Starting phenix.real_space_refine
on Sun May 11 08:22:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y9v_33693/05_2025/7y9v_33693_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y9v_33693/05_2025/7y9v_33693.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y9v_33693/05_2025/7y9v_33693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y9v_33693/05_2025/7y9v_33693.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y9v_33693/05_2025/7y9v_33693_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y9v_33693/05_2025/7y9v_33693_neut.cif"
  }
  resolution = 3.2
  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=   0.003 sd=   0.087
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    5062      2.51       5
     N    1272      2.21       5
     O    1344      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7734
  Number of models: 1
  Model: ""
    Number of chains: 5
    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: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'IAC': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 6.02, per 1000 atoms: 0.78
  Number of scatterers: 7734
  At special positions: 0
  Unit cell: (111.28, 119.6, 95.68, 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    1344      8.00
     N    1272      7.00
     C    5062      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: 1.77
  Conformation dependent library (CDL) restraints added in 1.2 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:
      42 helices and 6 sheets defined
      55.3% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 30
      removed outlier: 3.645A  pdb=" N   VAL A  10 " --> pdb=" O   ASP A   6 " (cutoff:3.500A)
      Proline residue:  A  16  - end of helix
      removed outlier: 3.620A  pdb=" N   ALA A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ALA A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 49
      removed outlier: 3.713A  pdb=" N   ILE A  42 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASN A  43 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG A  44 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 68 through 91
      removed outlier: 3.605A  pdb=" N   ALA A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LYS A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 110
      removed outlier: 3.685A  pdb=" N   THR A 101 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   SER A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A 110 " --> pdb=" O   SER A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 126
      removed outlier: 3.609A  pdb=" N   LEU A 120 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 143
      removed outlier: 4.109A  pdb=" N   VAL A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN A 135 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 165
      removed outlier: 3.517A  pdb=" N   LEU A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 157 " (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: 3.988A  pdb=" N   ARG A 463 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 466 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   MET A 468 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 492
      removed outlier: 4.086A  pdb=" N   TYR A 480 " --> pdb=" O   ASN A 476 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER A 481 " --> pdb=" O   PRO A 477 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER A 482 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A 491 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 507 through 512
    Processing helix  chain 'A' and resid 513 through 529
      removed outlier: 3.776A  pdb=" N   MET A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 547
      removed outlier: 4.021A  pdb=" N   PHE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A 545 " --> pdb=" O   ALA A 541 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG A 547 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 554
    Processing helix  chain 'A' and resid 558 through 563
      removed outlier: 3.876A  pdb=" N   GLY A 563 " --> pdb=" O   SER A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 3.543A  pdb=" N   HIS A 570 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 592
    Processing helix  chain 'A' and resid 596 through 608
      removed outlier: 4.052A  pdb=" N   VAL A 602 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 607 " --> pdb=" O   ILE A 603 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 620
      removed outlier: 3.504A  pdb=" N   ILE A 612 " --> pdb=" O   ILE A 608 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 615 " --> pdb=" O   PRO A 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 30
      removed outlier: 3.645A  pdb=" N   VAL B  10 " --> pdb=" O   ASP B   6 " (cutoff:3.500A)
      Proline residue:  B  16  - end of helix
      removed outlier: 3.620A  pdb=" N   ALA B  20 " --> pdb=" O   PRO B  16 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ALA B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 49
      removed outlier: 3.713A  pdb=" N   ILE B  42 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASN B  43 " --> pdb=" O   CYS B  39 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 60
    Processing helix  chain 'B' and resid 68 through 91
      removed outlier: 3.604A  pdb=" N   ALA B  74 " --> pdb=" O   ARG B  70 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP B  75 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LYS B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL B  80 " --> pdb=" O   SER B  76 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS B  91 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 110
