Starting phenix.real_space_refine
on Wed Mar 12 10:44:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y9u_33692/03_2025/7y9u_33692.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y9u_33692/03_2025/7y9u_33692.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y9u_33692/03_2025/7y9u_33692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y9u_33692/03_2025/7y9u_33692.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y9u_33692/03_2025/7y9u_33692.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y9u_33692/03_2025/7y9u_33692.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.116
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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5078      2.51       5
     N    1272      2.21       5
     O    1342      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7748
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2957
          Classifications: {'peptide': 379}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 360}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 895
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'E7O': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 6.08, per 1000 atoms: 0.78
  Number of scatterers: 7748
  At special positions: 0
  Unit cell: (100.1, 123.2, 96.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1342      8.00
     N    1272      7.00
     C    5078      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  26 " - pdb=" SG  CYS C 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D 100 " 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=0, symmetry=0
  Time building additional restraints: 1.94
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      51.6% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 30
      removed outlier: 3.846A  pdb=" N   PHE A   7 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA A  13 " --> pdb=" O   HIS A   9 " (cutoff:3.500A)
      Proline residue:  A  16  - end of helix
      removed outlier: 4.041A  pdb=" N   ALA A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET A  21 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 49
      removed outlier: 3.886A  pdb=" N   ASN A  43 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU A  48 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 60
      removed outlier: 3.874A  pdb=" N   PHE A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 76
      removed outlier: 3.523A  pdb=" N   ALA A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 70 through 76'
    Processing helix  chain 'A' and resid 77 through 86
      removed outlier: 4.120A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.662A  pdb=" N   LYS A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.510A  pdb=" N   ILE A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A 110 " --> pdb=" O   SER A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 126
    Processing helix  chain 'A' and resid 128 through 143
      removed outlier: 3.933A  pdb=" N   VAL A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN A 135 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 165
      removed outlier: 3.664A  pdb=" N   LEU A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 457 through 474
      removed outlier: 3.751A  pdb=" N   THR A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ARG A 463 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A 466 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS A 472 " --> pdb=" O   MET A 468 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 474 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 480
      removed outlier: 3.535A  pdb=" N   SER A 479 " --> pdb=" O   ASN A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 493
      removed outlier: 3.563A  pdb=" N   TRP A 488 " --> pdb=" O   PHE A 484 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 491 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE A 493 " --> pdb=" O   SER A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 508
    Processing helix  chain 'A' and resid 510 through 512
      No H-bonds generated for 'chain 'A' and resid 510 through 512'
    Processing helix  chain 'A' and resid 513 through 529
      removed outlier: 3.531A  pdb=" N   MET A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   MET A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY A 523 " --> pdb=" O   MET A 519 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   PHE A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   MET A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A 527 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASN A 529 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.541A  pdb=" N   ALA A 541 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 3.710A  pdb=" N   HIS A 570 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 574 " --> pdb=" O   HIS A 570 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 3.558A  pdb=" N   ALA A 588 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A 590 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 608
