Starting phenix.real_space_refine
on Fri Jan 17 14:42:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vpb_43406/01_2025/8vpb_43406.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vpb_43406/01_2025/8vpb_43406.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vpb_43406/01_2025/8vpb_43406.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vpb_43406/01_2025/8vpb_43406.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vpb_43406/01_2025/8vpb_43406.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vpb_43406/01_2025/8vpb_43406.cif"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.013
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      2      5.21       5
     S      56      5.16       5
     C    7064      2.51       5
     N    1784      2.21       5
     O    2018      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10928
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 697, 5436
          Classifications: {'peptide': 697}
          Link IDs: {'PTRANS': 13, 'TRANS': 683}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 697, 5436
          Classifications: {'peptide': 697}
          Link IDs: {'PTRANS': 13, 'TRANS': 683}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.97, per 1000 atoms: 0.64
  Number of scatterers: 10928
  At special positions: 0
  Unit cell: (94.462, 111.284, 135.87, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      56     16.00
     P       4     15.00
     Mg      2     11.99
     O    2018      8.00
     N    1784      7.00
     C    7064      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: 2.55
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2588

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 9 sheets defined
      65.7% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 33
    Processing helix  chain 'A' and resid 38 through 47
      removed outlier: 3.523A  pdb=" N   GLY A  47 " --> pdb=" O   ARG A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
    Processing helix  chain 'A' and resid 75 through 81
    Processing helix  chain 'A' and resid 124 through 131
    Processing helix  chain 'A' and resid 153 through 160
      removed outlier: 3.552A  pdb=" N   LYS A 157 " --> pdb=" O   ASN A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 166 through 187
      removed outlier: 3.749A  pdb=" N   LEU A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ALA A 175 " --> pdb=" O   CYS A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 196
      removed outlier: 3.666A  pdb=" N   ASP A 196 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 203 through 251
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 4.155A  pdb=" N   PHE A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN A 259 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 254 through 259'
    Processing helix  chain 'A' and resid 262 through 305
      removed outlier: 4.954A  pdb=" N   ARG A 269 " --> pdb=" O   GLU A 265 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   PHE A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   MET A 271 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LEU A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   MET A 288 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 353
      removed outlier: 3.584A  pdb=" N   PHE A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      Proline residue:  A 329  - end of helix
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 3.788A  pdb=" N   ILE A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 417
      removed outlier: 3.569A  pdb=" N   THR A 367 " --> pdb=" O   ALA A 363 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 443
      removed outlier: 3.945A  pdb=" N   LEU A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
      Proline residue:  A 438  - end of helix
    Processing helix  chain 'A' and resid 445 through 464
      removed outlier: 3.608A  pdb=" N   GLN A 450 " --> pdb=" O   GLN A 446 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   THR A 451 " --> pdb=" O   PRO A 447 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 455 " --> pdb=" O   THR A 451 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE A 462 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLU A 464 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 472
      removed outlier: 3.538A  pdb=" N   LEU A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 533
    Processing helix  chain 'A' and resid 551 through 553
      No H-bonds generated for 'chain 'A' and resid 551 through 553'
    Processing helix  chain 'A' and resid 554 through 561
      removed outlier: 3.582A  pdb=" N   ILE A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 581
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.502A  pdb=" N   ILE A 592 " --> pdb=" O   ASP A 588 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A 599 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 608
    Processing helix  chain 'A' and resid 626 through 639
    Processing helix  chain 'A' and resid 654 through 667
      removed outlier: 3.520A  pdb=" N   GLY A 667 " --> pdb=" O   ASP A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 684
      removed outlier: 3.646A  pdb=" N   ILE A 684 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 3.678A  pdb=" N   ALA A 709 " --> pdb=" O   THR A 705 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 710 " --> pdb=" O   GLU A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 722
    Processing helix  chain 'B' and resid 20 through 33
    Processing helix  chain 'B' and resid 38 through 46
    Processing helix  chain 'B' and resid 55 through 66
      removed outlier: 3.967A  pdb=" N   ILE B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 82
      removed outlier: 3.760A  pdb=" N   LEU B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LYS B  81 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP B  82 " --> pdb=" O   ASP B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 131
    Processing helix  chain 'B' and resid 153 through 160
    Processing helix  chain 'B' and resid 161 through 163
      No H-bonds generated for 'chain 'B' and resid 161 through 163'
    Processing helix  chain 'B' and resid 167 through 188
