Starting phenix.real_space_refine
on Wed Apr 30 23:52:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ik4_60648/04_2025/9ik4_60648.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ik4_60648/04_2025/9ik4_60648.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ik4_60648/04_2025/9ik4_60648.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ik4_60648/04_2025/9ik4_60648.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ik4_60648/04_2025/9ik4_60648.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ik4_60648/04_2025/9ik4_60648.cif"
  }
  resolution = 3.34
  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=  -0.002 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      14      5.49       5
     S      64      5.16       5
     C    6590      2.51       5
     N    1668      2.21       5
     O    1778      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 103 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10114
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 607, 5016
          Classifications: {'peptide': 607}
          Link IDs: {'PTRANS': 10, 'TRANS': 596}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 607, 5016
          Classifications: {'peptide': 607}
          Link IDs: {'PTRANS': 10, 'TRANS': 596}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'IHP': 1, 'PO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'IHP': 1, 'PO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.37, per 1000 atoms: 0.63
  Number of scatterers: 10114
  At special positions: 0
  Unit cell: (105.41, 118.69, 95.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      64     16.00
     P      14     15.00
     O    1778      8.00
     N    1668      7.00
     C    6590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 577 " - pdb=" SG  CYS A 592 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 577 " - pdb=" SG  CYS B 592 " distance=2.03

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.69
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2320

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 2 sheets defined
      54.7% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 39
      removed outlier: 3.838A  pdb=" N   LYS A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASP A  29 " --> pdb=" O   GLN A  25 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   HIS A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASN A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 151
      removed outlier: 3.765A  pdb=" N   PHE A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   CYS A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU A 112 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASP A 113 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   MET A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE A 122 " --> pdb=" O   LYS A 118 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   CYS A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   LEU A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LYS A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A 144 " --> pdb=" O   GLN A 140 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU A 146 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA A 150 " --> pdb=" O   GLU A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 317
      removed outlier: 4.134A  pdb=" N   LYS A 287 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   MET A 288 " --> pdb=" O   HIS A 284 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLY A 291 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   ALA A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   GLU A 295 " --> pdb=" O   GLY A 291 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   PHE A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASN A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 325
    Processing helix  chain 'A' and resid 328 through 333
      removed outlier: 3.798A  pdb=" N   ILE A 332 " --> pdb=" O   GLN A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 338
      removed outlier: 3.535A  pdb=" N   VAL A 337 " --> pdb=" O   TYR A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 350 through 355
    Processing helix  chain 'A' and resid 369 through 374
      removed outlier: 3.768A  pdb=" N   TYR A 374 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 403
      removed outlier: 3.611A  pdb=" N   PHE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 444
      removed outlier: 3.646A  pdb=" N   LEU A 437 " --> pdb=" O   MET A 433 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE A 438 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   PHE A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 453
      removed outlier: 3.618A  pdb=" N   LYS A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.657A  pdb=" N   ILE A 461 " --> pdb=" O   ASN A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 490
      removed outlier: 3.689A  pdb=" N   VAL A 489 " --> pdb=" O   ALA A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 500
      removed outlier: 3.747A  pdb=" N   LEU A 496 " --> pdb=" O   VAL A 492 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A 497 " --> pdb=" O   HIS A 493 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS A 499 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 3.516A  pdb=" N   GLN A 507 " --> pdb=" O   PHE A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 522
      removed outlier: 3.704A  pdb=" N   LEU A 515 " --> pdb=" O   GLY A 511 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A 522 " --> pdb=" O   LEU A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 557
    Processing helix  chain 'A' and resid 558 through 560
      No H-bonds generated for 'chain 'A' and resid 558 through 560'
    Processing helix  chain 'A' and resid 567 through 571
      removed outlier: 3.521A  pdb=" N   ARG A 570 " --> pdb=" O   PRO A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 578