      removed outlier: 3.529A  pdb=" N   ALA A 601 " --> pdb=" O   ILE A 597 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL A 602 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 603 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 622
      removed outlier: 3.820A  pdb=" N   LEU A 615 " --> pdb=" O   PRO A 611 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 618 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY A 621 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 30
      removed outlier: 3.846A  pdb=" N   PHE B   7 " --> pdb=" O   THR B   3 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR B   8 " --> pdb=" O   ALA B   4 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA B  13 " --> pdb=" O   HIS B   9 " (cutoff:3.500A)
      Proline residue:  B  16  - end of helix
      removed outlier: 4.041A  pdb=" N   ALA B  20 " --> pdb=" O   PRO B  16 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET B  21 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 49
      removed outlier: 3.886A  pdb=" N   ASN B  43 " --> pdb=" O   CYS B  39 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B  48 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 60
      removed outlier: 3.874A  pdb=" N   PHE B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 76
      removed outlier: 3.522A  pdb=" N   ALA B  74 " --> pdb=" O   ARG B  70 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP B  75 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 70 through 76'
    Processing helix  chain 'B' and resid 77 through 86
      removed outlier: 4.120A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.662A  pdb=" N   LYS B  91 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 110
      removed outlier: 3.510A  pdb=" N   ILE B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER B 108 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU B 110 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 126
    Processing helix  chain 'B' and resid 128 through 143
      removed outlier: 3.932A  pdb=" N   VAL B 134 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN B 135 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 165
      removed outlier: 3.663A  pdb=" N   LEU B 159 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 457 through 474
      removed outlier: 3.752A  pdb=" N   THR B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ARG B 463 " --> pdb=" O   SER B 459 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU B 466 " --> pdb=" O   THR B 462 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS B 472 " --> pdb=" O   MET B 468 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B 474 " --> pdb=" O   TRP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 480
      removed outlier: 3.534A  pdb=" N   SER B 479 " --> pdb=" O   ASN B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 3.563A  pdb=" N   TRP B 488 " --> pdb=" O   PHE B 484 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE B 491 " --> pdb=" O   THR B 487 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE B 493 " --> pdb=" O   SER B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 508
    Processing helix  chain 'B' and resid 510 through 512
      No H-bonds generated for 'chain 'B' and resid 510 through 512'
    Processing helix  chain 'B' and resid 513 through 529
      removed outlier: 3.532A  pdb=" N   MET B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   MET B 519 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B 523 " --> pdb=" O   MET B 519 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B 525 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   MET B 526 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 527 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASN B 529 " --> pdb=" O   PHE B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 542
      removed outlier: 3.541A  pdb=" N   ALA B 541 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 577
      removed outlier: 3.710A  pdb=" N   HIS B 570 " --> pdb=" O   GLY B 566 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA B 572 " --> pdb=" O   LEU B 568 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 574 " --> pdb=" O   HIS B 570 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA B 576 " --> pdb=" O   ALA B 572 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 591
      removed outlier: 3.558A  pdb=" N   ALA B 588 " --> pdb=" O   PRO B 584 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU B 590 " --> pdb=" O   VAL B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 608
      removed outlier: 3.529A  pdb=" N   ALA B 601 " --> pdb=" O   ILE B 597 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   VAL B 602 " --> pdb=" O   LEU B 598 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE B 603 " --> pdb=" O   SER B 599 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU B 607 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE B 608 " --> pdb=" O   PHE B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 622
      removed outlier: 3.820A  pdb=" N   LEU B 615 " --> pdb=" O   PRO B 611 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE B 618 " --> pdb=" O   LEU B 614 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177