      removed outlier: 3.684A  pdb=" N   THR B 101 " --> pdb=" O   SER B  97 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   THR B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU B 110 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 126
      removed outlier: 3.608A  pdb=" N   LEU B 120 " --> pdb=" O   MET B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 143
      removed outlier: 4.109A  pdb=" N   VAL B 134 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLN B 135 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 165
      removed outlier: 3.518A  pdb=" N   LEU B 159 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ILE B 161 " --> pdb=" O   ALA B 157 " (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: 3.988A  pdb=" N   ARG B 463 " --> pdb=" O   SER B 459 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU B 466 " --> pdb=" O   THR B 462 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   MET B 468 " --> pdb=" O   LEU B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 492
      removed outlier: 4.087A  pdb=" N   TYR B 480 " --> pdb=" O   ASN B 476 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER B 481 " --> pdb=" O   PRO B 477 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER B 482 " --> pdb=" O   ASN B 478 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE B 491 " --> pdb=" O   THR B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 507
    Processing helix  chain 'B' and resid 507 through 512
    Processing helix  chain 'B' and resid 513 through 529
      removed outlier: 3.776A  pdb=" N   MET B 519 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 547
      removed outlier: 4.020A  pdb=" N   PHE B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B 545 " --> pdb=" O   ALA B 541 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG B 547 " --> pdb=" O   ALA B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 554
    Processing helix  chain 'B' and resid 558 through 563
      removed outlier: 3.876A  pdb=" N   GLY B 563 " --> pdb=" O   SER B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 577
      removed outlier: 3.543A  pdb=" N   HIS B 570 " --> pdb=" O   GLY B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 592
    Processing helix  chain 'B' and resid 596 through 608
      removed outlier: 4.052A  pdb=" N   VAL B 602 " --> pdb=" O   LEU B 598 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU B 607 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE B 608 " --> pdb=" O   PHE B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 620
      removed outlier: 3.504A  pdb=" N   ILE B 612 " --> pdb=" O   ILE B 608 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU B 615 " --> pdb=" O   PRO B 611 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177
      removed outlier: 7.244A  pdb=" N   VAL A 204 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ILE A 175 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL A 206 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   VAL A 177 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR C 107 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR C  99 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR C  41 " --> pdb=" O   TYR C  99 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU C  39 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   TRP C  40 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLU C  50 " --> pdb=" O   ARG C  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11
      removed outlier: 3.920A  pdb=" N   SER C  29 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER C  11 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER C  25 " --> pdb=" O   SER C  11 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS C  26 " --> pdb=" O   VAL C  83 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL C  83 " --> pdb=" O   CYS C  26 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP C  77 " --> pdb=" O   THR C  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 17
      removed outlier: 5.744A  pdb=" N   GLY C  14 " --> pdb=" O   THR C 116 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   SER C 118 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL C  16 " --> pdb=" O   SER C 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 7 through 11
      removed outlier: 3.921A  pdb=" N   SER D  29 " --> pdb=" O   GLN D   7 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   SER D  11 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER D  25 " --> pdb=" O   SER D  11 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS D  26 " --> pdb=" O   VAL D  83 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL D  83 " --> pdb=" O   CYS D  26 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP D  77 " --> pdb=" O   THR D  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 17
      removed outlier: 5.744A  pdb=" N   GLY D  14 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   SER D 118 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL D  16 " --> pdb=" O   SER D 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 50 through 54
      removed outlier: 4.144A  pdb=" N   GLU D  50 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   TRP D  40 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU D  39 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR D  41 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR D  99 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   TYR D 107 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   ILE B 196 " --> pdb=" O   TYR D 107 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ARG D 109 " --> pdb=" O   ILE B 196 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   VAL B 204 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ILE B 175 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL B 206 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   VAL B 177 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    996 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: 2.05

