Starting phenix.real_space_refine
on Tue May 13 11:08:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ik4_60648/05_2025/9ik4_60648.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ik4_60648/05_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_60648/05_2025/9ik4_60648.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ik4_60648/05_2025/9ik4_60648.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ik4_60648/05_2025/9ik4_60648.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ik4_60648/05_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-5687/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: 2.64
  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: 1.06
  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: 2.53

  Time building geometry restraints manager: 3.02 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: 0.05
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:             2.560
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.100
  Find NCS groups from input model:        0.500
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.790
-------------------------------------------------------------------------------
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  : 1.123 
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: 0.2341
  time to fit residues: 66.6221
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  : 1.074 
-------------------------------------------------------------------------------
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: 0.4184 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
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  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 VAL cc_start: 0.3110 (OUTLIER) cc_final: 0.2845 (m)
REVERT: A  335 LYS cc_start: 0.7477 (mmmt) cc_final: 0.6220 (ptmt)
REVERT: A  349 MET cc_start: 0.7443 (mmt) cc_final: 0.7011 (mmm)
REVERT: A  410 LEU cc_start: 0.7108 (tt) cc_final: 0.6370 (mt)
REVERT: A  569 LEU cc_start: 0.7931 (mt) cc_final: 0.7720 (mt)
REVERT: B   89 VAL cc_start: 0.3075 (OUTLIER) cc_final: 0.2829 (m)
REVERT: B  335 LYS cc_start: 0.7649 (mmpt) cc_final: 0.6228 (ptmt)
REVERT: B  410 LEU cc_start: 0.7289 (tt) cc_final: 0.6498 (mt)
REVERT: B  569 LEU cc_start: 0.7991 (mt) cc_final: 0.7770 (mt)
REVERT: B  590 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7094 (mm-30)
  outliers start: 24
  outliers final: 11
  residues processed: 177
  average time/residue: 0.2091
  time to fit residues: 52.4218
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  : 1.004 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 98 optimal weight:    0.3980
   chunk 92 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 114 optimal weight:    4.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5031 r_free = 0.5031 target = 0.276123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.236092 restraints weight = 10890.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.4692 rms_B_bonded: 3.05
r_work: 0.4169 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.2689

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= 0.138
  Angle     :  0.721  11.439  13990  Z= 0.369
  Chirality :  0.045   0.369   1524
  Planarity :  0.004   0.048   1702
  Dihedral  : 12.904  93.937   1424
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.31 %
    Favored  : 87.69 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.17 %
    Favored  : 77.69 %
  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: -4.79 (0.21), residues: 1202
  helix: -2.69 (0.16), residues: 770
  sheet: -1.93 (1.02), residues: 24
  loop : -3.98 (0.26), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 621 
 HIS   0.013   0.001   HIS B 384 
 PHE   0.016   0.001   PHE A 622 
 TYR   0.020   0.002   TYR B 671 
 ARG   0.006   0.001   ARG A 599 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  297)
  hydrogen bonds       : angle       5.78662 (  837)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.50997 (    4)
  covalent geometry    : bond        0.00294 (10356)
  covalent geometry    : angle       0.72124 (13986)
  Misc. bond           : bond        0.00058 (    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
  174 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 140
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 VAL cc_start: 0.3298 (OUTLIER) cc_final: 0.2968 (m)
REVERT: A  301 ASN cc_start: 0.8344 (t0) cc_final: 0.7545 (m-40)
REVERT: A  335 LYS cc_start: 0.7462 (mmmt) cc_final: 0.6339 (ptmt)
REVERT: A  349 MET cc_start: 0.7553 (mmt) cc_final: 0.7184 (mmm)
REVERT: A  410 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6481 (mt)
REVERT: A  569 LEU cc_start: 0.8021 (mt) cc_final: 0.7747 (mt)
REVERT: A  590 GLU cc_start: 0.6524 (mm-30) cc_final: 0.5485 (mm-30)
REVERT: B   89 VAL cc_start: 0.3323 (OUTLIER) cc_final: 0.3033 (m)
REVERT: B  335 LYS cc_start: 0.7596 (mmpt) cc_final: 0.6309 (ptmt)
REVERT: B  569 LEU cc_start: 0.8089 (mt) cc_final: 0.7816 (mt)
  outliers start: 34
  outliers final: 20
  residues processed: 162
  average time/residue: 0.2024
  time to fit residues: 47.5542
Evaluate side-chains
  154 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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  410 LEU
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  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  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  430 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  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:    3.9990
   chunk 112 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0980