      removed outlier: 7.381A  pdb=" N   VAL A 204 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE A 175 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL A 206 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   VAL A 177 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR C 107 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL C  97 " --> pdb=" O   GLN C  43 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR C  99 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TYR C  41 " --> pdb=" O   TYR C  99 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG C 101 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLU C  39 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   TRP C  40 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11
      removed outlier: 3.630A  pdb=" N   GLN C   7 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER C  29 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 16
      removed outlier: 3.612A  pdb=" N   THR C 116 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 21 through 23
      removed outlier: 3.916A  pdb=" N   LEU C  22 " --> pdb=" O   MET C  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 11
      removed outlier: 3.630A  pdb=" N   GLN D   7 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER D  29 " --> pdb=" O   GLN D   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 14 through 16
      removed outlier: 3.613A  pdb=" N   THR D 116 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 21 through 23
      removed outlier: 3.915A  pdb=" N   LEU D  22 " --> pdb=" O   MET D  87 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 54
      removed outlier: 7.021A  pdb=" N   TRP D  40 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLU D  39 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG D 101 " --> pdb=" O   GLU D  39 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR D  41 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR D  99 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL D  97 " --> pdb=" O   GLN D  43 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TYR D 107 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ILE B 196 " --> pdb=" O   TYR D 107 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ARG D 109 " --> pdb=" O   ILE B 196 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   VAL B 204 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ILE B 175 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL B 206 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   VAL B 177 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    750 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: 2.01

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1184
        1.28 -     1.41: 2092
        1.41 -     1.54: 4528
        1.54 -     1.67: 32
        1.67 -     1.80: 100
  Bond restraints: 7936
  Sorted by residual:
  bond pdb=" CA  ASN A 112 "
       pdb=" C   ASN A 112 "
    ideal  model  delta    sigma   weight residual
    1.525  1.374  0.151 1.29e-02 6.01e+03 1.38e+02
  bond pdb=" CA  ASN B 112 "
       pdb=" C   ASN B 112 "
    ideal  model  delta    sigma   weight residual
    1.525  1.374  0.151 1.29e-02 6.01e+03 1.37e+02
  bond pdb=" C04 E7O A 701 "
       pdb=" C05 E7O A 701 "
    ideal  model  delta    sigma   weight residual
    1.421  1.250  0.171 2.00e-02 2.50e+03 7.34e+01
  bond pdb=" C04 E7O B 701 "
       pdb=" C05 E7O B 701 "
    ideal  model  delta    sigma   weight residual
    1.421  1.250  0.171 2.00e-02 2.50e+03 7.29e+01
  bond pdb=" C04 E7O B 701 "
       pdb=" C10 E7O B 701 "
    ideal  model  delta    sigma   weight residual
    1.428  1.272  0.156 2.00e-02 2.50e+03 6.11e+01
  ... (remaining 7931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 10201
        2.12 -     4.24: 493
        4.24 -     6.37: 78
        6.37 -     8.49: 12
        8.49 -    10.61: 6
  Bond angle restraints: 10790
  Sorted by residual:
  angle pdb=" C   ASN B 112 "
        pdb=" CA  ASN B 112 "
        pdb=" CB  ASN B 112 "
      ideal   model   delta    sigma   weight residual
     111.31  100.98   10.33 1.68e+00 3.54e-01 3.78e+01
  angle pdb=" C   ASN A 112 "
        pdb=" CA  ASN A 112 "
        pdb=" CB  ASN A 112 "
      ideal   model   delta    sigma   weight residual
     111.31  100.99   10.32 1.68e+00 3.54e-01 3.77e+01
  angle pdb=" C   GLN D  56 "
        pdb=" N   SER D  57 "
        pdb=" CA  SER D  57 "
      ideal   model   delta    sigma   weight residual
     121.19  127.35   -6.16 1.59e+00 3.96e-01 1.50e+01
  angle pdb=" C   GLN C  56 "
        pdb=" N   SER C  57 "
        pdb=" CA  SER C  57 "
      ideal   model   delta    sigma   weight residual
     121.19  127.34   -6.15 1.59e+00 3.96e-01 1.50e+01
  angle pdb=" C   PRO B 111 "
        pdb=" N   ASN B 112 "
        pdb=" CA  ASN B 112 "
      ideal   model   delta    sigma   weight residual
     122.85  128.12   -5.27 1.39e+00 5.18e-01 1.44e+01
  ... (remaining 10785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.31: 4416