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1180
        1.27 -     1.41: 2058
        1.41 -     1.54: 4482
        1.54 -     1.67: 96
        1.67 -     1.80: 100
  Bond restraints: 7916
  Sorted by residual:
  bond pdb=" CA  LEU B 147 "
       pdb=" C   LEU B 147 "
    ideal  model  delta    sigma   weight residual
    1.519  1.361  0.158 1.01e-02 9.80e+03 2.46e+02
  bond pdb=" CA  LEU A 147 "
       pdb=" C   LEU A 147 "
    ideal  model  delta    sigma   weight residual
    1.519  1.361  0.158 1.01e-02 9.80e+03 2.46e+02
  bond pdb=" CA  ASN B 112 "
       pdb=" C   ASN B 112 "
    ideal  model  delta    sigma   weight residual
    1.526  1.405  0.121 1.11e-02 8.12e+03 1.19e+02
  bond pdb=" CA  ASN A 112 "
       pdb=" C   ASN A 112 "
    ideal  model  delta    sigma   weight residual
    1.526  1.406  0.121 1.11e-02 8.12e+03 1.18e+02
  bond pdb=" CA  ALA B 561 "
       pdb=" C   ALA B 561 "
    ideal  model  delta    sigma   weight residual
    1.522  1.421  0.101 1.39e-02 5.18e+03 5.31e+01
  ... (remaining 7911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 10466
        3.17 -     6.34: 252
        6.34 -     9.51: 32
        9.51 -    12.69: 8
       12.69 -    15.86: 4
  Bond angle restraints: 10762
  Sorted by residual:
  angle pdb=" N   SER A 479 "
        pdb=" CA  SER A 479 "
        pdb=" C   SER A 479 "
      ideal   model   delta    sigma   weight residual
     114.04   98.18   15.86 1.24e+00 6.50e-01 1.64e+02
  angle pdb=" N   SER B 479 "
        pdb=" CA  SER B 479 "
        pdb=" C   SER B 479 "
      ideal   model   delta    sigma   weight residual
     114.04   98.19   15.85 1.24e+00 6.50e-01 1.63e+02
  angle pdb=" N   LEU A 147 "
        pdb=" CA  LEU A 147 "
        pdb=" C   LEU A 147 "
      ideal   model   delta    sigma   weight residual
     112.72   98.40   14.32 1.28e+00 6.10e-01 1.25e+02
  angle pdb=" N   LEU B 147 "
        pdb=" CA  LEU B 147 "
        pdb=" C   LEU B 147 "
      ideal   model   delta    sigma   weight residual
     112.72   98.45   14.27 1.28e+00 6.10e-01 1.24e+02
  angle pdb=" C   ASN A 112 "
        pdb=" CA  ASN A 112 "
        pdb=" CB  ASN A 112 "
      ideal   model   delta    sigma   weight residual
     112.05  102.06    9.99 1.52e+00 4.33e-01 4.32e+01
  ... (remaining 10757 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.93: 4408
       16.93 -    33.85: 198
       33.85 -    50.78: 44
       50.78 -    67.71: 2
       67.71 -    84.63: 4
  Dihedral angle restraints: 4656
    sinusoidal: 1794
      harmonic: 2862
  Sorted by residual:
  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 -138.53  -41.47     0      5.00e+00 4.00e-02 6.88e+01
  dihedral pdb=" CA  GLN D  56 "
           pdb=" C   GLN D  56 "
           pdb=" N   SER D  57 "
           pdb=" CA  SER D  57 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.55  -41.45     0      5.00e+00 4.00e-02 6.87e+01
  dihedral pdb=" C   LEU A 147 "
           pdb=" N   LEU A 147 "
           pdb=" CA  LEU A 147 "
           pdb=" CB  LEU A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.71  -14.89     0      2.50e+00 1.60e-01 3.55e+01
  ... (remaining 4653 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 939
       0.065 -    0.130: 253
       0.130 -    0.196: 44
       0.196 -    0.261: 7
       0.261 -    0.326: 3
  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    2.32    0.33 2.00e-01 2.50e+01 2.66e+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    2.32    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CB  ILE D  35 "
            pdb=" CA  ILE D  35 "
            pdb=" CG1 ILE D  35 "
            pdb=" CG2 ILE D  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1243 not shown)

  Planarity restraints: 1322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 551 "    0.044 5.00e-02 4.00e+02   6.64e-02 7.05e+00
        pdb=" N   PRO A 552 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 552 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 552 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 551 "   -0.044 5.00e-02 4.00e+02   6.61e-02 7.00e+00
        pdb=" N   PRO B 552 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 552 "   -0.034 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=" CA  GLN A 140 "   -0.013 2.00e-02 2.50e+03   2.47e-02 6.12e+00
        pdb=" C   GLN A 140 "    0.043 2.00e-02 2.50e+03
        pdb=" O   GLN A 140 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS A 141 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1319 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 71
        2.63 -     3.19: 6442
        3.19 -     3.76: 11289
        3.76 -     4.33: 16504
        4.33 -     4.90: 26861
  Nonbonded interactions: 61167
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG D  71 "
            pdb=" O   SER D  89 "
     model   vdw
     2.057 3.120
  nonbonded pdb=" NH2 ARG C  71 "
            pdb=" O   SER C  89 "
     model   vdw
     2.057 3.120
  nonbonded pdb=" NE1 TRP D  37 "
            pdb=" OE2 GLU D  39 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" NE1 TRP C  37 "
            pdb=" OE2 GLU C  39 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   THR B 458 "
            pdb=" OG1 THR B 462 "
     model   vdw
     2.320 3.040
  ... (remaining 61162 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:             0.860
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.410
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.158   7918  Z= 0.742
  Angle     :  1.209  15.856  10766  Z= 0.690
  Chirality :  0.063   0.326   1246
  Planarity :  0.009   0.066   1322