   chunk 51 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4995 r_free = 0.4995 target = 0.271368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.228184 restraints weight = 10809.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.4623 rms_B_bonded: 3.12
r_work: 0.4101 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10360  Z= 0.185
  Angle     :  0.720  11.911  13990  Z= 0.370
  Chirality :  0.044   0.220   1524
  Planarity :  0.004   0.044   1702
  Dihedral  : 12.603  89.551   1424
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.40 %
    Favored  : 87.60 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.19 %
    Favored  : 76.02 %
  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: -4.45 (0.21), residues: 1202
  helix: -2.42 (0.17), residues: 768
  sheet: -1.76 (1.01), residues: 24
  loop : -3.86 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 621 
 HIS   0.006   0.001   HIS B 384 
 PHE   0.017   0.002   PHE A 767 
 TYR   0.030   0.002   TYR A 306 
 ARG   0.004   0.001   ARG A 594 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  297)
  hydrogen bonds       : angle       5.42745 (  837)
  SS BOND              : bond        0.00109 (    2)
  SS BOND              : angle       0.27316 (    4)
  covalent geometry    : bond        0.00415 (10356)
  covalent geometry    : angle       0.71997 (13986)
  Misc. bond           : bond        0.00071 (    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
  183 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  335 LYS cc_start: 0.7417 (mmmt) cc_final: 0.6393 (ptmt)
REVERT: A  349 MET cc_start: 0.7649 (mmt) cc_final: 0.7302 (mmm)
REVERT: A  410 LEU cc_start: 0.7329 (tt) cc_final: 0.6549 (mt)
REVERT: B   25 GLN cc_start: 0.6837 (tm130) cc_final: 0.6290 (tp40)
REVERT: B  335 LYS cc_start: 0.7592 (mmpt) cc_final: 0.6342 (ptmt)
  outliers start: 41
  outliers final: 30
  residues processed: 171
  average time/residue: 0.1890
  time to fit residues: 47.5102
Evaluate side-chains
  167 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  673 LEU
Chi-restraints excluded: chain A residue  704 ILE
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  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  578 TYR
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  593 MET
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  770 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 91 optimal weight:    0.3980
   chunk 79 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 113 optimal weight:    0.0050
   chunk 61 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    0.3980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 115 GLN
A 301 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 HIS
B 117 ASN
B 301 ASN
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5033 r_free = 0.5033 target = 0.276550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.232893 restraints weight = 10786.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.4666 rms_B_bonded: 2.94
r_work: 0.4173 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10360  Z= 0.115
  Angle     :  0.677  11.564  13990  Z= 0.342
  Chirality :  0.040   0.189   1524
  Planarity :  0.003   0.038   1702
  Dihedral  : 12.206  87.102   1424
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.11 %
    Favored  : 74.72 %
  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: -4.16 (0.22), residues: 1202
  helix: -2.21 (0.18), residues: 770
  sheet: -2.18 (0.93), residues: 28
  loop : -3.67 (0.27), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  16 
 HIS   0.006   0.001   HIS B 384 
 PHE   0.010   0.001   PHE A 767 
 TYR   0.023   0.001   TYR B 306 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  297)
  hydrogen bonds       : angle       5.09788 (  837)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       0.39791 (    4)
  covalent geometry    : bond        0.00242 (10356)
  covalent geometry    : angle       0.67744 (13986)
  Misc. bond           : bond        0.00062 (    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
  193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 148
  time to evaluate  : 1.151 
Fit side-chains
REVERT: A   25 GLN cc_start: 0.6833 (tm130) cc_final: 0.6335 (tp40)
REVERT: A  335 LYS cc_start: 0.7653 (mmmt) cc_final: 0.6692 (ptmt)
REVERT: A  349 MET cc_start: 0.7691 (mmt) cc_final: 0.7440 (mmm)
REVERT: A  410 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6428 (mt)
REVERT: A  503 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6039 (t80)
REVERT: A  569 LEU cc_start: 0.8033 (mt) cc_final: 0.7821 (mt)
REVERT: B   25 GLN cc_start: 0.6775 (tm130) cc_final: 0.6300 (tp40)
REVERT: B  335 LYS cc_start: 0.7604 (mmpt) cc_final: 0.6476 (ptmt)
REVERT: B  503 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6459 (t80)
REVERT: B  569 LEU cc_start: 0.8059 (mt) cc_final: 0.7834 (mt)
  outliers start: 45
  outliers final: 29
  residues processed: 178
  average time/residue: 0.1989
  time to fit residues: 51.5143
Evaluate side-chains
  167 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLN
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  410 LEU
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  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   94 LEU
Chi-restraints excluded: chain B residue  293 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  503 PHE
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  548 LEU
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:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 35 optimal weight:   20.0000
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0270
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.6440

-------------------------------------------------------------------------------
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 117 ASN