       15.31 -    30.61: 190
       30.61 -    45.92: 54
       45.92 -    61.23: 6
       61.23 -    76.54: 2
  Dihedral angle restraints: 4668
    sinusoidal: 1806
      harmonic: 2862
  Sorted by residual:
  dihedral pdb=" C   ASN B 112 "
           pdb=" N   ASN B 112 "
           pdb=" CA  ASN B 112 "
           pdb=" CB  ASN B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.69  -14.91     0      2.50e+00 1.60e-01 3.56e+01
  dihedral pdb=" C   ASN A 112 "
           pdb=" N   ASN A 112 "
           pdb=" CA  ASN A 112 "
           pdb=" CB  ASN A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.70  -14.90     0      2.50e+00 1.60e-01 3.55e+01
  dihedral pdb=" CA  GLN C  56 "
           pdb=" C   GLN C  56 "
           pdb=" N   SER C  57 "
           pdb=" CA  SER C  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.54  -28.46     0      5.00e+00 4.00e-02 3.24e+01
  ... (remaining 4665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 984
       0.069 -    0.137: 239
       0.137 -    0.206: 17
       0.206 -    0.275: 4
       0.275 -    0.343: 2
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CB  ILE C  55 "
            pdb=" CA  ILE C  55 "
            pdb=" CG1 ILE C  55 "
            pdb=" CG2 ILE C  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CB  ILE D  55 "
            pdb=" CA  ILE D  55 "
            pdb=" CG1 ILE D  55 "
            pdb=" CG2 ILE D  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CB  VAL B 554 "
            pdb=" CA  VAL B 554 "
            pdb=" CG1 VAL B 554 "
            pdb=" CG2 VAL B 554 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 1243 not shown)

  Planarity restraints: 1326
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 551 "   -0.045 5.00e-02 4.00e+02   6.79e-02 7.37e+00
        pdb=" N   PRO A 552 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 552 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 552 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 551 "    0.045 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO B 552 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 552 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 552 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  15 "   -0.041 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO B  16 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1323 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2395
        2.83 -     3.35: 6381
        3.35 -     3.86: 11760
        3.86 -     4.38: 13681
        4.38 -     4.90: 23874
  Nonbonded interactions: 58091
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 193 "
            pdb=" NE  ARG C 109 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" OE2 GLU A 191 "
            pdb=" NH2 ARG C 101 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" NH2 ARG C  71 "
            pdb=" O   SER C  89 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" NH2 ARG D  71 "
            pdb=" O   SER D  89 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" O   TRP A  89 "
            pdb=" OG  SER A  93 "
     model   vdw
     2.369 3.040
  ... (remaining 58086 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.570
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
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      :  0.011   0.171   7936  Z= 0.713
  Angle     :  1.056  10.612  10790  Z= 0.561
  Chirality :  0.060   0.343   1246
  Planarity :  0.009   0.068   1326
  Dihedral  : 10.083  76.536   2822
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.22 %
  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: -6.23 (0.17), residues: 976
  helix: -4.89 (0.07), residues: 524
  sheet: -2.72 (0.40), residues: 106
  loop : -2.86 (0.27), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B  31 
 HIS   0.009   0.003   HIS A   9 
 PHE   0.022   0.003   PHE A 587 
 TYR   0.016   0.002   TYR C  41 
 ARG   0.005   0.001   ARG C 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8414 (m-30) cc_final: 0.8115 (m-30)
REVERT: A  463 ARG cc_start: 0.7245 (ttt180) cc_final: 0.6832 (ttt90)
REVERT: A  505 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7823 (mptt)
REVERT: A  560 TYR cc_start: 0.7942 (t80) cc_final: 0.7742 (t80)
REVERT: A  589 LYS cc_start: 0.8289 (tttp) cc_final: 0.8004 (ttpt)
REVERT: D    9 VAL cc_start: 0.8814 (t) cc_final: 0.8478 (p)
REVERT: B   21 MET cc_start: 0.8848 (ttp) cc_final: 0.8588 (ttt)
REVERT: B   88 LEU cc_start: 0.7906 (mp) cc_final: 0.7466 (tt)
REVERT: B   99 ASP cc_start: 0.8336 (m-30) cc_final: 0.8048 (m-30)
REVERT: B  142 ILE cc_start: 0.8423 (tp) cc_final: 0.8215 (pt)
REVERT: B  178 ASP cc_start: 0.7456 (m-30) cc_final: 0.7204 (m-30)
REVERT: B  463 ARG cc_start: 0.7291 (ttt180) cc_final: 0.6775 (ttt90)
REVERT: B  472 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8732 (mmmm)
REVERT: B  499 MET cc_start: 0.8762 (ttp) cc_final: 0.8541 (ttm)
REVERT: B  505 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7844 (mptt)
REVERT: B  589 LYS cc_start: 0.8286 (tttp) cc_final: 0.7995 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2434