  Dihedral  : 10.859  84.631   2810
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.13 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.65 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.91 (0.18), residues: 976
  helix: -4.55 (0.09), residues: 540
  sheet: -2.50 (0.46), residues: 116
  loop : -2.74 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP B  31 
 HIS   0.006   0.002   HIS B 594 
 PHE   0.021   0.003   PHE B  58 
 TYR   0.034   0.003   TYR A 617 
 ARG   0.013   0.001   ARG D 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.32654 (  338)
  hydrogen bonds       : angle      11.55483 (  996)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       0.80771 (    4)
  covalent geometry    : bond        0.01320 ( 7916)
  covalent geometry    : angle       1.20907 (10762)

*********************** 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
  190 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 186
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8376 (mmtt)
REVERT: A  122 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8307 (mtpp)
REVERT: A  147 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8377 (tp)
REVERT: A  181 ILE cc_start: 0.8457 (mt) cc_final: 0.8224 (mt)
REVERT: A  201 LYS cc_start: 0.7289 (mttt) cc_final: 0.6916 (mmtt)
REVERT: A  459 SER cc_start: 0.8610 (t) cc_final: 0.8205 (p)
REVERT: A  505 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8356 (mmmt)
REVERT: A  512 ASP cc_start: 0.8374 (m-30) cc_final: 0.7925 (m-30)
REVERT: C   55 ILE cc_start: 0.7367 (tp) cc_final: 0.7102 (tt)
REVERT: B    9 HIS cc_start: 0.8203 (m-70) cc_final: 0.7902 (m170)
REVERT: B   29 LYS cc_start: 0.7516 (tppt) cc_final: 0.7224 (tppt)
REVERT: B   32 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8204 (mmtm)
REVERT: B  122 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8303 (mtpp)
REVERT: B  181 ILE cc_start: 0.8458 (mt) cc_final: 0.8236 (mt)
REVERT: B  201 LYS cc_start: 0.7210 (mttt) cc_final: 0.6783 (mmtt)
REVERT: B  459 SER cc_start: 0.8487 (t) cc_final: 0.8204 (p)
REVERT: B  467 ILE cc_start: 0.8984 (mm) cc_final: 0.8641 (mt)
REVERT: B  505 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8313 (mmmt)
REVERT: B  512 ASP cc_start: 0.8358 (m-30) cc_final: 0.7759 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2412
  time to fit residues: 57.5788
Evaluate side-chains
  129 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    0.1980
   chunk 75 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 164 GLN
B  43 ASN
B 164 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.172373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116103 restraints weight = 8878.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.93
r_work: 0.3129 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7918  Z= 0.135
  Angle     :  0.629   6.872  10766  Z= 0.331
  Chirality :  0.043   0.146   1246
  Planarity :  0.006   0.046   1322
  Dihedral  :  6.804  82.853   1074
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.76 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.72 (0.23), residues: 976
  helix: -2.46 (0.18), residues: 544
  sheet: -2.36 (0.44), residues: 124
  loop : -2.01 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  40 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.014   0.001   PHE D  72 
 TYR   0.013   0.001   TYR C  41 
 ARG   0.005   0.001   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04511 (  338)
  hydrogen bonds       : angle       5.96218 (  996)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       0.37328 (    4)
  covalent geometry    : bond        0.00305 ( 7916)
  covalent geometry    : angle       0.62947 (10762)

*********************** 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
  163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5563 (ppp) cc_final: 0.5176 (ppp)
REVERT: A   21 MET cc_start: 0.9003 (ttp) cc_final: 0.8654 (ttt)
REVERT: A   29 LYS cc_start: 0.8197 (tppt) cc_final: 0.7912 (ttmt)
REVERT: A   32 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8412 (mmtt)
REVERT: A  208 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7723 (mmm-85)
REVERT: A  459 SER cc_start: 0.8568 (t) cc_final: 0.8341 (p)
REVERT: A  505 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8387 (mmmt)
REVERT: A  512 ASP cc_start: 0.8342 (m-30) cc_final: 0.7983 (m-30)
REVERT: A  517 MET cc_start: 0.9041 (mmm) cc_final: 0.8833 (mmm)
REVERT: A  554 VAL cc_start: 0.8730 (p) cc_final: 0.8509 (p)
REVERT: C   56 GLN cc_start: 0.7004 (pp30) cc_final: 0.6523 (pt0)
REVERT: B    1 MET cc_start: 0.5382 (ppp) cc_final: 0.4964 (ppp)
REVERT: B   21 MET cc_start: 0.8963 (ttp) cc_final: 0.8676 (ttt)
REVERT: B   32 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8313 (mmtt)
REVERT: B  131 ASP cc_start: 0.7976 (t70) cc_final: 0.7708 (m-30)
REVERT: B  173 VAL cc_start: 0.9005 (t) cc_final: 0.8722 (m)
REVERT: B  467 ILE cc_start: 0.9094 (mm) cc_final: 0.8735 (mt)
REVERT: B  505 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8455 (mmmt)
REVERT: B  512 ASP cc_start: 0.8402 (m-30) cc_final: 0.8074 (m-30)
REVERT: B  517 MET cc_start: 0.9039 (mmm) cc_final: 0.8812 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 159
  average time/residue: 0.1941
  time to fit residues: 41.3268
Evaluate side-chains
  140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  479 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    0.0980
   chunk 69 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.171816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.115297 restraints weight = 9036.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.91
r_work: 0.3121 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7918  Z= 0.116
  Angle     :  0.539   5.689  10766  Z= 0.283