      removed outlier: 3.617A  pdb=" N   ALA B 175 " --> pdb=" O   CYS B 171 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE B 188 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 196
      removed outlier: 3.671A  pdb=" N   ASP B 196 " --> pdb=" O   PHE B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'B' and resid 203 through 251
    Processing helix  chain 'B' and resid 254 through 259
      removed outlier: 3.969A  pdb=" N   PHE B 258 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 305
      removed outlier: 4.887A  pdb=" N   ARG B 269 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   PHE B 270 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   MET B 271 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR B 284 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   LEU B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   MET B 288 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 354
      Proline residue:  B 329  - end of helix
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 3.548A  pdb=" N   ILE B 358 " --> pdb=" O   GLY B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 417
      removed outlier: 3.663A  pdb=" N   THR B 367 " --> pdb=" O   ALA B 363 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS B 374 " --> pdb=" O   SER B 370 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   THR B 377 " --> pdb=" O   ASP B 373 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS B 384 " --> pdb=" O   LYS B 380 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLU B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 444
      removed outlier: 4.131A  pdb=" N   LEU B 426 " --> pdb=" O   GLY B 422 " (cutoff:3.500A)
      Proline residue:  B 438  - end of helix
    Processing helix  chain 'B' and resid 445 through 464
      removed outlier: 4.267A  pdb=" N   ILE B 462 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B 463 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLU B 464 " --> pdb=" O   GLY B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 472
      removed outlier: 3.587A  pdb=" N   ARG B 472 " --> pdb=" O   GLU B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 525 through 533
    Processing helix  chain 'B' and resid 551 through 553
      No H-bonds generated for 'chain 'B' and resid 551 through 553'
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 575 through 581
    Processing helix  chain 'B' and resid 588 through 599
      removed outlier: 3.887A  pdb=" N   ILE B 592 " --> pdb=" O   ASP B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 608
    Processing helix  chain 'B' and resid 626 through 639
    Processing helix  chain 'B' and resid 649 through 653
      removed outlier: 3.590A  pdb=" N   ASN B 652 " --> pdb=" O   ALA B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 667
    Processing helix  chain 'B' and resid 703 through 710
    Processing helix  chain 'B' and resid 712 through 722
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37
      removed outlier: 7.426A  pdb=" N   LYS A  36 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73
      removed outlier: 5.973A  pdb=" N   GLY A 135 " --> pdb=" O   ASN A  90 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN A  90 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   THR A 112 " --> pdb=" O   TYR A 104 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE A 111 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR A 123 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509
    Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494
      removed outlier: 6.603A  pdb=" N   PHE A 493 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 562 through 565
      removed outlier: 6.150A  pdb=" N   ALA A 563 " --> pdb=" O   ILE A 645 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   ASP A 647 " --> pdb=" O   ALA A 563 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   VAL A 565 " --> pdb=" O   ASP A 647 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LEU A 644 " --> pdb=" O   ILE A 675 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ILE A 677 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU A 646 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY A 519 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU A 692 " --> pdb=" O   GLU A 700 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   GLU A 700 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37
      removed outlier: 7.143A  pdb=" N   LYS B  36 " --> pdb=" O   TYR B 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 73
      removed outlier: 5.446A  pdb=" N   GLY B 135 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA B  87 " --> pdb=" O   ILE B 103 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VAL B 102 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   THR B 112 " --> pdb=" O   TYR B 104 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 110 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ILE B 110 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 500 through 509
      removed outlier: 6.980A  pdb=" N   VAL B 501 " --> pdb=" O   ARG B 494 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   ARG B 494 " --> pdb=" O   VAL B 501 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LYS B 503 " --> pdb=" O   ASP B 492 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ASP B 492 " --> pdb=" O   LYS B 503 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE B 505 " --> pdb=" O   ASN B 490 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ASN B 490 " --> pdb=" O   ILE B 505 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 562 through 565
      removed outlier: 6.434A  pdb=" N   ALA B 563 " --> pdb=" O   ILE B 645 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ASP B 647 " --> pdb=" O   ALA B 563 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL B 565 " --> pdb=" O   ASP B 647 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU B 644 " --> pdb=" O   ILE B 675 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   ILE B 677 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU B 646 " --> pdb=" O   ILE B 677 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA B 516 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLU B 700 " --> pdb=" O   LEU B 692 " (cutoff:3.500A)

    685 hydrogen bonds defined for protein.