  time to fit residues: 54.5156
Evaluate side-chains
  128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:   30.0000
   chunk 38 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.172391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.114842 restraints weight = 8925.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.36
r_work: 0.2878 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7936  Z= 0.193
  Angle     :  0.599   5.728  10790  Z= 0.324
  Chirality :  0.044   0.156   1246
  Planarity :  0.006   0.053   1326
  Dihedral  :  5.426  22.976   1084
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  8.80 %
    Favored  : 88.92 %
  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: -4.75 (0.21), residues: 976
  helix: -3.63 (0.14), residues: 532
  sheet: -1.85 (0.45), residues: 100
  loop : -2.33 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 144 
 HIS   0.005   0.001   HIS A   9 
 PHE   0.013   0.002   PHE D  72 
 TYR   0.016   0.001   TYR D  41 
 ARG   0.006   0.001   ARG D 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8657 (m-30) cc_final: 0.8069 (m-30)
REVERT: A   11 MET cc_start: 0.8610 (mmt) cc_final: 0.8195 (mmt)
REVERT: A   88 LEU cc_start: 0.7871 (mp) cc_final: 0.7174 (tt)
REVERT: A   99 ASP cc_start: 0.8531 (m-30) cc_final: 0.8321 (m-30)
REVERT: A  163 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8091 (tp30)
REVERT: A  463 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6969 (mtp85)
REVERT: A  505 LYS cc_start: 0.7799 (mmtp) cc_final: 0.7382 (mptt)
REVERT: A  589 LYS cc_start: 0.8649 (tttp) cc_final: 0.8084 (ttpt)
REVERT: C   38 MET cc_start: 0.7667 (mtt) cc_final: 0.7438 (mtp)
REVERT: D   38 MET cc_start: 0.7804 (mtt) cc_final: 0.7366 (mtm)
REVERT: B    6 ASP cc_start: 0.8674 (m-30) cc_final: 0.8055 (m-30)
REVERT: B   88 LEU cc_start: 0.7739 (mp) cc_final: 0.7473 (tt)
REVERT: B   99 ASP cc_start: 0.8508 (m-30) cc_final: 0.8300 (m-30)
REVERT: B  163 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8168 (tp30)
REVERT: B  199 ASP cc_start: 0.7472 (p0) cc_final: 0.6697 (t0)
REVERT: B  463 ARG cc_start: 0.7339 (ttt180) cc_final: 0.6981 (mtp85)
REVERT: B  499 MET cc_start: 0.8732 (ttp) cc_final: 0.8375 (ttm)
REVERT: B  505 LYS cc_start: 0.7761 (mmtp) cc_final: 0.7354 (mptt)
REVERT: B  589 LYS cc_start: 0.8647 (tttp) cc_final: 0.8079 (ttpt)
  outliers start: 19
  outliers final: 10
  residues processed: 156
  average time/residue: 0.2015
  time to fit residues: 42.1728
Evaluate side-chains
  137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 CYS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   39 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 52 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 38 optimal weight:   40.0000
   chunk 21 optimal weight:    0.3980
   chunk 77 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 580 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.170917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114358 restraints weight = 9113.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.60
r_work: 0.2837 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7936  Z= 0.228
  Angle     :  0.569   5.347  10790  Z= 0.302
  Chirality :  0.044   0.151   1246
  Planarity :  0.005   0.046   1326
  Dihedral  :  5.008  22.916   1084
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  :  9.64 %
    Favored  : 86.51 %
  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: -3.80 (0.23), residues: 976
  helix: -2.75 (0.18), residues: 532
  sheet: -1.50 (0.47), residues: 104
  loop : -2.08 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 144 
 HIS   0.005   0.001   HIS B   9 
 PHE   0.016   0.002   PHE B  87 
 TYR   0.015   0.001   TYR C  41 
 ARG   0.005   0.000   ARG D 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8693 (m-30) cc_final: 0.8062 (m-30)
REVERT: A   67 MET cc_start: 0.8332 (mtt) cc_final: 0.8025 (mtt)
REVERT: A   88 LEU cc_start: 0.7898 (mp) cc_final: 0.7302 (tt)
REVERT: A   92 LEU cc_start: 0.7259 (mp) cc_final: 0.6741 (tt)
REVERT: A  163 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8109 (tp30)
REVERT: A  184 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.4980 (pp)
REVERT: A  505 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7580 (mptt)
REVERT: A  589 LYS cc_start: 0.8693 (tttp) cc_final: 0.8081 (ttpt)
REVERT: B    6 ASP cc_start: 0.8681 (m-30) cc_final: 0.8059 (m-30)
REVERT: B   67 MET cc_start: 0.8331 (mtt) cc_final: 0.8037 (mtt)
REVERT: B   88 LEU cc_start: 0.7705 (mp) cc_final: 0.7430 (tt)
REVERT: B  163 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8110 (tp30)
REVERT: B  184 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.5003 (pp)
REVERT: B  499 MET cc_start: 0.8842 (ttp) cc_final: 0.8536 (ttm)
REVERT: B  505 LYS cc_start: 0.8011 (mmtp) cc_final: 0.7553 (mptt)
REVERT: B  589 LYS cc_start: 0.8688 (tttp) cc_final: 0.8080 (ttpt)
  outliers start: 32
  outliers final: 21
  residues processed: 158
  average time/residue: 0.2060
  time to fit residues: 43.5809
Evaluate side-chains
  141 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 CYS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 GLN