  Chirality :  0.042   0.137   1246
  Planarity :  0.005   0.042   1322
  Dihedral  :  6.070  76.488   1072
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.60 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.56 (0.25), residues: 976
  helix: -1.21 (0.21), residues: 540
  sheet: -2.33 (0.40), residues: 164
  loop : -1.77 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  40 
 HIS   0.006   0.001   HIS B  57 
 PHE   0.012   0.001   PHE A 585 
 TYR   0.013   0.001   TYR C  41 
 ARG   0.004   0.000   ARG A 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  338)
  hydrogen bonds       : angle       5.09161 (  996)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       0.59845 (    4)
  covalent geometry    : bond        0.00268 ( 7916)
  covalent geometry    : angle       0.53913 (10762)

*********************** 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
  169 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5506 (ppp) cc_final: 0.5232 (ppp)
REVERT: A   21 MET cc_start: 0.8980 (ttp) cc_final: 0.8683 (ttt)
REVERT: A   29 LYS cc_start: 0.8192 (tppt) cc_final: 0.7892 (ttmt)
REVERT: A   32 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8505 (mmtt)
REVERT: A  467 ILE cc_start: 0.9076 (mm) cc_final: 0.8702 (mt)
REVERT: A  505 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8408 (mmmt)
REVERT: A  512 ASP cc_start: 0.8355 (m-30) cc_final: 0.8101 (m-30)
REVERT: A  517 MET cc_start: 0.8982 (mmm) cc_final: 0.8695 (mmm)
REVERT: C   56 GLN cc_start: 0.7069 (pp30) cc_final: 0.6712 (pt0)
REVERT: D   56 GLN cc_start: 0.7213 (pt0) cc_final: 0.6887 (pt0)
REVERT: B    1 MET cc_start: 0.5716 (ppp) cc_final: 0.5267 (ppp)
REVERT: B   21 MET cc_start: 0.8933 (ttp) cc_final: 0.8655 (ttt)
REVERT: B   32 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8303 (mmtt)
REVERT: B  173 VAL cc_start: 0.9074 (t) cc_final: 0.8776 (m)
REVERT: B  201 LYS cc_start: 0.7211 (mttt) cc_final: 0.6764 (mmtt)
REVERT: B  467 ILE cc_start: 0.9080 (mm) cc_final: 0.8724 (mt)
REVERT: B  505 LYS cc_start: 0.8824 (mmtp) cc_final: 0.8524 (mmmt)
REVERT: B  512 ASP cc_start: 0.8396 (m-30) cc_final: 0.8164 (m-30)
REVERT: B  517 MET cc_start: 0.9006 (mmm) cc_final: 0.8691 (mmm)
REVERT: B  546 MET cc_start: 0.8735 (mmm) cc_final: 0.8535 (mmt)
  outliers start: 20
  outliers final: 9
  residues processed: 165
  average time/residue: 0.1857
  time to fit residues: 41.5221
Evaluate side-chains
  140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  479 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 140 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.170523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.113480 restraints weight = 8999.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.93
r_work: 0.3086 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7918  Z= 0.133
  Angle     :  0.545   5.635  10766  Z= 0.283
  Chirality :  0.043   0.146   1246
  Planarity :  0.005   0.043   1322
  Dihedral  :  5.903  77.680   1072
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 11.33 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.84 (0.26), residues: 976
  helix: -0.70 (0.22), residues: 540
  sheet: -1.89 (0.43), residues: 154
  loop : -1.43 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 488 
 HIS   0.005   0.001   HIS B  57 
 PHE   0.010   0.001   PHE A 585 
 TYR   0.014   0.001   TYR B 617 
 ARG   0.004   0.000   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  338)
  hydrogen bonds       : angle       4.89666 (  996)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       0.49894 (    4)
  covalent geometry    : bond        0.00323 ( 7916)
  covalent geometry    : angle       0.54546 (10762)

*********************** 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
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5639 (ppp) cc_final: 0.5414 (ppp)
REVERT: A   29 LYS cc_start: 0.8209 (tppt) cc_final: 0.7890 (ttmt)
REVERT: A   32 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8502 (mmtt)
REVERT: A  467 ILE cc_start: 0.9064 (mm) cc_final: 0.8680 (mt)
REVERT: A  505 LYS cc_start: 0.8764 (mmtp) cc_final: 0.8443 (mmmt)
REVERT: A  512 ASP cc_start: 0.8441 (m-30) cc_final: 0.8201 (m-30)
REVERT: D   56 GLN cc_start: 0.7200 (pt0) cc_final: 0.6903 (pt0)
REVERT: B    1 MET cc_start: 0.5526 (ppp) cc_final: 0.5188 (ppp)
REVERT: B   21 MET cc_start: 0.8950 (ttp) cc_final: 0.8683 (ttt)
REVERT: B   32 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8329 (mmtt)
REVERT: B  173 VAL cc_start: 0.9135 (t) cc_final: 0.8801 (m)
REVERT: B  201 LYS cc_start: 0.7215 (mttt) cc_final: 0.6768 (mmtt)
REVERT: B  467 ILE cc_start: 0.9075 (mm) cc_final: 0.8700 (mt)
REVERT: B  505 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8442 (mmmt)
REVERT: B  512 ASP cc_start: 0.8425 (m-30) cc_final: 0.8183 (m-30)
REVERT: B  517 MET cc_start: 0.9020 (mmm) cc_final: 0.8717 (mmm)
  outliers start: 23
  outliers final: 14
  residues processed: 150
  average time/residue: 0.1861
  time to fit residues: 37.9017
Evaluate side-chains
  142 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  589 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   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 140 GLN
C  56 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.170273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.113008 restraints weight = 8945.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.93
r_work: 0.3092 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7918  Z= 0.128
  Angle     :  0.534   5.840  10766  Z= 0.276
  Chirality :  0.042   0.143   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.767  79.438   1072
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 10.84 %
    Favored  : 85.66 %
  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: -1.28 (0.27), residues: 976