    Processing helix  chain 'A' and resid 595 through 599
    Processing helix  chain 'A' and resid 608 through 615
      removed outlier: 3.746A  pdb=" N   ALA A 614 " --> pdb=" O   TYR A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 642
      removed outlier: 3.698A  pdb=" N   VAL A 631 " --> pdb=" O   THR A 627 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   LEU A 633 " --> pdb=" O   HIS A 629 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   TYR A 636 " --> pdb=" O   ASN A 632 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 637 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA A 639 " --> pdb=" O   LYS A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 648
      removed outlier: 3.811A  pdb=" N   ALA A 648 " --> pdb=" O   GLY A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 672
      removed outlier: 3.627A  pdb=" N   THR A 669 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A 670 " --> pdb=" O   SER A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 678
      removed outlier: 3.988A  pdb=" N   PHE A 677 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 711
      removed outlier: 3.609A  pdb=" N   PHE A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER A 708 " --> pdb=" O   ILE A 704 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET A 709 " --> pdb=" O   TYR A 705 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL A 710 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 717
    Processing helix  chain 'A' and resid 740 through 748
      removed outlier: 3.901A  pdb=" N   VAL A 745 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ILE A 746 " --> pdb=" O   ALA A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 762
      removed outlier: 3.643A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 39
      removed outlier: 3.838A  pdb=" N   LYS B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASP B  29 " --> pdb=" O   GLN B  25 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   HIS B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASN B  38 " --> pdb=" O   HIS B  34 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 151
      removed outlier: 3.766A  pdb=" N   PHE B 109 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   CYS B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU B 112 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASP B 113 " --> pdb=" O   PHE B 109 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   MET B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE B 122 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   CYS B 136 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 5.880A  pdb=" N   LEU B 137 " --> pdb=" O   ARG B 133 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   LYS B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU B 144 " --> pdb=" O   GLN B 140 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU B 146 " --> pdb=" O   ASP B 142 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA B 150 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 317
      removed outlier: 4.134A  pdb=" N   LYS B 287 " --> pdb=" O   SER B 283 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   MET B 288 " --> pdb=" O   HIS B 284 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE B 289 " --> pdb=" O   ALA B 285 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY B 291 " --> pdb=" O   LYS B 287 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   ALA B 292 " --> pdb=" O   MET B 288 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   GLU B 295 " --> pdb=" O   GLY B 291 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS B 298 " --> pdb=" O   THR B 294 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 300 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASN B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 325
    Processing helix  chain 'B' and resid 328 through 333
      removed outlier: 3.799A  pdb=" N   ILE B 332 " --> pdb=" O   GLN B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 338
      removed outlier: 3.535A  pdb=" N   VAL B 337 " --> pdb=" O   TYR B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 345
      removed outlier: 3.501A  pdb=" N   SER B 345 " --> pdb=" O   TYR B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 355
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 3.767A  pdb=" N   TYR B 374 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 403
      removed outlier: 3.612A  pdb=" N   PHE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 444
      removed outlier: 3.646A  pdb=" N   LEU B 437 " --> pdb=" O   MET B 433 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE B 438 " --> pdb=" O   PHE B 434 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   PHE B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 453
      removed outlier: 3.618A  pdb=" N   LYS B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 462
      removed outlier: 3.658A  pdb=" N   ILE B 461 " --> pdb=" O   ASN B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 482
    Processing helix  chain 'B' and resid 483 through 490
      removed outlier: 3.689A  pdb=" N   VAL B 489 " --> pdb=" O   ALA B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 500
      removed outlier: 3.747A  pdb=" N   LEU B 496 " --> pdb=" O   VAL B 492 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU B 497 " --> pdb=" O   HIS B 493 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS B 499 " --> pdb=" O   SER B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 507
      removed outlier: 3.515A  pdb=" N   GLN B 507 " --> pdb=" O   PHE B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 522
      removed outlier: 3.703A  pdb=" N   LEU B 515 " --> pdb=" O   GLY B 511 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE B 522 " --> pdb=" O   LEU B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 557