Chi-restraints excluded: chain A residue  582 ILE
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   39 CYS
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 72 optimal weight:    0.3980
   chunk 48 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 580 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.169617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.111307 restraints weight = 9045.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.44
r_work: 0.2841 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7936  Z= 0.197
  Angle     :  0.534   5.293  10790  Z= 0.285
  Chirality :  0.043   0.155   1246
  Planarity :  0.005   0.044   1326
  Dihedral  :  4.792  21.674   1084
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.69 %
    Favored  : 85.30 %
  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: -3.29 (0.24), residues: 976
  helix: -2.31 (0.20), residues: 530
  sheet: -1.08 (0.47), residues: 102
  loop : -1.96 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 144 
 HIS   0.004   0.001   HIS A   9 
 PHE   0.015   0.001   PHE A  87 
 TYR   0.015   0.001   TYR C  41 
 ARG   0.005   0.000   ARG D 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8744 (m-30) cc_final: 0.8137 (m-30)
REVERT: A   67 MET cc_start: 0.8269 (mtt) cc_final: 0.7979 (mtt)
REVERT: A   88 LEU cc_start: 0.7787 (mp) cc_final: 0.7282 (tt)
REVERT: A   92 LEU cc_start: 0.7025 (mp) cc_final: 0.6634 (tt)
REVERT: A  589 LYS cc_start: 0.8670 (tttp) cc_final: 0.8078 (ttpt)
REVERT: D   38 MET cc_start: 0.7690 (mtt) cc_final: 0.7153 (mtm)
REVERT: D   87 MET cc_start: 0.6019 (pmm) cc_final: 0.5043 (ppp)
REVERT: B    6 ASP cc_start: 0.8651 (m-30) cc_final: 0.8093 (m-30)
REVERT: B   67 MET cc_start: 0.8280 (mtt) cc_final: 0.7990 (mtt)
REVERT: B   88 LEU cc_start: 0.7633 (mp) cc_final: 0.7371 (tt)
REVERT: B  163 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8094 (tp30)
REVERT: B  184 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.4922 (pp)
REVERT: B  499 MET cc_start: 0.8827 (ttp) cc_final: 0.8499 (ttm)
REVERT: B  589 LYS cc_start: 0.8668 (tttp) cc_final: 0.8036 (ttpt)
  outliers start: 25
  outliers final: 16
  residues processed: 146
  average time/residue: 0.2028
  time to fit residues: 40.8572
Evaluate side-chains
  137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 75 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.169962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.105814 restraints weight = 9044.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.03
r_work: 0.2844 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7936  Z= 0.181
  Angle     :  0.515   5.256  10790  Z= 0.272
  Chirality :  0.043   0.145   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.623  21.713   1084
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.77 %
    Favored  : 84.46 %
  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: -2.89 (0.25), residues: 976
  helix: -1.98 (0.20), residues: 530
  sheet: -0.84 (0.48), residues: 102
  loop : -1.83 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.011   0.001   PHE A  87 
 TYR   0.014   0.001   TYR D  41 
 ARG   0.004   0.000   ARG C 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 1.159 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8780 (m-30) cc_final: 0.8193 (m-30)
REVERT: A   67 MET cc_start: 0.8340 (mtt) cc_final: 0.8038 (mtt)
REVERT: A   88 LEU cc_start: 0.7899 (mp) cc_final: 0.7420 (tt)
REVERT: A   92 LEU cc_start: 0.7070 (mp) cc_final: 0.6675 (tt)
REVERT: A  589 LYS cc_start: 0.8715 (tttp) cc_final: 0.8174 (ttpt)
REVERT: D   38 MET cc_start: 0.7703 (mtt) cc_final: 0.7164 (mtm)
REVERT: D   87 MET cc_start: 0.6302 (pmm) cc_final: 0.5404 (ppp)
REVERT: B    6 ASP cc_start: 0.8755 (m-30) cc_final: 0.8217 (m-30)
REVERT: B   67 MET cc_start: 0.8351 (mtt) cc_final: 0.8066 (mtt)
REVERT: B   88 LEU cc_start: 0.7695 (mp) cc_final: 0.7495 (tt)
REVERT: B   92 LEU cc_start: 0.7064 (mp) cc_final: 0.6573 (tt)
REVERT: B  184 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5033 (pp)
REVERT: B  499 MET cc_start: 0.8905 (ttp) cc_final: 0.8588 (ttm)
REVERT: B  589 LYS cc_start: 0.8706 (tttp) cc_final: 0.8125 (ttpt)
  outliers start: 23
  outliers final: 17
  residues processed: 141
  average time/residue: 0.2003
  time to fit residues: 38.9799
Evaluate side-chains
  140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0060
   chunk 60 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0870
   chunk 74 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0570
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.2692

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

Flipped N/Q/H residues before XYZ refinement:
A 580 GLN
B 580 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.174207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.110941 restraints weight = 8985.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.01
r_work: 0.2904 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7936  Z= 0.112
  Angle     :  0.469   5.186  10790  Z= 0.248
  Chirality :  0.041   0.149   1246
  Planarity :  0.004   0.045   1326