  helix: -0.30 (0.22), residues: 534
  sheet: -1.68 (0.43), residues: 154
  loop : -1.03 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 488 
 HIS   0.005   0.001   HIS B  57 
 PHE   0.011   0.001   PHE A 585 
 TYR   0.013   0.001   TYR B 617 
 ARG   0.004   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  338)
  hydrogen bonds       : angle       4.75744 (  996)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.48764 (    4)
  covalent geometry    : bond        0.00309 ( 7916)
  covalent geometry    : angle       0.53364 (10762)

*********************** 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
  159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 1.416 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5640 (ppp) cc_final: 0.5420 (ppp)
REVERT: A   32 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8406 (mmtt)
REVERT: A  467 ILE cc_start: 0.9061 (mm) cc_final: 0.8677 (mt)
REVERT: A  505 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8463 (mmmt)
REVERT: A  512 ASP cc_start: 0.8371 (m-30) cc_final: 0.8133 (m-30)
REVERT: A  547 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8175 (tpt90)
REVERT: D   56 GLN cc_start: 0.7082 (pt0) cc_final: 0.6715 (pt0)
REVERT: B    1 MET cc_start: 0.5570 (ppp) cc_final: 0.5267 (ppp)
REVERT: B   21 MET cc_start: 0.8941 (ttp) cc_final: 0.8629 (ttt)
REVERT: B   32 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8346 (mmtt)
REVERT: B  173 VAL cc_start: 0.9127 (t) cc_final: 0.8793 (m)
REVERT: B  180 ASP cc_start: 0.8429 (t0) cc_final: 0.8148 (t0)
REVERT: B  201 LYS cc_start: 0.7233 (mttt) cc_final: 0.6823 (mmtt)
REVERT: B  208 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7902 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9065 (mm) cc_final: 0.8689 (mt)
REVERT: B  505 LYS cc_start: 0.8772 (mmtp) cc_final: 0.8436 (mmmt)
REVERT: B  512 ASP cc_start: 0.8401 (m-30) cc_final: 0.8159 (m-30)
  outliers start: 29
  outliers final: 20
  residues processed: 151
  average time/residue: 0.2789
  time to fit residues: 56.4945
Evaluate side-chains
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Chi-restraints excluded: chain B residue  589 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.184517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.126768 restraints weight = 8803.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.82
r_work: 0.3062 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7918  Z= 0.124
  Angle     :  0.531   5.705  10766  Z= 0.273
  Chirality :  0.042   0.143   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.635  77.655   1072
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 11.08 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.27), residues: 976
  helix: -0.02 (0.22), residues: 536
  sheet: -1.60 (0.43), residues: 154
  loop : -1.01 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  37 
 HIS   0.005   0.001   HIS A  57 
 PHE   0.010   0.001   PHE A 585 
 TYR   0.013   0.001   TYR B 617 
 ARG   0.003   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  338)
  hydrogen bonds       : angle       4.67937 (  996)
  SS BOND              : bond        0.00083 (    2)
  SS BOND              : angle       0.42485 (    4)
  covalent geometry    : bond        0.00301 ( 7916)
  covalent geometry    : angle       0.53065 (10762)

*********************** 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
  161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8346 (mmtt)
REVERT: A  131 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7468 (m-30)
REVERT: A  208 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7866 (mmm-85)
REVERT: A  467 ILE cc_start: 0.8988 (mm) cc_final: 0.8609 (mt)
REVERT: A  505 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8426 (mmmt)
REVERT: A  512 ASP cc_start: 0.8377 (m-30) cc_final: 0.8142 (m-30)
REVERT: D   56 GLN cc_start: 0.6985 (pt0) cc_final: 0.6669 (pt0)
REVERT: B    1 MET cc_start: 0.5658 (ppp) cc_final: 0.5366 (ppp)
REVERT: B   21 MET cc_start: 0.8930 (ttp) cc_final: 0.8613 (ttt)
REVERT: B   32 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8323 (mmtt)
REVERT: B  131 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7563 (m-30)
REVERT: B  180 ASP cc_start: 0.8441 (t0) cc_final: 0.8117 (t0)
REVERT: B  208 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7813 (mmm-85)
REVERT: B  461 MET cc_start: 0.8438 (mmm) cc_final: 0.8184 (tpp)
REVERT: B  467 ILE cc_start: 0.8993 (mm) cc_final: 0.8618 (mt)
REVERT: B  505 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8444 (mmmt)
REVERT: B  512 ASP cc_start: 0.8385 (m-30) cc_final: 0.8153 (m-30)
  outliers start: 27
  outliers final: 21
  residues processed: 152
  average time/residue: 0.2228
  time to fit residues: 44.3433
Evaluate side-chains
  153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   87 MET
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
D  56 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.182092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.128653 restraints weight = 8908.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.41
r_work: 0.2950 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7918  Z= 0.176
  Angle     :  0.582   8.809  10766  Z= 0.295
  Chirality :  0.044   0.155   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.749  79.895   1072
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 10.84 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.27), residues: 976
  helix:  0.01 (0.22), residues: 536
  sheet: -1.54 (0.44), residues: 154
  loop : -1.03 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  37 
 HIS   0.004   0.001   HIS A  57 
 PHE   0.009   0.002   PHE A 587 
 TYR   0.017   0.001   TYR B 617 
