angle       0.54982 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8446 (t)
REVERT: A  551 GLN cc_start: 0.7999 (mp10) cc_final: 0.7769 (mp10)
REVERT: B  161 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7810 (m-10)
  outliers start: 32
  outliers final: 20
  residues processed: 126
  average time/residue: 0.2516
  time to fit residues: 46.9699
Evaluate side-chains
  124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 2.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  227 ASP
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 67 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 523 GLN ** 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 = 0.2850 r_free = 0.2850 target = 0.075296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.065855 restraints weight = 20288.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 1.98
r_work: 0.2576 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2463 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10260  Z= 0.123
  Angle     :  0.573  11.620  14032  Z= 0.291
  Chirality :  0.047   0.161   1564
  Planarity :  0.004   0.046   1812
  Dihedral  :  8.202  89.772   1494
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 12.66 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    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: -0.88 (0.23), residues: 1286
  helix:  0.28 (0.27), residues: 412
  sheet: -0.14 (0.37), residues: 188
  loop : -1.26 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.011   0.001   PHE A 228 
 TYR   0.019   0.001   TYR B  75 
 ARG   0.002   0.000   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  348)
  hydrogen bonds       : angle       4.44883 (  984)
  covalent geometry    : bond        0.00290 (10260)
  covalent geometry    : angle       0.57269 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8489 (t)
REVERT: B  161 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7783 (m-10)
  outliers start: 31
  outliers final: 24
  residues processed: 131
  average time/residue: 0.2116
  time to fit residues: 41.8459
Evaluate side-chains
  129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  227 ASP
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  601 ASP
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 113 optimal weight:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.074471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.065143 restraints weight = 20421.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.2651 rms_B_bonded: 1.97
r_work: 0.2557 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2443 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10260  Z= 0.141
  Angle     :  0.595  12.762  14032  Z= 0.303
  Chirality :  0.048   0.214   1564
  Planarity :  0.004   0.046   1812
  Dihedral  :  8.025  87.197   1492
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.50 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    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: -0.81 (0.24), residues: 1286
  helix:  0.30 (0.26), residues: 412
  sheet: -0.08 (0.37), residues: 188
  loop : -1.18 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.013   0.001   PHE A 228 
 TYR   0.020   0.001   TYR B  75 
 ARG   0.002   0.000   ARG A 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04547 (  348)
  hydrogen bonds       : angle       4.46990 (  984)
  covalent geometry    : bond        0.00339 (10260)
  covalent geometry    : angle       0.59539 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6550 (m-10)
REVERT: A  226 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8580 (t)
REVERT: B  161 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7710 (m-10)
REVERT: B  226 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8042 (t)
  outliers start: 31
  outliers final: 24
  residues processed: 128
  average time/residue: 0.2473
  time to fit residues: 49.1238
Evaluate side-chains
  129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  227 ASP
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  601 ASP
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0770
   chunk 80 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.075244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.066213 restraints weight = 20470.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 1.92
r_work: 0.2592 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2480 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10260  Z= 0.121
  Angle     :  0.572  11.744  14032  Z= 0.292
  Chirality :  0.047   0.218   1564
  Planarity :  0.004   0.046   1812
  Dihedral  :  7.968  85.274   1492
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.78 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.24), residues: 1286
  helix:  0.38 (0.27), residues: 400
  sheet: -0.04 (0.37), residues: 188
  loop : -1.12 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.015   0.001   PHE A 699 
 TYR   0.022   0.001   TYR B  75 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  348)
  hydrogen bonds       : angle       4.39232 (  984)
  covalent geometry    : bond        0.00285 (10260)
  covalent geometry    : angle       0.57156 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 1.742 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6979 (m-10)
REVERT: A  226 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8599 (t)
REVERT: B  161 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7720 (m-10)
REVERT: B  226 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8063 (t)
  outliers start: 33
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1910
  time to fit residues: 37.8220
Evaluate side-chains
  129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  227 ASP
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  601 ASP
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 4 optimal weight:    0.0000
   chunk 70 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.073786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.064792 restraints weight = 20380.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 1.89
r_work: 0.2564 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2453 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10260  Z= 0.158
  Angle     :  0.607   9.306  14032  Z= 0.309
  Chirality :  0.049   0.263   1564
  Planarity :  0.004   0.047   1812
  Dihedral  :  7.957  84.146   1492
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.97 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.78 (0.24), residues: 1286
  helix:  0.27 (0.26), residues: 412
  sheet: -0.04 (0.37), residues: 188
  loop : -1.14 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 127 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.013   0.001   PHE A 228 
 TYR   0.023   0.001   TYR B  75 
 ARG   0.002   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04688 (  348)
  hydrogen bonds       : angle       4.47795 (  984)
  covalent geometry    : bond        0.00386 (10260)
  covalent geometry    : angle       0.60677 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7036 (m-10)
REVERT: A  226 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8608 (t)
REVERT: B  161 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7658 (m-10)
REVERT: B  226 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8111 (t)
  outliers start: 29
  outliers final: 24
  residues processed: 126
  average time/residue: 0.2079
  time to fit residues: 39.8976
Evaluate side-chains
  131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  227 ASP
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  601 ASP
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.073563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.064519 restraints weight = 20548.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 1.92
r_work: 0.2564 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2453 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10260  Z= 0.155
  Angle     :  0.609   9.121  14032  Z= 0.311
  Chirality :  0.049   0.249   1564
  Planarity :  0.004   0.047   1812
  Dihedral  :  7.974  82.735   1492
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.87 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.80 (0.24), residues: 1286
  helix:  0.25 (0.26), residues: 412
  sheet: -0.06 (0.37), residues: 188
  loop : -1.14 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 127 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.022   0.001   PHE A 699 
 TYR   0.022   0.001   TYR B  75 
 ARG   0.002   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04666 (  348)
  hydrogen bonds       : angle       4.50132 (  984)
  covalent geometry    : bond        0.00375 (10260)
  covalent geometry    : angle       0.60863 (14032)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7393 (m-10)
REVERT: A  499 PHE cc_start: 0.8030 (p90) cc_final: 0.7728 (p90)
REVERT: A  551 GLN cc_start: 0.7989 (mp10) cc_final: 0.7466 (mp10)
REVERT: B  161 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7726 (m-10)
REVERT: B  226 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8111 (t)
REVERT: B  499 PHE cc_start: 0.8122 (p90) cc_final: 0.7909 (p90)
  outliers start: 31
  outliers final: 22
  residues processed: 128
  average time/residue: 0.1852
  time to fit residues: 36.0484
Evaluate side-chains
  127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  601 ASP
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  648 VAL
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0670
   chunk 4 optimal weight:    0.2980
   chunk 96 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.5920

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.075910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.066954 restraints weight = 20041.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2687 rms_B_bonded: 1.89
r_work: 0.2599 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2489 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10260  Z= 0.115
  Angle     :  0.573   8.607  14032  Z= 0.295
  Chirality :  0.047   0.213   1564
  Planarity :  0.004   0.046   1812
  Dihedral  :  7.874  82.134   1492
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.34 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.68 (0.24), residues: 1286
  helix:  0.41 (0.27), residues: 400
  sheet: -0.09 (0.37), residues: 188
  loop : -1.06 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 127 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.013   0.001   PHE A 228 
 TYR   0.019   0.001   TYR B  75 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  348)
  hydrogen bonds       : angle       4.37202 (  984)
  covalent geometry    : bond        0.00264 (10260)
  covalent geometry    : angle       0.57342 (14032)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4417.26 seconds
wall clock time: 78 minutes 11.63 seconds (4691.63 seconds total)