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 = 0.5027 r_free = 0.5027 target = 0.275619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.231927 restraints weight = 10888.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.4662 rms_B_bonded: 2.92
r_work: 0.4175 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10360  Z= 0.120
  Angle     :  0.686  12.707  13990  Z= 0.343
  Chirality :  0.041   0.180   1524
  Planarity :  0.003   0.034   1702
  Dihedral  : 12.053  85.710   1424
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.31 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 21.30 %
    Favored  : 74.07 %
  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: -4.05 (0.22), residues: 1202
  helix: -2.10 (0.18), residues: 766
  sheet: -2.03 (0.94), residues: 28
  loop : -3.71 (0.27), residues: 408

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   0.011   0.001   PHE A 767 
 TYR   0.021   0.001   TYR B 341 
 ARG   0.006   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03797 (  297)
  hydrogen bonds       : angle       5.04390 (  837)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       0.38441 (    4)
  covalent geometry    : bond        0.00257 (10356)
  covalent geometry    : angle       0.68560 (13986)
  Misc. bond           : bond        0.00049 (    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
  194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 144
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6797 (tm130) cc_final: 0.6303 (tp40)
REVERT: A  335 LYS cc_start: 0.7650 (mmmt) cc_final: 0.6770 (ptmt)
REVERT: A  349 MET cc_start: 0.7794 (mmt) cc_final: 0.7565 (mmm)
REVERT: A  410 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6422 (mt)
REVERT: A  503 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.6224 (t80)
REVERT: A  569 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7782 (mt)
REVERT: A  593 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5584 (ppp)
REVERT: A  756 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6155 (mm)
REVERT: B   25 GLN cc_start: 0.6789 (tm130) cc_final: 0.6255 (tp40)
REVERT: B  503 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.6483 (t80)
REVERT: B  569 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7816 (mt)
REVERT: B  756 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6159 (mm)
  outliers start: 50
  outliers final: 30
  residues processed: 176
  average time/residue: 0.1891
  time to fit residues: 48.9358
Evaluate side-chains
  176 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 LEU
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  410 LEU
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  593 MET
Chi-restraints excluded: chain A residue  605 VAL
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  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  363 LEU
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  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  658 LEU
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=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:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 52 optimal weight:    8.9990
   chunk 50 optimal weight:    0.6980
   chunk 11 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0370
   chunk 111 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.8260

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.276031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.231760 restraints weight = 10949.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.4654 rms_B_bonded: 3.19
r_work: 0.4134 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.3531

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= 0.130
  Angle     :  0.695  11.628  13990  Z= 0.344
  Chirality :  0.041   0.177   1524
  Planarity :  0.003   0.036   1702
  Dihedral  : 11.824  83.083   1424
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.56 %
    Favored  : 88.44 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 22.04 %
    Favored  : 73.61 %
  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: -3.92 (0.23), residues: 1202
  helix: -1.99 (0.18), residues: 766
  sheet: -1.79 (0.96), residues: 28
  loop : -3.68 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 675 
 HIS   0.004   0.001   HIS A 384 
 PHE   0.012   0.001   PHE A 767 
 TYR   0.023   0.001   TYR A 306 
 ARG   0.005   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  297)
  hydrogen bonds       : angle       4.95716 (  837)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.41886 (    4)
  covalent geometry    : bond        0.00284 (10356)
  covalent geometry    : angle       0.69553 (13986)
  Misc. bond           : bond        0.00054 (    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
  188 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 141
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6791 (tm130) cc_final: 0.6252 (tp40)
REVERT: A  335 LYS cc_start: 0.7621 (mmmt) cc_final: 0.6802 (ptmt)
REVERT: A  349 MET cc_start: 0.7858 (mmt) cc_final: 0.7605 (mmm)
REVERT: A  410 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6416 (mt)
REVERT: A  503 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6411 (t80)
REVERT: A  569 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7796 (mt)
REVERT: A  636 TYR cc_start: 0.8538 (m-80) cc_final: 0.8066 (m-80)
REVERT: A  756 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6248 (mm)
REVERT: B   25 GLN cc_start: 0.6803 (tm130) cc_final: 0.6258 (tp40)
REVERT: B  503 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6581 (t80)
REVERT: B  569 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7789 (mt)
REVERT: B  756 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6240 (mm)