 ARG   0.003   0.000   ARG C 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  338)
  hydrogen bonds       : angle       4.82304 (  996)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       0.40740 (    4)
  covalent geometry    : bond        0.00438 ( 7916)
  covalent geometry    : angle       0.58166 (10762)

*********************** 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
  159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8382 (mmtm)
REVERT: A  131 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7609 (m-30)
REVERT: A  208 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7927 (mmm-85)
REVERT: A  467 ILE cc_start: 0.9001 (mm) cc_final: 0.8633 (mt)
REVERT: A  505 LYS cc_start: 0.8768 (mmtp) cc_final: 0.8442 (mmmt)
REVERT: A  512 ASP cc_start: 0.8419 (m-30) cc_final: 0.8144 (m-30)
REVERT: A  517 MET cc_start: 0.9040 (mmm) cc_final: 0.8833 (mmm)
REVERT: A  547 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8283 (tpt90)
REVERT: D   56 GLN cc_start: 0.6985 (pt0) cc_final: 0.6654 (pt0)
REVERT: B    1 MET cc_start: 0.5814 (ppp) cc_final: 0.5488 (ppp)
REVERT: B   21 MET cc_start: 0.8980 (ttp) cc_final: 0.8683 (ttt)
REVERT: B   32 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8380 (mmtt)
REVERT: B  131 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7588 (m-30)
REVERT: B  180 ASP cc_start: 0.8347 (t0) cc_final: 0.7904 (t0)
REVERT: B  201 LYS cc_start: 0.7238 (mttt) cc_final: 0.6821 (mmtt)
REVERT: B  208 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7804 (mmm-85)
REVERT: B  467 ILE cc_start: 0.8999 (mm) cc_final: 0.8632 (mt)
REVERT: B  505 LYS cc_start: 0.8786 (mmtp) cc_final: 0.8437 (mmmt)
REVERT: B  512 ASP cc_start: 0.8402 (m-30) cc_final: 0.8132 (m-30)
  outliers start: 30
  outliers final: 21
  residues processed: 149
  average time/residue: 0.2258
  time to fit residues: 43.4640
Evaluate side-chains
  152 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   87 MET
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Chi-restraints excluded: chain B residue  589 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 56 optimal weight:    8.9990
   chunk 45 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 30 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  78 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.183891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.126038 restraints weight = 8901.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.83
r_work: 0.3269 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
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   0.029   7918  Z= 0.124
  Angle     :  0.543   7.892  10766  Z= 0.275
  Chirality :  0.042   0.145   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.588  78.435   1072
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 11.69 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.27), residues: 976
  helix:  0.24 (0.22), residues: 536
  sheet: -1.45 (0.43), residues: 154
  loop : -0.97 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 488 
 HIS   0.004   0.001   HIS A  57 
 PHE   0.010   0.001   PHE A 585 
 TYR   0.017   0.001   TYR B 617 
 ARG   0.004   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03567 (  338)
  hydrogen bonds       : angle       4.71323 (  996)
  SS BOND              : bond        0.00090 (    2)
  SS BOND              : angle       0.39000 (    4)
  covalent geometry    : bond        0.00299 ( 7916)
  covalent geometry    : angle       0.54294 (10762)

*********************** 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
  161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8526 (mmtm)
REVERT: A  131 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7548 (m-30)
REVERT: A  158 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8238 (ttmt)
REVERT: A  208 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7923 (mmm-85)
REVERT: A  467 ILE cc_start: 0.9088 (mm) cc_final: 0.8715 (mt)
REVERT: A  505 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8719 (mmmt)
REVERT: A  512 ASP cc_start: 0.8501 (m-30) cc_final: 0.8282 (m-30)
REVERT: A  517 MET cc_start: 0.9065 (mmm) cc_final: 0.8853 (mmm)
REVERT: A  547 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8389 (tpt90)
REVERT: D   56 GLN cc_start: 0.7200 (pt0) cc_final: 0.6866 (pt0)
REVERT: B    1 MET cc_start: 0.5925 (ppp) cc_final: 0.5626 (ppp)
REVERT: B   21 MET cc_start: 0.8952 (ttp) cc_final: 0.8682 (ttt)
REVERT: B   32 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8518 (mmtm)
REVERT: B  201 LYS cc_start: 0.7404 (mttt) cc_final: 0.7040 (mmtt)
REVERT: B  208 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7774 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9088 (mm) cc_final: 0.8729 (mt)
REVERT: B  505 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8678 (mmmt)
REVERT: B  512 ASP cc_start: 0.8486 (m-30) cc_final: 0.8267 (m-30)
REVERT: B  517 MET cc_start: 0.9056 (mmm) cc_final: 0.8837 (mmm)
  outliers start: 29
  outliers final: 26
  residues processed: 150
  average time/residue: 0.2246
  time to fit residues: 43.5885
Evaluate side-chains
  158 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  592 ASN
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   87 MET
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  458 THR
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Chi-restraints excluded: chain B residue  589 LYS
Chi-restraints excluded: chain B residue  592 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 87 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.184615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.126293 restraints weight = 8911.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.86
r_work: 0.3312 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7918  Z= 0.118
  Angle     :  0.543  11.055  10766  Z= 0.274