    2010 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: 3.76

  Time building geometry restraints manager: 3.01 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: 3198
        1.34 -     1.46: 1505
        1.46 -     1.57: 6293
        1.57 -     1.69: 6
        1.69 -     1.81: 96
  Bond restraints: 11098
  Sorted by residual:
  bond pdb=" CA  SER A 566 "
       pdb=" C   SER A 566 "
    ideal  model  delta    sigma   weight residual
    1.528  1.476  0.052 1.37e-02 5.33e+03 1.41e+01
  bond pdb=" CA  ASP A 568 "
       pdb=" C   ASP A 568 "
    ideal  model  delta    sigma   weight residual
    1.523  1.492  0.031 1.34e-02 5.57e+03 5.42e+00
  bond pdb=" CA  LEU A 610 "
       pdb=" C   LEU A 610 "
    ideal  model  delta    sigma   weight residual
    1.532  1.510  0.022 1.12e-02 7.97e+03 3.88e+00
  bond pdb=" C   ASP A 568 "
       pdb=" O   ASP A 568 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.019 1.26e-02 6.30e+03 2.21e+00
  bond pdb=" C   LEU A 608 "
       pdb=" N   PRO A 609 "
    ideal  model  delta    sigma   weight residual
    1.332  1.351 -0.019 1.33e-02 5.65e+03 2.00e+00
  ... (remaining 11093 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 14646
        1.44 -     2.87: 226
        2.87 -     4.31: 59
        4.31 -     5.75: 30
        5.75 -     7.19: 7
  Bond angle restraints: 14968
  Sorted by residual:
  angle pdb=" N   SER A 566 "
        pdb=" CA  SER A 566 "
        pdb=" C   SER A 566 "
      ideal   model   delta    sigma   weight residual
     110.53  115.21   -4.68 1.29e+00 6.01e-01 1.32e+01
  angle pdb=" N   VAL A 569 "
        pdb=" CA  VAL A 569 "
        pdb=" C   VAL A 569 "
      ideal   model   delta    sigma   weight residual
     109.51  113.99   -4.48 1.43e+00 4.89e-01 9.80e+00
  angle pdb=" CA  GLU B 245 "
        pdb=" CB  GLU B 245 "
        pdb=" CG  GLU B 245 "
      ideal   model   delta    sigma   weight residual
     114.10  119.97   -5.87 2.00e+00 2.50e-01 8.61e+00
  angle pdb=" C   LEU A 610 "
        pdb=" CA  LEU A 610 "
        pdb=" CB  LEU A 610 "
      ideal   model   delta    sigma   weight residual
     116.34  112.37    3.97 1.40e+00 5.10e-01 8.06e+00
  angle pdb=" CA  TYR A 714 "
        pdb=" CB  TYR A 714 "
        pdb=" CG  TYR A 714 "
      ideal   model   delta    sigma   weight residual
     113.90  118.95   -5.05 1.80e+00 3.09e-01 7.87e+00
  ... (remaining 14963 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 5800
       17.86 -    35.72: 729
       35.72 -    53.57: 134
       53.57 -    71.43: 31
       71.43 -    89.29: 4
  Dihedral angle restraints: 6698
    sinusoidal: 2674
      harmonic: 4024
  Sorted by residual:
  dihedral pdb=" CA  SER A 360 "
           pdb=" C   SER A 360 "
           pdb=" N   PHE A 361 "
           pdb=" CA  PHE A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.45   19.55     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  VAL B 685 "
           pdb=" C   VAL B 685 "
           pdb=" N   ASN B 686 "
           pdb=" CA  ASN B 686 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.33  -18.67     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  SER A 421 "
           pdb=" C   SER A 421 "
           pdb=" N   GLY A 422 "
           pdb=" CA  GLY A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.47   18.53     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 6695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1313
       0.039 -    0.077: 333
       0.077 -    0.116: 108
       0.116 -    0.155: 18
       0.155 -    0.193: 2
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CB  ILE B  92 "
            pdb=" CA  ILE B  92 "
            pdb=" CG1 ILE B  92 "
            pdb=" CG2 ILE B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.35e-01
  chirality pdb=" CG  LEU A 637 "
            pdb=" CB  LEU A 637 "
            pdb=" CD1 LEU A 637 "
            pdb=" CD2 LEU A 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  ILE B 543 "
            pdb=" N   ILE B 543 "
            pdb=" C   ILE B 543 "
            pdb=" CB  ILE B 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.07e-01
  ... (remaining 1771 not shown)

  Planarity restraints: 1846
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 565 "    0.019 2.00e-02 2.50e+03   3.80e-02 1.44e+01
        pdb=" C   VAL A 565 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   VAL A 565 "    0.025 2.00e-02 2.50e+03
        pdb=" N   SER A 566 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 608 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO A 609 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 609 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 609 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A  20 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.45e+00
        pdb=" CG  ASP A  20 "    0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASP A  20 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A  20 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1843 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 100
        2.61 -     3.18: 9622