  outliers start: 47
  outliers final: 33
  residues processed: 170
  average time/residue: 0.1930
  time to fit residues: 48.4028
Evaluate side-chains
  178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 138
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 ASN
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  410 LEU
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  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  704 ILE
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  293 LEU
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 102 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 112 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    2.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
A 343 ASN
A 384 HIS
** 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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.269174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.224118 restraints weight = 11022.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.4593 rms_B_bonded: 3.02
r_work: 0.4073 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  10360  Z= 0.242
  Angle     :  0.790  10.919  13990  Z= 0.394
  Chirality :  0.045   0.199   1524
  Planarity :  0.004   0.043   1702
  Dihedral  : 11.543  78.585   1424
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.81 %
    Favored  : 87.19 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.96 %
    Favored  : 72.78 %
  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: -3.98 (0.22), residues: 1202
  helix: -2.06 (0.18), residues: 770
  sheet: -1.80 (0.96), residues: 28
  loop : -3.67 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 675 
 HIS   0.004   0.001   HIS A 760 
 PHE   0.021   0.002   PHE A 767 
 TYR   0.027   0.002   TYR B 636 
 ARG   0.003   0.001   ARG B 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  297)
  hydrogen bonds       : angle       5.14584 (  837)
  SS BOND              : bond        0.00102 (    2)
  SS BOND              : angle       0.31986 (    4)
  covalent geometry    : bond        0.00555 (10356)
  covalent geometry    : angle       0.79012 (13986)
  Misc. bond           : bond        0.00074 (    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
  184 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 138
  time to evaluate  : 1.110 
Fit side-chains
REVERT: A   25 GLN cc_start: 0.6795 (tm130) cc_final: 0.6287 (tp40)
REVERT: A  335 LYS cc_start: 0.7581 (mmmt) cc_final: 0.6695 (ptmt)
REVERT: A  349 MET cc_start: 0.7917 (mmt) cc_final: 0.7566 (mmm)
REVERT: A  410 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6585 (mt)
REVERT: A  503 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6606 (t80)
REVERT: A  709 MET cc_start: 0.8051 (mtm) cc_final: 0.7802 (mtp)
REVERT: A  756 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6394 (mm)
REVERT: B   25 GLN cc_start: 0.6823 (tm130) cc_final: 0.6281 (tp40)
REVERT: B  433 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7490 (ttt)
REVERT: B  756 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6399 (mm)
  outliers start: 46
  outliers final: 34
  residues processed: 169
  average time/residue: 0.1981
  time to fit residues: 49.7960
Evaluate side-chains
  173 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
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  410 LEU
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  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  704 ILE
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  372 MET
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  433 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  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:    9.9990
   chunk 49 optimal weight:    0.0770
   chunk 68 optimal weight:    8.9990
   chunk 85 optimal weight:    9.9990
   chunk 86 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 112 optimal weight:    4.9990
   chunk 109 optimal weight:    0.0770
   chunk 60 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.5300

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
A 343 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 HIS
** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.275957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.230906 restraints weight = 10872.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.4647 rms_B_bonded: 2.83
r_work: 0.4154 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10360  Z= 0.120
  Angle     :  0.730  11.411  13990  Z= 0.353
  Chirality :  0.041   0.180   1524
  Planarity :  0.003   0.046   1702
  Dihedral  : 10.874  74.348   1424
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 25.00 %
    Favored  : 72.41 %
  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: -3.70 (0.23), residues: 1202
  helix: -1.83 (0.18), residues: 760
  sheet: -1.73 (0.95), residues: 28
  loop : -3.54 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 675 
 HIS   0.007   0.001   HIS B 384 
 PHE   0.014   0.001   PHE B 122 
 TYR   0.019   0.001   TYR A 306 
 ARG   0.005   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  297)
  hydrogen bonds       : angle       4.85785 (  837)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       0.61739 (    4)
  covalent geometry    : bond        0.00251 (10356)
  covalent geometry    : angle       0.72976 (13986)
  Misc. bond           : bond        0.00058 (    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: 28
    poor density    : 142
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6876 (tm130) cc_final: 0.6397 (tp40)
REVERT: A  335 LYS cc_start: 0.7541 (mmmt) cc_final: 0.6794 (ptmt)
REVERT: A  349 MET cc_start: 0.7888 (mmt) cc_final: 0.7569 (mmm)