    Processing helix  chain 'B' and resid 558 through 560
      No H-bonds generated for 'chain 'B' and resid 558 through 560'
    Processing helix  chain 'B' and resid 567 through 571
      removed outlier: 3.520A  pdb=" N   ARG B 570 " --> pdb=" O   PRO B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 578
    Processing helix  chain 'B' and resid 595 through 599
    Processing helix  chain 'B' and resid 608 through 615
      removed outlier: 3.746A  pdb=" N   ALA B 614 " --> pdb=" O   TYR B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 642
      removed outlier: 3.698A  pdb=" N   VAL B 631 " --> pdb=" O   THR B 627 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   LEU B 633 " --> pdb=" O   HIS B 629 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TYR B 636 " --> pdb=" O   ASN B 632 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL B 637 " --> pdb=" O   LEU B 633 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA B 639 " --> pdb=" O   LYS B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 648
      removed outlier: 3.811A  pdb=" N   ALA B 648 " --> pdb=" O   GLY B 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 672
      removed outlier: 3.627A  pdb=" N   THR B 669 " --> pdb=" O   SER B 665 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 670 " --> pdb=" O   SER B 666 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 678
      removed outlier: 3.988A  pdb=" N   PHE B 677 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 703 through 711
      removed outlier: 3.608A  pdb=" N   PHE B 707 " --> pdb=" O   SER B 703 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER B 708 " --> pdb=" O   ILE B 704 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET B 709 " --> pdb=" O   TYR B 705 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL B 710 " --> pdb=" O   TYR B 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 717
    Processing helix  chain 'B' and resid 740 through 748
      removed outlier: 3.902A  pdb=" N   VAL B 745 " --> pdb=" O   ALA B 741 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ILE B 746 " --> pdb=" O   ALA B 742 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 762
      removed outlier: 3.642A  pdb=" N   ASN B 758 " --> pdb=" O   TYR B 754 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79
      removed outlier: 3.815A  pdb=" N   LYS A  79 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.816A  pdb=" N   LYS B  79 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.59

  Time building geometry restraints manager: 2.87 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1576
        1.32 -     1.44: 2955
        1.44 -     1.56: 5707
        1.56 -     1.69: 12
        1.69 -     1.81: 106
  Bond restraints: 10356
  Sorted by residual:
  bond pdb=" N   VAL B 430 "
       pdb=" CA  VAL B 430 "
    ideal  model  delta    sigma   weight residual
    1.459  1.504 -0.045 9.10e-03 1.21e+04 2.45e+01
  bond pdb=" O16 IHP B1002 "
       pdb=" P6  IHP B1002 "
    ideal  model  delta    sigma   weight residual
    1.672  1.579  0.093 2.00e-02 2.50e+03 2.16e+01
  bond pdb=" O16 IHP A 801 "
       pdb=" P6  IHP A 801 "
    ideal  model  delta    sigma   weight residual
    1.672  1.579  0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" N   VAL A 430 "
       pdb=" CA  VAL A 430 "
    ideal  model  delta    sigma   weight residual
    1.459  1.509 -0.050 1.25e-02 6.40e+03 1.62e+01
  bond pdb=" O14 IHP B1002 "
       pdb=" P4  IHP B1002 "
    ideal  model  delta    sigma   weight residual
    1.671  1.597  0.074 2.00e-02 2.50e+03 1.38e+01
  ... (remaining 10351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.48: 13739
        4.48 -     8.97: 213
        8.97 -    13.45: 26
       13.45 -    17.94: 6
       17.94 -    22.42: 2
  Bond angle restraints: 13986
  Sorted by residual:
  angle pdb=" N   GLY A 412 "
        pdb=" CA  GLY A 412 "
        pdb=" C   GLY A 412 "
      ideal   model   delta    sigma   weight residual
     115.36  137.78  -22.42 1.33e+00 5.65e-01 2.84e+02
  angle pdb=" N   GLY B 412 "
        pdb=" CA  GLY B 412 "
        pdb=" C   GLY B 412 "
      ideal   model   delta    sigma   weight residual
     115.36  137.73  -22.37 1.33e+00 5.65e-01 2.83e+02
  angle pdb=" N   MET B 413 "
        pdb=" CA  MET B 413 "
        pdb=" C   MET B 413 "
      ideal   model   delta    sigma   weight residual
     113.88  103.69   10.19 1.23e+00 6.61e-01 6.86e+01
  angle pdb=" N   MET A 413 "
        pdb=" CA  MET A 413 "
        pdb=" C   MET A 413 "
      ideal   model   delta    sigma   weight residual
     113.88  103.71   10.17 1.23e+00 6.61e-01 6.84e+01
  angle pdb=" N   LEU B 431 "
        pdb=" CA  LEU B 431 "
        pdb=" C   LEU B 431 "
      ideal   model   delta    sigma   weight residual
     113.30  102.45   10.85 1.34e+00 5.57e-01 6.55e+01
  ... (remaining 13981 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.98: 5891
       32.98 -    65.95: 241
       65.95 -    98.93: 30
       98.93 -   131.90: 2
      131.90 -   164.88: 6
  Dihedral angle restraints: 6170
    sinusoidal: 2566
      harmonic: 3604
  Sorted by residual:
  dihedral pdb=" CA  HIS A 730 "
           pdb=" C   HIS A 730 "
           pdb=" N   VAL A 731 "
           pdb=" CA  VAL A 731 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.70  -29.30     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  HIS B 730 "
           pdb=" C   HIS B 730 "
           pdb=" N   VAL B 731 "
           pdb=" CA  VAL B 731 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.72  -29.28     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  GLU A 759 "
           pdb=" C   GLU A 759 "
           pdb=" N   HIS A 760 "
           pdb=" CA  HIS A 760 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.88   27.12     0      5.00e+00 4.00e-02 2.94e+01
  ... (remaining 6167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.996: 1520