  Dihedral  :  4.298  20.352   1084
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.73 %
    Favored  : 83.86 %
  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: -2.20 (0.26), residues: 976
  helix: -1.21 (0.22), residues: 522
  sheet: -1.37 (0.46), residues: 126
  loop : -1.59 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  40 
 HIS   0.003   0.001   HIS B   9 
 PHE   0.009   0.001   PHE A  87 
 TYR   0.015   0.001   TYR D  41 
 ARG   0.004   0.000   ARG C 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8784 (m-30) cc_final: 0.8308 (m-30)
REVERT: A   88 LEU cc_start: 0.7853 (mp) cc_final: 0.7465 (tt)
REVERT: A  184 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.4734 (pp)
REVERT: A  531 ARG cc_start: 0.7820 (tpt170) cc_final: 0.6843 (ttm110)
REVERT: A  589 LYS cc_start: 0.8702 (tttp) cc_final: 0.8173 (ttpt)
REVERT: D   38 MET cc_start: 0.7371 (mtt) cc_final: 0.6941 (mtm)
REVERT: D   87 MET cc_start: 0.6300 (pmm) cc_final: 0.5411 (ppp)
REVERT: B    6 ASP cc_start: 0.8775 (m-30) cc_final: 0.8320 (m-30)
REVERT: B   11 MET cc_start: 0.8663 (mmt) cc_final: 0.8191 (mmt)
REVERT: B   92 LEU cc_start: 0.6992 (mp) cc_final: 0.6484 (tt)
REVERT: B  162 SER cc_start: 0.8341 (p) cc_final: 0.8133 (p)
REVERT: B  184 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.4756 (pp)
REVERT: B  461 MET cc_start: 0.8420 (mmm) cc_final: 0.8131 (mmm)
REVERT: B  499 MET cc_start: 0.8914 (ttp) cc_final: 0.8693 (ttt)
REVERT: B  531 ARG cc_start: 0.7816 (tpt170) cc_final: 0.6843 (ttm110)
REVERT: B  589 LYS cc_start: 0.8702 (tttp) cc_final: 0.8172 (ttpt)
  outliers start: 20
  outliers final: 13
  residues processed: 151
  average time/residue: 0.1857
  time to fit residues: 38.3550
Evaluate side-chains
  137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 GLN
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    0.0030
   chunk 29 optimal weight:    0.0370
   chunk 82 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 43 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.4868

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.171582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.107665 restraints weight = 9085.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.02
r_work: 0.2891 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7936  Z= 0.137
  Angle     :  0.491   9.615  10790  Z= 0.253
  Chirality :  0.042   0.143   1246
  Planarity :  0.005   0.050   1326
  Dihedral  :  4.219  19.365   1084
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.58 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.26), residues: 976
  helix: -0.95 (0.22), residues: 528
  sheet: -0.39 (0.50), residues: 102
  loop : -1.67 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 144 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.007   0.001   PHE A  87 
 TYR   0.016   0.001   TYR B 617 
 ARG   0.004   0.000   ARG C 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.878 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8789 (m-30) cc_final: 0.8380 (m-30)
REVERT: A   88 LEU cc_start: 0.7882 (mp) cc_final: 0.7466 (tt)
REVERT: A  184 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.4862 (pp)
REVERT: A  505 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7640 (mptt)
REVERT: A  589 LYS cc_start: 0.8721 (tttp) cc_final: 0.8186 (ttpt)
REVERT: D   38 MET cc_start: 0.7301 (mtt) cc_final: 0.6853 (mtm)
REVERT: D   87 MET cc_start: 0.6260 (pmm) cc_final: 0.5361 (ppp)
REVERT: B    6 ASP cc_start: 0.8774 (m-30) cc_final: 0.8400 (m-30)
REVERT: B   11 MET cc_start: 0.8681 (mmt) cc_final: 0.8176 (mmt)
REVERT: B   92 LEU cc_start: 0.6769 (mp) cc_final: 0.6346 (tt)
REVERT: B  184 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.4818 (pp)
REVERT: B  461 MET cc_start: 0.8441 (mmm) cc_final: 0.8165 (mmm)
REVERT: B  499 MET cc_start: 0.8930 (ttp) cc_final: 0.8722 (ttt)
REVERT: B  531 ARG cc_start: 0.7803 (tpt170) cc_final: 0.6792 (ttm110)
REVERT: B  589 LYS cc_start: 0.8715 (tttp) cc_final: 0.8192 (ttpt)
  outliers start: 18
  outliers final: 12
  residues processed: 135
  average time/residue: 0.2106
  time to fit residues: 38.1225
Evaluate side-chains
  132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 56 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.170016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.106194 restraints weight = 9131.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.03
r_work: 0.2847 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7936  Z= 0.225
  Angle     :  0.533   8.744  10790  Z= 0.272
  Chirality :  0.044   0.138   1246
  Planarity :  0.005   0.048   1326
  Dihedral  :  4.381  18.663   1084
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.18 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.25), residues: 976
  helix: -1.04 (0.21), residues: 532
  sheet: -0.34 (0.50), residues: 102
  loop : -1.78 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A 594 
 PHE   0.007   0.001   PHE B 493 
 TYR   0.012   0.001   TYR C  41 
 ARG   0.007   0.000   ARG D 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8870 (m-30) cc_final: 0.8378 (m-30)