REVERT: A  410 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6449 (mt)
REVERT: A  503 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6656 (t80)
REVERT: B   25 GLN cc_start: 0.6829 (tm130) cc_final: 0.6314 (tp40)
REVERT: B  553 MET cc_start: 0.8312 (tpp) cc_final: 0.7983 (tpp)
REVERT: B  569 LEU cc_start: 0.7995 (mt) cc_final: 0.7713 (mt)
  outliers start: 28
  outliers final: 24
  residues processed: 161
  average time/residue: 0.1852
  time to fit residues: 44.6271
Evaluate side-chains
  167 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  410 LEU
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  588 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain B residue  293 LEU
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  578 TYR
Chi-restraints excluded: chain B residue  588 ASP
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  704 ILE
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:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 81 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 78 optimal weight:    7.9990
   chunk 24 optimal weight:    0.1980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
A 343 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN
** B 725 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 = 0.5014 r_free = 0.5014 target = 0.274004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.228077 restraints weight = 10862.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.4624 rms_B_bonded: 3.04
r_work: 0.4125 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10360  Z= 0.151
  Angle     :  0.743  11.385  13990  Z= 0.362
  Chirality :  0.043   0.214   1524
  Planarity :  0.003   0.043   1702
  Dihedral  : 10.268  69.245   1424
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.48 %
    Favored  : 87.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 24.81 %
    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: -3.65 (0.23), residues: 1202
  helix: -1.76 (0.18), residues: 756
  sheet: -1.66 (0.95), residues: 28
  loop : -3.57 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 675 
 HIS   0.015   0.001   HIS B 384 
 PHE   0.015   0.001   PHE B 728 
 TYR   0.022   0.002   TYR B 636 
 ARG   0.004   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03750 (  297)
  hydrogen bonds       : angle       4.87084 (  837)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       0.51369 (    4)
  covalent geometry    : bond        0.00335 (10356)
  covalent geometry    : angle       0.74258 (13986)
  Misc. bond           : bond        0.00072 (    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
  170 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A   25 GLN cc_start: 0.6823 (tm130) cc_final: 0.6317 (tp40)
REVERT: A  301 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7510 (m-40)
REVERT: A  335 LYS cc_start: 0.7464 (mmmt) cc_final: 0.6777 (ptmt)
REVERT: A  349 MET cc_start: 0.7942 (mmt) cc_final: 0.7618 (mmm)
REVERT: A  410 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6459 (mt)
REVERT: A  503 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6690 (t80)
REVERT: A  756 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6321 (mm)
REVERT: B   25 GLN cc_start: 0.6797 (tm130) cc_final: 0.6288 (tp40)
REVERT: B  306 TYR cc_start: 0.6642 (t80) cc_final: 0.6438 (t80)
REVERT: B  756 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6312 (mm)
  outliers start: 31
  outliers final: 23
  residues processed: 159
  average time/residue: 0.1783
  time to fit residues: 42.3739
Evaluate side-chains
  166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
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  410 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  532 SER
Chi-restraints excluded: chain A residue  548 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  704 ILE
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  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  673 LEU
Chi-restraints excluded: chain B residue  704 ILE
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:    0.0980
   chunk 108 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 117 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 106 optimal weight:    0.6980
   chunk 68 optimal weight:    9.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
A 343 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5080 r_free = 0.5080 target = 0.279567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.233264 restraints weight = 10553.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.4681 rms_B_bonded: 3.30
r_work: 0.4145 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10360  Z= 0.141
  Angle     :  0.741  11.353  13990  Z= 0.361
  Chirality :  0.042   0.237   1524
  Planarity :  0.003   0.042   1702
  Dihedral  :  9.693  64.412   1424
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.81 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 25.74 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.23), residues: 1202
  helix: -1.74 (0.18), residues: 758
  sheet: -1.64 (0.95), residues: 28
  loop : -3.54 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 675 
 HIS   0.009   0.001   HIS A 384 
 PHE   0.013   0.001   PHE A 767 
 TYR   0.021   0.001   TYR B 636 
 ARG   0.004   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  297)
  hydrogen bonds       : angle       4.83462 (  837)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.59389 (    4)
  covalent geometry    : bond        0.00311 (10356)
  covalent geometry    : angle       0.74064 (13986)
  Misc. bond           : bond        0.00105 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5160.42 seconds
wall clock time: 90 minutes 32.88 seconds (5432.88 seconds total)