       0.996 -    1.992: 0
       1.992 -    2.989: 0
       2.989 -    3.985: 0
       3.985 -    4.981: 4
  Chirality restraints: 1524
  Sorted by residual:
  chirality pdb=" C2  IHP A 801 "
            pdb=" C1  IHP A 801 "
            pdb=" C3  IHP A 801 "
            pdb=" O12 IHP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.46   -4.98 2.00e-01 2.50e+01 6.20e+02
  chirality pdb=" C2  IHP B1002 "
            pdb=" C1  IHP B1002 "
            pdb=" C3  IHP B1002 "
            pdb=" O12 IHP B1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.46   -4.98 2.00e-01 2.50e+01 6.20e+02
  chirality pdb=" C3  IHP B1002 "
            pdb=" C2  IHP B1002 "
            pdb=" C4  IHP B1002 "
            pdb=" O13 IHP B1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.34    2.46   -4.79 2.00e-01 2.50e+01 5.75e+02
  ... (remaining 1521 not shown)

  Planarity restraints: 1702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 428 "    0.075 5.00e-02 4.00e+02   1.15e-01 2.13e+01
        pdb=" N   PRO A 429 "   -0.200 5.00e-02 4.00e+02
        pdb=" CA  PRO A 429 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO A 429 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 671 "   -0.029 2.00e-02 2.50e+03   2.59e-02 1.34e+01
        pdb=" CG  TYR B 671 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 671 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 671 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 671 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 671 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 671 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 671 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 671 "    0.028 2.00e-02 2.50e+03   2.57e-02 1.32e+01
        pdb=" CG  TYR A 671 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 671 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 671 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 671 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 671 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 671 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 671 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1699 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 77
        2.48 -     3.09: 6250
        3.09 -     3.69: 15588
        3.69 -     4.30: 21985
        4.30 -     4.90: 35392
  Nonbonded interactions: 79292
  Sorted by model distance:
  nonbonded pdb=" CD2 TYR A 733 "
            pdb=" CG2 THR A 736 "
     model   vdw
     1.881 3.760
  nonbonded pdb=" CD2 TYR B 733 "
            pdb=" CG2 THR B 736 "
     model   vdw
     1.882 3.760
  nonbonded pdb=" CE2 TYR A 733 "
            pdb=" CG2 THR A 736 "
     model   vdw
     1.982 3.760
  nonbonded pdb=" CE2 TYR B 733 "
            pdb=" CG2 THR B 736 "
     model   vdw
     1.985 3.760
  nonbonded pdb=" O   GLN B 587 "
            pdb=" OD1 ASP B 588 "
     model   vdw
     2.018 3.040
  ... (remaining 79287 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: 0.08
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 11 through 772)
  selection = (chain 'B' and resid 11 through 772)
}

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:             2.410
  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:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.720
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.764  10360  Z= 1.134
  Angle     :  1.414  22.423  13990  Z= 0.796
  Chirality :  0.257   4.981   1524
  Planarity :  0.007   0.115   1702
  Dihedral  : 19.372 164.880   3844
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 14.06 %
    Favored  : 85.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.67 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.52 (0.15), residues: 1202
  helix: -4.31 (0.10), residues: 746
  sheet: -2.30 (0.99), residues: 24
  loop : -4.15 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A 657 
 HIS   0.016   0.002   HIS B 284 
 PHE   0.048   0.004   PHE B  20 
 TYR   0.063   0.003   TYR B 671 
 ARG   0.015   0.001   ARG A 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.33596 (  297)
  hydrogen bonds       : angle      10.98867 (  837)
  SS BOND              : bond        0.00110 (    2)
  SS BOND              : angle       0.30453 (    4)
  covalent geometry    : bond        0.00835 (10356)
  covalent geometry    : angle       1.41438 (13986)
  Misc. bond           : bond        0.76218 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 VAL cc_start: 0.6120 (t) cc_final: 0.5881 (m)
REVERT: B  335 LYS cc_start: 0.6748 (mmpt) cc_final: 0.6214 (ptmt)
REVERT: B  410 LEU cc_start: 0.7367 (tt) cc_final: 0.6683 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.2555
  time to fit residues: 73.2029
Evaluate side-chains
  162 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0570
   chunk 94 optimal weight:    0.2980
   chunk 36 optimal weight:    0.4980
   chunk 57 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0770
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
A 120 ASN
A 157 ASN
A 284 HIS
A 316 ASN
** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 ASN
A 629 HIS
B  11 GLN
B 120 ASN
B 157 ASN
B 284 HIS
B 301 ASN
B 316 ASN
** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 629 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5045 r_free = 0.5045 target = 0.277480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.234841 restraints weight = 10790.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.4682 rms_B_bonded: 3.04
r_work: 0.4185 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10360  Z= 0.135
  Angle     :  0.798  13.414  13990  Z= 0.403
  Chirality :  0.049   0.605   1524
  Planarity :  0.005   0.071   1702
  Dihedral  : 13.387  97.696   1424
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.22 %
    Favored  : 80.56 %
  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: -5.28 (0.19), residues: 1202
  helix: -3.17 (0.15), residues: 752