        3.18 -     3.76: 17000
        3.76 -     4.33: 21946
        4.33 -     4.90: 37200
  Nonbonded interactions: 85868
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 526 "
            pdb="MG    MG A 802 "
     model   vdw
     2.041 2.170
  nonbonded pdb=" OG1 THR B 526 "
            pdb="MG    MG B 802 "
     model   vdw
     2.063 2.170
  nonbonded pdb=" O3B ADP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.121 2.170
  nonbonded pdb=" O1B ADP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.170 2.170
  nonbonded pdb=" NZ  LYS A 525 "
            pdb="MG    MG A 802 "
     model   vdw
     2.185 2.250
  ... (remaining 85863 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:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     27.220
  Find NCS groups from input model:        0.340
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  11098  Z= 0.149
  Angle     :  0.535   7.187  14968  Z= 0.276
  Chirality :  0.040   0.193   1774
  Planarity :  0.003   0.041   1846
  Dihedral  : 15.784  89.288   4110
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 22.15 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.23), residues: 1382
  helix:  1.60 (0.19), residues: 810
  sheet:  0.09 (0.44), residues: 142
  loop : -1.33 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.009   0.001   HIS A  60 
 PHE   0.011   0.001   PHE B 535 
 TYR   0.011   0.001   TYR A 225 
 ARG   0.001   0.000   ARG B 630 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 156
  time to evaluate  : 1.173 
Fit side-chains
REVERT: B  691 TYR cc_start: 0.7333 (m-80) cc_final: 0.6816 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1985
  time to fit residues: 46.5727
Evaluate side-chains
  144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 108 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 125 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 629 GLN
A 704 HIS
B 660 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.187382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.124517 restraints weight = 14728.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.75
r_work: 0.3468 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11098  Z= 0.167
  Angle     :  0.524   8.457  14968  Z= 0.266
  Chirality :  0.040   0.159   1774
  Planarity :  0.003   0.043   1846
  Dihedral  :  4.409  29.777   1498
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.05 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.23), residues: 1382
  helix:  1.70 (0.18), residues: 848
  sheet:  0.40 (0.46), residues: 124
  loop : -1.36 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 718 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.011   0.001   PHE A 194 
 TYR   0.014   0.001   TYR B  32 
 ARG   0.002   0.000   ARG B 269 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 162
  time to evaluate  : 1.177 
Fit side-chains
REVERT: A  100 PHE cc_start: 0.6491 (m-80) cc_final: 0.6244 (m-80)
REVERT: A  434 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.5511 (t80)
REVERT: A  648 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5856 (tm-30)
REVERT: B  152 GLN cc_start: 0.7983 (tt0) cc_final: 0.7494 (tm-30)
REVERT: B  265 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7904 (tt0)
REVERT: B  588 ASP cc_start: 0.8149 (t0) cc_final: 0.7936 (t0)
REVERT: B  598 MET cc_start: 0.7925 (tpp) cc_final: 0.7659 (tpp)
REVERT: B  691 TYR cc_start: 0.7048 (m-80) cc_final: 0.6791 (m-80)
  outliers start: 39
  outliers final: 19
  residues processed: 186
  average time/residue: 0.1910
  time to fit residues: 53.8412
Evaluate side-chains
  174 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 534 ASN
A 629 GLN
A 652 ASN
B 660 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.185507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122125 restraints weight = 14845.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.72
r_work: 0.3433 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11098  Z= 0.205
  Angle     :  0.536  10.275  14968  Z= 0.271
  Chirality :  0.041   0.165   1774
  Planarity :  0.003   0.039   1846
  Dihedral  :  4.458  29.366   1498
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.22 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.23), residues: 1382
  helix:  1.66 (0.18), residues: 852
  sheet:  0.44 (0.47), residues: 124
  loop : -1.34 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 718 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.012   0.001   PHE A 194 
 TYR   0.012   0.001   TYR B 225 
 ARG   0.002   0.000   ARG B 269 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 153
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.6647 (m-80) cc_final: 0.6398 (m-80)
REVERT: A  434 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.5645 (t80)
REVERT: A  648 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6142 (tt0)
REVERT: B  152 GLN cc_start: 0.7985 (tt0) cc_final: 0.7500 (tm-30)
REVERT: B  265 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7926 (tt0)
REVERT: B  691 TYR cc_start: 0.7065 (m-80) cc_final: 0.6761 (m-80)