REVERT: A   88 LEU cc_start: 0.7907 (mp) cc_final: 0.7484 (tt)
REVERT: A  182 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7094 (tmm)
REVERT: A  184 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.4885 (pp)
REVERT: A  505 LYS cc_start: 0.8080 (mmtp) cc_final: 0.7705 (mmtm)
REVERT: A  589 LYS cc_start: 0.8638 (tttp) cc_final: 0.8125 (ttpt)
REVERT: D   87 MET cc_start: 0.6078 (pmm) cc_final: 0.5170 (ppp)
REVERT: B    6 ASP cc_start: 0.8871 (m-30) cc_final: 0.8346 (m-30)
REVERT: B  184 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.4906 (pp)
REVERT: B  499 MET cc_start: 0.8873 (ttp) cc_final: 0.8600 (ttm)
REVERT: B  589 LYS cc_start: 0.8653 (tttp) cc_final: 0.8132 (ttpt)
  outliers start: 19
  outliers final: 15
  residues processed: 129
  average time/residue: 0.2006
  time to fit residues: 34.8319
Evaluate side-chains
  132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 49 optimal weight:   40.0000
   chunk 92 optimal weight:    0.8980
   chunk 43 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.168158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.103563 restraints weight = 9165.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.01
r_work: 0.2859 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7936  Z= 0.176
  Angle     :  0.499   7.840  10790  Z= 0.257
  Chirality :  0.042   0.137   1246
  Planarity :  0.005   0.046   1326
  Dihedral  :  4.302  18.106   1084
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.18 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.26), residues: 976
  helix: -0.78 (0.22), residues: 532
  sheet: -0.28 (0.51), residues: 102
  loop : -1.72 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  37 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.021   0.001   PHE A  87 
 TYR   0.017   0.001   TYR B 617 
 ARG   0.008   0.000   ARG D 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.8885 (m-30) cc_final: 0.8426 (m-30)
REVERT: A   88 LEU cc_start: 0.7880 (mp) cc_final: 0.7480 (tt)
REVERT: A  505 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7746 (mmtm)
REVERT: A  589 LYS cc_start: 0.8684 (tttp) cc_final: 0.8184 (ttpt)
REVERT: D   87 MET cc_start: 0.6164 (pmm) cc_final: 0.5219 (ppp)
REVERT: B    6 ASP cc_start: 0.8886 (m-30) cc_final: 0.8448 (m-30)
REVERT: B  184 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5132 (pp)
REVERT: B  589 LYS cc_start: 0.8690 (tttp) cc_final: 0.8189 (ttpt)
  outliers start: 21
  outliers final: 17
  residues processed: 132
  average time/residue: 0.2386
  time to fit residues: 42.5649
Evaluate side-chains
  129 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0060
   chunk 92 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.171825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.108090 restraints weight = 9119.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.02
r_work: 0.2873 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7936  Z= 0.156
  Angle     :  0.504   7.353  10790  Z= 0.257
  Chirality :  0.042   0.135   1246
  Planarity :  0.005   0.046   1326
  Dihedral  :  4.234  17.943   1084
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.42 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.26), residues: 976
  helix: -0.52 (0.22), residues: 534
  sheet: -0.19 (0.52), residues: 102
  loop : -1.67 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.019   0.001   PHE A  87 
 TYR   0.020   0.001   TYR A 617 
 ARG   0.008   0.000   ARG D 109 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8856 (m-30) cc_final: 0.8420 (m-30)
REVERT: A   88 LEU cc_start: 0.7863 (mp) cc_final: 0.7511 (tt)
REVERT: A  472 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8897 (tptt)
REVERT: A  505 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7705 (mmtm)
REVERT: A  589 LYS cc_start: 0.8660 (tttp) cc_final: 0.8154 (ttpt)
REVERT: D   87 MET cc_start: 0.6074 (pmm) cc_final: 0.5153 (ppp)
REVERT: B    6 ASP cc_start: 0.8859 (m-30) cc_final: 0.8426 (m-30)
REVERT: B  589 LYS cc_start: 0.8677 (tttp) cc_final: 0.8165 (ttpt)
  outliers start: 17
  outliers final: 13
  residues processed: 124
  average time/residue: 0.2055
  time to fit residues: 34.4286
Evaluate side-chains
  123 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.170958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.106607 restraints weight = 9013.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.04
r_work: 0.2878 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7936  Z= 0.139
  Angle     :  0.493   6.790  10790  Z= 0.251
  Chirality :  0.042   0.134   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.167  18.435   1084
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.78 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.27), residues: 976
  helix: -0.26 (0.23), residues: 534
  sheet: -0.21 (0.52), residues: 102
  loop : -1.61 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.018   0.001   PHE A  87 
 TYR   0.015   0.001   TYR A 617 
 ARG   0.008   0.000   ARG D 109 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5266.84 seconds
wall clock time: 92 minutes 56.59 seconds (5576.59 seconds total)