  sheet: -2.16 (1.02), residues: 24
  loop : -3.97 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 612 
 HIS   0.015   0.002   HIS A 384 
 PHE   0.029   0.001   PHE A 622 
 TYR   0.025   0.002   TYR B 671 
 ARG   0.003   0.001   ARG B 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04817 (  297)
  hydrogen bonds       : angle       6.50465 (  837)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.82972 (    4)
  covalent geometry    : bond        0.00268 (10356)
  covalent geometry    : angle       0.79826 (13986)
  Misc. bond           : bond        0.00327 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 VAL cc_start: 0.3049 (OUTLIER) cc_final: 0.2788 (m)
REVERT: A  335 LYS cc_start: 0.7484 (mmmt) cc_final: 0.6222 (ptmt)
REVERT: A  349 MET cc_start: 0.7440 (mmt) cc_final: 0.7004 (mmm)
REVERT: A  410 LEU cc_start: 0.7108 (tt) cc_final: 0.6368 (mt)
REVERT: A  569 LEU cc_start: 0.7935 (mt) cc_final: 0.7726 (mt)
REVERT: B   89 VAL cc_start: 0.3025 (OUTLIER) cc_final: 0.2785 (m)
REVERT: B  335 LYS cc_start: 0.7659 (mmpt) cc_final: 0.6229 (ptmt)
REVERT: B  410 LEU cc_start: 0.7289 (tt) cc_final: 0.6499 (mt)
REVERT: B  569 LEU cc_start: 0.8001 (mt) cc_final: 0.7779 (mt)
REVERT: B  590 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7093 (mm-30)
  outliers start: 24
  outliers final: 11
  residues processed: 177
  average time/residue: 0.2933
  time to fit residues: 73.1806
Evaluate side-chains
  155 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 2.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0270
   chunk 92 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 114 optimal weight:    4.9990
   overall best weight:    1.1442

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 HIS
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN
B 115 GLN
B 301 ASN
B 316 ASN
B 384 HIS
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 ASN
B 587 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.273950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.231171 restraints weight = 10895.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.4657 rms_B_bonded: 3.33
r_work: 0.4114 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10360  Z= 0.161
  Angle     :  0.736  11.281  13990  Z= 0.377
  Chirality :  0.046   0.357   1524
  Planarity :  0.004   0.049   1702
  Dihedral  : 12.916  93.443   1424
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.48 %
    Favored  : 87.52 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.17 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.80 (0.21), residues: 1202
  helix: -2.71 (0.16), residues: 770
  sheet: -1.93 (1.02), residues: 24
  loop : -3.97 (0.26), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 621 
 HIS   0.013   0.001   HIS B 384 
 PHE   0.016   0.002   PHE A 767 
 TYR   0.022   0.002   TYR B 671 
 ARG   0.005   0.001   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04496 (  297)
  hydrogen bonds       : angle       5.81030 (  837)
  SS BOND              : bond        0.00090 (    2)
  SS BOND              : angle       0.47328 (    4)
  covalent geometry    : bond        0.00349 (10356)
  covalent geometry    : angle       0.73562 (13986)
  Misc. bond           : bond        0.00061 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 VAL cc_start: 0.3295 (OUTLIER) cc_final: 0.2976 (m)
REVERT: A  335 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6338 (ptmt)
REVERT: A  349 MET cc_start: 0.7595 (mmt) cc_final: 0.7198 (mmm)
REVERT: A  410 LEU cc_start: 0.7286 (tt) cc_final: 0.6519 (mt)
REVERT: A  569 LEU cc_start: 0.8075 (mt) cc_final: 0.7785 (mt)
REVERT: B   89 VAL cc_start: 0.3253 (OUTLIER) cc_final: 0.2959 (m)
REVERT: B  335 LYS cc_start: 0.7631 (mmpt) cc_final: 0.6322 (ptmt)
REVERT: B  569 LEU cc_start: 0.8101 (mt) cc_final: 0.7827 (mt)
  outliers start: 37
  outliers final: 24
  residues processed: 168
  average time/residue: 0.1984
  time to fit residues: 48.0260
Evaluate side-chains
  158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  578 TYR
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 112 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 114 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
A 310 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.275813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.231128 restraints weight = 10757.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.4652 rms_B_bonded: 3.05
r_work: 0.4150 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10360  Z= 0.123
  Angle     :  0.676  12.407  13990  Z= 0.345
  Chirality :  0.042   0.228   1524
  Planarity :  0.003   0.041   1702
  Dihedral  : 12.525  90.063   1424
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.56 %
    Favored  : 88.44 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.28 %
    Favored  : 75.93 %
  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: -4.38 (0.22), residues: 1202
  helix: -2.40 (0.17), residues: 776
  sheet: -1.76 (1.02), residues: 24
  loop : -3.76 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  16 
 HIS   0.006   0.001   HIS B 384 
 PHE   0.015   0.001   PHE A 122 
 TYR   0.028   0.002   TYR A 306 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  297)
  hydrogen bonds       : angle       5.33145 (  837)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.33625 (    4)
  covalent geometry    : bond        0.00262 (10356)
  covalent geometry    : angle       0.67657 (13986)
  Misc. bond           : bond        0.00056 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 VAL cc_start: 0.3144 (OUTLIER) cc_final: 0.2818 (m)
REVERT: A  335 LYS cc_start: 0.7474 (mmmt) cc_final: 0.6456 (ptmt)
REVERT: A  349 MET cc_start: 0.7607 (mmt) cc_final: 0.7262 (mmm)
REVERT: A  569 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7751 (mt)
REVERT: B   25 GLN cc_start: 0.6962 (tm130) cc_final: 0.6460 (tp40)
REVERT: B   89 VAL cc_start: 0.3083 (OUTLIER) cc_final: 0.2774 (m)