REVERT: B  717 MET cc_start: 0.8498 (mmm) cc_final: 0.7474 (ttm)
  outliers start: 44
  outliers final: 26
  residues processed: 183
  average time/residue: 0.1927
  time to fit residues: 53.3565
Evaluate side-chains
  176 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue  132 TRP
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  663 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   chunk 135 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 88 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 652 ASN
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.183359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.119053 restraints weight = 14744.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.74
r_work: 0.3396 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11098  Z= 0.268
  Angle     :  0.570  12.103  14968  Z= 0.288
  Chirality :  0.041   0.159   1774
  Planarity :  0.003   0.037   1846
  Dihedral  :  4.585  31.634   1498
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 20.72 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1382
  helix:  1.55 (0.18), residues: 850
  sheet:  0.39 (0.47), residues: 124
  loop : -1.31 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 132 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.015   0.001   PHE A 194 
 TYR   0.014   0.001   TYR B 225 
 ARG   0.002   0.000   ARG B 269 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 157
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.5697 (t80)
REVERT: A  629 GLN cc_start: 0.8763 (pt0) cc_final: 0.8520 (mt0)
REVERT: A  648 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6167 (tt0)
REVERT: B  434 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.5816 (t80)
REVERT: B  598 MET cc_start: 0.7913 (tpp) cc_final: 0.7676 (tpp)
REVERT: B  691 TYR cc_start: 0.7083 (m-80) cc_final: 0.6755 (m-80)
  outliers start: 54
  outliers final: 34
  residues processed: 191
  average time/residue: 0.1899
  time to fit residues: 55.7387
Evaluate side-chains
  185 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 148
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  350 GLU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 110 optimal weight:    0.5980
   chunk 66 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 534 ASN
A 629 GLN
B 152 GLN
** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.185762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.122630 restraints weight = 14665.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.71
r_work: 0.3443 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11098  Z= 0.172
  Angle     :  0.537  13.205  14968  Z= 0.268
  Chirality :  0.040   0.158   1774
  Planarity :  0.003   0.036   1846
  Dihedral  :  4.469  29.287   1498
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.98 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.23), residues: 1382
  helix:  1.61 (0.18), residues: 862
  sheet:  0.44 (0.47), residues: 124
  loop : -1.28 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 132 
 HIS   0.007   0.001   HIS A  60 
 PHE   0.009   0.001   PHE A 428 
 TYR   0.013   0.001   TYR A 225 
 ARG   0.001   0.000   ARG B 109 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 153
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6884 (t)
REVERT: A  434 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.5563 (t80)
REVERT: A  598 MET cc_start: 0.7887 (tpt) cc_final: 0.7633 (tpt)
REVERT: A  648 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6230 (tm-30)
REVERT: B  434 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.5784 (t80)
REVERT: B  691 TYR cc_start: 0.7043 (m-80) cc_final: 0.6756 (m-80)
REVERT: B  717 MET cc_start: 0.8488 (mmm) cc_final: 0.7414 (ttm)
  outliers start: 45
  outliers final: 29
  residues processed: 181
  average time/residue: 0.1989
  time to fit residues: 55.6853
Evaluate side-chains
  177 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  350 GLU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 132 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 133 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 111 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.186255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.125423 restraints weight = 14773.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 3.07
r_work: 0.3430 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11098  Z= 0.170
  Angle     :  0.535  13.080  14968  Z= 0.267
  Chirality :  0.040   0.157   1774
  Planarity :  0.003   0.038   1846
  Dihedral  :  4.397  29.112   1498
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 22.57 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.23), residues: 1382
  helix:  1.68 (0.18), residues: 860
  sheet:  0.42 (0.47), residues: 128
  loop : -1.36 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 132 
 HIS   0.007   0.001   HIS A  60 
 PHE   0.011   0.001   PHE A 570 
 TYR   0.012   0.001   TYR A 225 
 ARG   0.003   0.000   ARG A 630 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 150
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6717 (t)