REVERT: B  335 LYS cc_start: 0.7572 (mmpt) cc_final: 0.6376 (ptmt)
REVERT: B  569 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7897 (mt)
  outliers start: 41
  outliers final: 27
  residues processed: 173
  average time/residue: 0.1969
  time to fit residues: 49.4942
Evaluate side-chains
  164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  578 TYR
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:   30.0000
   chunk 113 optimal weight:    0.0030
   chunk 61 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0000
   chunk 67 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0070
   chunk 93 optimal weight:    6.9990
   overall best weight:    0.2614

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 301 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 HIS
B 301 ASN
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5052 r_free = 0.5052 target = 0.279242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.236484 restraints weight = 10783.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4695 rms_B_bonded: 2.92
r_work: 0.4210 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10360  Z= 0.107
  Angle     :  0.675  11.940  13990  Z= 0.334
  Chirality :  0.040   0.194   1524
  Planarity :  0.003   0.035   1702
  Dihedral  : 12.191  87.903   1424
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.15 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.74 %
    Favored  : 75.00 %
  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: -4.04 (0.22), residues: 1202
  helix: -2.15 (0.18), residues: 750
  sheet: -1.59 (1.02), residues: 24
  loop : -3.54 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 675 
 HIS   0.006   0.001   HIS B 384 
 PHE   0.009   0.001   PHE B 422 
 TYR   0.023   0.001   TYR B 306 
 ARG   0.007   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  297)
  hydrogen bonds       : angle       5.04826 (  837)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.49591 (    4)
  covalent geometry    : bond        0.00214 (10356)
  covalent geometry    : angle       0.67523 (13986)
  Misc. bond           : bond        0.00050 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 148
  time to evaluate  : 1.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6772 (tm130) cc_final: 0.6250 (tp40)
REVERT: A   89 VAL cc_start: 0.3272 (OUTLIER) cc_final: 0.2929 (m)
REVERT: A  335 LYS cc_start: 0.7589 (mmmt) cc_final: 0.6762 (ptmt)
REVERT: A  503 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6017 (t80)
REVERT: A  569 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7665 (mt)
REVERT: B   25 GLN cc_start: 0.6861 (tm130) cc_final: 0.6293 (tp40)
REVERT: B   89 VAL cc_start: 0.3052 (OUTLIER) cc_final: 0.2740 (m)
REVERT: B  335 LYS cc_start: 0.7511 (mmpt) cc_final: 0.6480 (ptmt)
REVERT: B  569 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7720 (mt)
REVERT: B  593 MET cc_start: 0.6853 (mpp) cc_final: 0.6138 (ppp)
REVERT: B  621 TRP cc_start: 0.7580 (t60) cc_final: 0.7345 (t-100)
  outliers start: 46
  outliers final: 30
  residues processed: 178
  average time/residue: 0.2053
  time to fit residues: 53.3524
Evaluate side-chains
  173 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  578 TYR
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 71 optimal weight:   10.0000
   chunk 91 optimal weight:    0.5980
   chunk 84 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 98 optimal weight:    0.1980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 ASN
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5040 r_free = 0.5040 target = 0.277355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.233196 restraints weight = 10862.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.4673 rms_B_bonded: 3.01
r_work: 0.4171 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10360  Z= 0.119
  Angle     :  0.678  11.850  13990  Z= 0.336
  Chirality :  0.041   0.183   1524
  Planarity :  0.003   0.035   1702
  Dihedral  : 12.031  86.232   1424
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 22.13 %
    Favored  : 73.80 %
  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: -3.88 (0.23), residues: 1202
  helix: -1.99 (0.18), residues: 744
  sheet: -2.10 (0.93), residues: 28
  loop : -3.53 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 675 
 HIS   0.005   0.001   HIS B 384 
 PHE   0.010   0.001   PHE A 767 
 TYR   0.021   0.001   TYR B 341 
 ARG   0.005   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  297)
  hydrogen bonds       : angle       4.97540 (  837)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       0.37465 (    4)
  covalent geometry    : bond        0.00255 (10356)
  covalent geometry    : angle       0.67813 (13986)
  Misc. bond           : bond        0.00052 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 143
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6811 (tm130) cc_final: 0.6281 (tp40)
REVERT: A   89 VAL cc_start: 0.3294 (OUTLIER) cc_final: 0.2962 (m)
REVERT: A  301 ASN cc_start: 0.8349 (t0) cc_final: 0.7569 (m-40)
REVERT: A  335 LYS cc_start: 0.7707 (mmmt) cc_final: 0.6840 (ptmt)
REVERT: A  503 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6194 (t80)
REVERT: A  569 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7695 (mt)
REVERT: B   25 GLN cc_start: 0.6888 (tm130) cc_final: 0.6315 (tp40)
REVERT: B   89 VAL cc_start: 0.2922 (OUTLIER) cc_final: 0.2587 (m)
REVERT: B  335 LYS cc_start: 0.7474 (mmpt) cc_final: 0.6484 (ptmt)
REVERT: B  503 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6382 (t80)
REVERT: B  569 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7717 (mt)
REVERT: B  593 MET cc_start: 0.6762 (mpp) cc_final: 0.6119 (ppp)
REVERT: B  621 TRP cc_start: 0.7593 (t60) cc_final: 0.7339 (t-100)
  outliers start: 44
  outliers final: 24
  residues processed: 171
  average time/residue: 0.2171
  time to fit residues: 55.7920
Evaluate side-chains
  164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  503 PHE
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 343 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 ASN
B 362 HIS
B 384 HIS
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5005 r_free = 0.5005 target = 0.272547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.231305 restraints weight = 10965.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.4653 rms_B_bonded: 3.11
r_work: 0.4105 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10360  Z= 0.180
  Angle     :  0.733  10.729  13990  Z= 0.364
  Chirality :  0.043   0.186   1524
  Planarity :  0.004   0.040   1702
  Dihedral  : 11.890  82.496   1424
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.31 %
    Favored  : 87.69 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 22.78 %
    Favored  : 73.24 %
  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: -3.89 (0.23), residues: 1202
  helix: -1.94 (0.18), residues: 744
  sheet: -1.93 (0.95), residues: 28
  loop : -3.66 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 675 
 HIS   0.005   0.001   HIS A 384 
 PHE   0.017   0.002   PHE A 728 
 TYR   0.022   0.002   TYR B 636 
 ARG   0.003   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  297)
  hydrogen bonds       : angle       5.04605 (  837)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.29258 (    4)
  covalent geometry    : bond        0.00403 (10356)
  covalent geometry    : angle       0.73303 (13986)
  Misc. bond           : bond        0.00071 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 138
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6784 (tm130) cc_final: 0.6237 (tp40)
REVERT: A  335 LYS cc_start: 0.7605 (mmmt) cc_final: 0.6741 (ptmt)
REVERT: A  503 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6355 (t80)
REVERT: A  569 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7826 (mt)
REVERT: A  756 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6342 (mm)
REVERT: B   25 GLN cc_start: 0.6789 (tm130) cc_final: 0.6205 (tp40)
REVERT: B  503 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6595 (t80)
REVERT: B  569 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7818 (mt)
REVERT: B  593 MET cc_start: 0.6658 (mpp) cc_final: 0.6155 (ppp)
REVERT: B  621 TRP cc_start: 0.7647 (t60) cc_final: 0.7338 (t-100)
REVERT: B  756 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6336 (mm)
  outliers start: 43
  outliers final: 28
  residues processed: 168
  average time/residue: 0.1870
  time to fit residues: 46.7558
Evaluate side-chains
  168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  578 TYR
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  503 PHE
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 102 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 62 optimal weight:   20.0000
   chunk 47 optimal weight:    2.9990
   chunk 112 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
A 301 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
B 301 ASN
B 343 ASN
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4981 r_free = 0.4981 target = 0.269761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.224410 restraints weight = 10985.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.4597 rms_B_bonded: 3.26
r_work: 0.4058 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10360  Z= 0.219
  Angle     :  0.775  11.040  13990  Z= 0.384
  Chirality :  0.045   0.198   1524
  Planarity :  0.004   0.045   1702
  Dihedral  : 11.430  77.343   1424
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.06 %
    Favored  : 86.94 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.33 %
    Favored  : 72.50 %
  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: -3.99 (0.23), residues: 1202
  helix: -2.05 (0.18), residues: 764
  sheet: -1.80 (0.97), residues: 28
  loop : -3.70 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 675 
 HIS   0.006   0.001   HIS A 384 
 PHE   0.020   0.002   PHE A 767 
 TYR   0.023   0.002   TYR B 671 
 ARG   0.003   0.000   ARG A 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (  297)
  hydrogen bonds       : angle       5.09625 (  837)
  SS BOND              : bond        0.00055 (    2)
  SS BOND              : angle       0.16230 (    4)
  covalent geometry    : bond        0.00501 (10356)
  covalent geometry    : angle       0.77527 (13986)
  Misc. bond           : bond        0.00052 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6844 (tm130) cc_final: 0.6315 (tp40)
REVERT: A  335 LYS cc_start: 0.7665 (mmmt) cc_final: 0.6741 (ptmt)
REVERT: A  503 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6605 (t80)
REVERT: A  756 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6433 (mm)
REVERT: B   25 GLN cc_start: 0.6827 (tm130) cc_final: 0.6286 (tp40)
REVERT: B  593 MET cc_start: 0.6583 (mpp) cc_final: 0.6170 (ppp)
REVERT: B  756 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6394 (mm)
  outliers start: 45
  outliers final: 33
  residues processed: 163
  average time/residue: 0.1987
  time to fit residues: 48.1959
Evaluate side-chains
  166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  578 TYR
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 68 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0060
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    9.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    1.3600

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 343 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 GLN
B 301 ASN
B 343 ASN
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5004 r_free = 0.5004 target = 0.271906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.225629 restraints weight = 10741.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.4599 rms_B_bonded: 3.27
r_work: 0.4071 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10360  Z= 0.170
  Angle     :  0.754  11.035  13990  Z= 0.369