REVERT: A  387 MET cc_start: 0.7675 (tpp) cc_final: 0.7268 (tpt)
REVERT: A  434 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.5497 (t80)
REVERT: A  598 MET cc_start: 0.7889 (tpt) cc_final: 0.7572 (tpt)
REVERT: A  648 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6128 (tm-30)
REVERT: B  265 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7768 (tt0)
REVERT: B  434 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5599 (t80)
REVERT: B  598 MET cc_start: 0.7864 (tpp) cc_final: 0.7650 (tpp)
REVERT: B  630 ARG cc_start: 0.8475 (ptp-110) cc_final: 0.8219 (ptp-110)
REVERT: B  691 TYR cc_start: 0.6956 (m-80) cc_final: 0.6734 (m-80)
REVERT: B  717 MET cc_start: 0.8485 (mmm) cc_final: 0.7447 (ttm)
  outliers start: 46
  outliers final: 35
  residues processed: 179
  average time/residue: 0.1885
  time to fit residues: 51.5627
Evaluate side-chains
  184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  350 GLU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 42 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9980
   chunk 116 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
A 534 ASN
** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.185634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.123766 restraints weight = 14934.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.92
r_work: 0.3428 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11098  Z= 0.188
  Angle     :  0.542  13.348  14968  Z= 0.270
  Chirality :  0.040   0.154   1774
  Planarity :  0.003   0.037   1846
  Dihedral  :  4.384  29.131   1498
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 23.07 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.23), residues: 1382
  helix:  1.67 (0.18), residues: 862
  sheet:  0.42 (0.47), residues: 128
  loop : -1.31 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 132 
 HIS   0.008   0.001   HIS A  60 
 PHE   0.009   0.001   PHE A 194 
 TYR   0.012   0.001   TYR A 225 
 ARG   0.001   0.000   ARG B 458 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 148
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6716 (t)
REVERT: A  387 MET cc_start: 0.7676 (tpp) cc_final: 0.7287 (tpt)
REVERT: A  434 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.5507 (t80)
REVERT: A  598 MET cc_start: 0.7859 (tpt) cc_final: 0.7510 (tpt)
REVERT: A  648 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6127 (tm-30)
REVERT: B  434 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.5577 (t80)
REVERT: B  598 MET cc_start: 0.7845 (tpp) cc_final: 0.7609 (tpp)
  outliers start: 49
  outliers final: 41
  residues processed: 183
  average time/residue: 0.1934
  time to fit residues: 53.6737
Evaluate side-chains
  189 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 144
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  350 GLU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0770
   chunk 131 optimal weight:    8.9990
   chunk 121 optimal weight:    0.9980
   chunk 116 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 110 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 73 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 629 GLN
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.186817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.124292 restraints weight = 14725.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.73
r_work: 0.3465 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11098  Z= 0.162
  Angle     :  0.544  14.035  14968  Z= 0.270
  Chirality :  0.040   0.164   1774
  Planarity :  0.003   0.038   1846
  Dihedral  :  4.347  29.011   1498
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.49 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.23), residues: 1382
  helix:  1.73 (0.18), residues: 862
  sheet:  0.46 (0.47), residues: 128
  loop : -1.32 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 132 
 HIS   0.009   0.001   HIS A  60 
 PHE   0.008   0.001   PHE B 535 
 TYR   0.012   0.001   TYR A 225 
 ARG   0.003   0.000   ARG B 630 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 154
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6728 (t)
REVERT: A  387 MET cc_start: 0.7881 (tpp) cc_final: 0.7492 (tpt)
REVERT: A  434 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.5627 (t80)
REVERT: A  598 MET cc_start: 0.7876 (tpt) cc_final: 0.7541 (tpt)
REVERT: A  648 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6442 (tm-30)
REVERT: B  265 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7845 (tt0)
REVERT: B  434 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.5741 (t80)
REVERT: B  598 MET cc_start: 0.7877 (tpp) cc_final: 0.7629 (tpp)
REVERT: B  691 TYR cc_start: 0.7010 (m-80) cc_final: 0.6712 (m-80)
  outliers start: 45
  outliers final: 37
  residues processed: 181
  average time/residue: 0.1847
  time to fit residues: 51.3512
Evaluate side-chains
  189 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  350 GLU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0370
   chunk 39 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 117 optimal weight:    3.9990