  Chirality :  0.043   0.184   1524
  Planarity :  0.003   0.045   1702
  Dihedral  : 10.847  72.627   1424
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.81 %
    Favored  : 87.19 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 24.44 %
    Favored  : 72.22 %
  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: -3.83 (0.23), residues: 1202
  helix: -1.94 (0.18), residues: 758
  sheet: -1.70 (0.96), residues: 28
  loop : -3.57 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 675 
 HIS   0.006   0.001   HIS A 384 
 PHE   0.017   0.002   PHE A 728 
 TYR   0.023   0.002   TYR A 306 
 ARG   0.003   0.000   ARG A 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  297)
  hydrogen bonds       : angle       5.00942 (  837)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.26851 (    4)
  covalent geometry    : bond        0.00381 (10356)
  covalent geometry    : angle       0.75378 (13986)
  Misc. bond           : bond        0.00074 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6879 (tm130) cc_final: 0.6366 (tp40)
REVERT: A  335 LYS cc_start: 0.7584 (mmmt) cc_final: 0.6779 (ptmt)
REVERT: A  503 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6634 (t80)
REVERT: A  636 TYR cc_start: 0.8573 (m-80) cc_final: 0.8244 (m-80)
REVERT: A  756 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6382 (mm)
REVERT: B   25 GLN cc_start: 0.6860 (tm130) cc_final: 0.6339 (tp40)
REVERT: B  593 MET cc_start: 0.6512 (mpp) cc_final: 0.6098 (ppp)
  outliers start: 36
  outliers final: 29
  residues processed: 158
  average time/residue: 0.1937
  time to fit residues: 45.3133
Evaluate side-chains
  160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 99 optimal weight:    0.7980
   chunk 80 optimal weight:    0.2980
   chunk 8 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   chunk 78 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 343 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 GLN
B 301 ASN
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5016 r_free = 0.5016 target = 0.274346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.229732 restraints weight = 10873.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.4640 rms_B_bonded: 2.89
r_work: 0.4131 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10360  Z= 0.131
  Angle     :  0.735  11.588  13990  Z= 0.356
  Chirality :  0.042   0.221   1524
  Planarity :  0.003   0.042   1702
  Dihedral  : 10.265  69.108   1424
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.56 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 25.00 %
    Favored  : 72.04 %
  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: -3.76 (0.23), residues: 1202
  helix: -1.89 (0.18), residues: 770
  sheet: -1.66 (0.96), residues: 28
  loop : -3.57 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 675 
 HIS   0.013   0.001   HIS B 384 
 PHE   0.014   0.001   PHE A 767 
 TYR   0.022   0.001   TYR B 341 
 ARG   0.004   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  297)
  hydrogen bonds       : angle       4.92744 (  837)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.40026 (    4)
  covalent geometry    : bond        0.00280 (10356)
  covalent geometry    : angle       0.73479 (13986)
  Misc. bond           : bond        0.00061 (    2)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6788 (tm130) cc_final: 0.6302 (tp40)
REVERT: A  335 LYS cc_start: 0.7508 (mmmt) cc_final: 0.6802 (ptmt)
REVERT: A  503 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6648 (t80)
REVERT: A  553 MET cc_start: 0.8336 (tpp) cc_final: 0.8038 (tpp)
REVERT: B   25 GLN cc_start: 0.6859 (tm130) cc_final: 0.6305 (tp40)
REVERT: B  115 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.6198 (mt0)
REVERT: B  553 MET cc_start: 0.8333 (tpp) cc_final: 0.8023 (tpp)
REVERT: B  593 MET cc_start: 0.6612 (mpp) cc_final: 0.6091 (ppp)
REVERT: B  756 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6245 (mm)
  outliers start: 32
  outliers final: 26
  residues processed: 156
  average time/residue: 0.1894
  time to fit residues: 44.0860
Evaluate side-chains
  163 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  115 GLN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  492 VAL
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 108 optimal weight:    8.9990
   chunk 87 optimal weight:    0.3980
   chunk 62 optimal weight:   30.0000
   chunk 24 optimal weight:    4.9990
   chunk 117 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4984 r_free = 0.4984 target = 0.270088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.228020 restraints weight = 10682.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.4637 rms_B_bonded: 2.85
r_work: 0.4096 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10360  Z= 0.191
  Angle     :  0.768  11.639  13990  Z= 0.377
  Chirality :  0.044   0.233   1524
  Planarity :  0.004   0.043   1702
  Dihedral  :  9.837  64.049   1424
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.65 %
    Favored  : 87.35 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 24.91 %
    Favored  : 72.31 %
  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: -3.74 (0.23), residues: 1202
  helix: -1.84 (0.18), residues: 768
  sheet: -1.58 (0.98), residues: 28
  loop : -3.65 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 675 
 HIS   0.010   0.001   HIS B 384 
 PHE   0.018   0.002   PHE A 767 
 TYR   0.024   0.002   TYR A 306 
 ARG   0.003   0.000   ARG A 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  297)
  hydrogen bonds       : angle       5.00089 (  837)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.23100 (    4)
  covalent geometry    : bond        0.00432 (10356)
  covalent geometry    : angle       0.76805 (13986)
  Misc. bond           : bond        0.00103 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5585.53 seconds
wall clock time: 99 minutes 36.42 seconds (5976.42 seconds total)