   chunk 136 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0970
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 534 ASN
B 629 GLN
B 652 ASN
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.187584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.125296 restraints weight = 14942.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.77
r_work: 0.3476 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11098  Z= 0.152
  Angle     :  0.544  14.347  14968  Z= 0.268
  Chirality :  0.040   0.160   1774
  Planarity :  0.003   0.038   1846
  Dihedral  :  4.305  28.888   1498
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.66 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.23), residues: 1382
  helix:  1.77 (0.18), residues: 862
  sheet:  0.50 (0.48), residues: 128
  loop : -1.27 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 132 
 HIS   0.010   0.001   HIS A  60 
 PHE   0.013   0.001   PHE A 570 
 TYR   0.012   0.001   TYR A 225 
 ARG   0.005   0.000   ARG B 630 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 152
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6666 (t)
REVERT: A  598 MET cc_start: 0.7885 (tpt) cc_final: 0.7532 (tpt)
REVERT: A  648 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6449 (tt0)
REVERT: B  265 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7741 (tt0)
REVERT: B  434 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.5759 (t80)
REVERT: B  691 TYR cc_start: 0.7072 (m-80) cc_final: 0.6765 (m-80)
  outliers start: 43
  outliers final: 37
  residues processed: 178
  average time/residue: 0.1881
  time to fit residues: 51.8161
Evaluate side-chains
  187 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 147
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  350 GLU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  629 GLN
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 107 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 629 GLN
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.185053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.124074 restraints weight = 14857.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 3.07
r_work: 0.3418 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11098  Z= 0.205
  Angle     :  0.569  14.201  14968  Z= 0.283
  Chirality :  0.041   0.166   1774
  Planarity :  0.003   0.038   1846
  Dihedral  :  4.396  29.022   1498
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.83 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.23), residues: 1382
  helix:  1.67 (0.18), residues: 862
  sheet:  0.43 (0.48), residues: 128
  loop : -1.30 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 132 
 HIS   0.011   0.001   HIS A  60 
 PHE   0.012   0.001   PHE A 570 
 TYR   0.015   0.001   TYR A 714 
 ARG   0.008   0.000   ARG B 630 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 146
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6922 (t)
REVERT: A  434 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.5520 (t80)
REVERT: A  598 MET cc_start: 0.7895 (tpt) cc_final: 0.7554 (tpt)
REVERT: B  434 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.5577 (t80)
REVERT: B  527 THR cc_start: 0.6519 (t) cc_final: 0.6265 (m)
REVERT: B  691 TYR cc_start: 0.7023 (m-80) cc_final: 0.6729 (m-80)
REVERT: B  717 MET cc_start: 0.8396 (mmm) cc_final: 0.7360 (ttm)
  outliers start: 45
  outliers final: 39
  residues processed: 178
  average time/residue: 0.1793
  time to fit residues: 49.1754
Evaluate side-chains
  187 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  350 GLU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  533 MET
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  699 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 114 optimal weight:    6.9990
   chunk 129 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 127 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 136 optimal weight:   20.0000
   chunk 125 optimal weight:    0.9980
   chunk 75 optimal weight:   20.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 659 ASN
B 660 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.185139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.122087 restraints weight = 14803.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.70
r_work: 0.3437 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.159  11098  Z= 0.310
  Angle     :  0.933  59.200  14968  Z= 0.553
  Chirality :  0.048   0.803   1774
  Planarity :  0.004   0.141   1846
  Dihedral  :  4.435  29.018   1498
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 24.08 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.23), residues: 1382
  helix:  1.66 (0.18), residues: 862
  sheet:  0.43 (0.48), residues: 128
  loop : -1.30 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 132 
 HIS   0.010   0.001   HIS A  60 
 PHE   0.010   0.001   PHE B 435 
 TYR   0.013   0.001   TYR B 225 
 ARG   0.006   0.000   ARG B 630 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6483.38 seconds
wall clock time: 115 minutes 57.63 seconds (6957.63 seconds total)