  Chirality :  0.042   0.142   1246
  Planarity :  0.004   0.044   1322
  Dihedral  :  5.461  77.269   1072
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 11.93 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.27), residues: 976
  helix:  0.40 (0.22), residues: 536
  sheet: -1.40 (0.43), residues: 154
  loop : -0.91 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 488 
 HIS   0.004   0.001   HIS A  57 
 PHE   0.009   0.001   PHE A 585 
 TYR   0.015   0.001   TYR B 617 
 ARG   0.004   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  338)
  hydrogen bonds       : angle       4.63881 (  996)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.35035 (    4)
  covalent geometry    : bond        0.00286 ( 7916)
  covalent geometry    : angle       0.54298 (10762)

*********************** 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
  159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8516 (mmtm)
REVERT: A  131 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7454 (m-30)
REVERT: A  158 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8215 (ttmt)
REVERT: A  467 ILE cc_start: 0.9087 (mm) cc_final: 0.8719 (mt)
REVERT: A  505 LYS cc_start: 0.8959 (mmtp) cc_final: 0.8717 (mmmt)
REVERT: A  512 ASP cc_start: 0.8473 (m-30) cc_final: 0.8262 (m-30)
REVERT: A  547 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8406 (tpt90)
REVERT: D   56 GLN cc_start: 0.7185 (pt0) cc_final: 0.6842 (pt0)
REVERT: B    1 MET cc_start: 0.6016 (ppp) cc_final: 0.5711 (ppp)
REVERT: B   21 MET cc_start: 0.8920 (ttp) cc_final: 0.8647 (ttt)
REVERT: B   32 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8479 (mmtm)
REVERT: B  201 LYS cc_start: 0.7420 (mttt) cc_final: 0.7056 (mmtt)
REVERT: B  467 ILE cc_start: 0.9084 (mm) cc_final: 0.8721 (mt)
REVERT: B  505 LYS cc_start: 0.8993 (mmtp) cc_final: 0.8714 (mmmt)
REVERT: B  512 ASP cc_start: 0.8485 (m-30) cc_final: 0.8280 (m-30)
REVERT: B  517 MET cc_start: 0.9067 (mmm) cc_final: 0.8749 (mmm)
  outliers start: 27
  outliers final: 25
  residues processed: 151
  average time/residue: 0.2340
  time to fit residues: 45.7619
Evaluate side-chains
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   87 MET
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Chi-restraints excluded: chain B residue  589 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    0.3980
   chunk 85 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 45 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.184242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125729 restraints weight = 8905.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.86
r_work: 0.3267 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7918  Z= 0.131
  Angle     :  0.551  10.784  10766  Z= 0.279
  Chirality :  0.043   0.145   1246
  Planarity :  0.004   0.044   1322
  Dihedral  :  5.447  76.934   1072
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 11.20 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.27), residues: 976
  helix:  0.53 (0.22), residues: 536
  sheet: -1.36 (0.44), residues: 154
  loop : -0.89 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C  63 
 HIS   0.004   0.001   HIS A  57 
 PHE   0.008   0.001   PHE A 585 
 TYR   0.017   0.001   TYR B 617 
 ARG   0.003   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03560 (  338)
  hydrogen bonds       : angle       4.65933 (  996)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       0.31152 (    4)
  covalent geometry    : bond        0.00319 ( 7916)
  covalent geometry    : angle       0.55069 (10762)

********************** 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
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8520 (mmtm)
REVERT: A  131 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7563 (m-30)
REVERT: A  467 ILE cc_start: 0.9088 (mm) cc_final: 0.8721 (mt)
REVERT: A  505 LYS cc_start: 0.9008 (mmtp) cc_final: 0.8769 (mmmt)
REVERT: A  512 ASP cc_start: 0.8510 (m-30) cc_final: 0.8302 (m-30)
REVERT: A  547 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8548 (tpt90)
REVERT: D   56 GLN cc_start: 0.7175 (pt0) cc_final: 0.6846 (pt0)
REVERT: B    1 MET cc_start: 0.5940 (ppp) cc_final: 0.5685 (ppp)
REVERT: B   21 MET cc_start: 0.8942 (ttp) cc_final: 0.8670 (ttt)
REVERT: B   32 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8523 (mmtm)
REVERT: B  131 ASP cc_start: 0.7915 (m-30) cc_final: 0.7401 (m-30)
REVERT: B  201 LYS cc_start: 0.7422 (mttt) cc_final: 0.7091 (mmtt)
REVERT: B  467 ILE cc_start: 0.9082 (mm) cc_final: 0.8723 (mt)
REVERT: B  505 LYS cc_start: 0.9020 (mmtp) cc_final: 0.8737 (mmmt)
REVERT: B  512 ASP cc_start: 0.8478 (m-30) cc_final: 0.8266 (m-30)
REVERT: B  517 MET cc_start: 0.9078 (mmm) cc_final: 0.8844 (mmm)
  outliers start: 30
  outliers final: 27
  residues processed: 151
  average time/residue: 0.2184
  time to fit residues: 43.2256
Evaluate side-chains
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  592 ASN
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   87 MET
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Chi-restraints excluded: chain B residue  589 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.184155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.126266 restraints weight = 8881.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.84
r_work: 0.3018 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7918  Z= 0.132
  Angle     :  0.553  10.283  10766  Z= 0.280
  Chirality :  0.043   0.146   1246
  Planarity :  0.004   0.044   1322
  Dihedral  :  5.414  76.909   1072
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 11.33 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.27), residues: 976
  helix:  0.67 (0.23), residues: 536
  sheet: -1.35 (0.43), residues: 154
  loop : -0.82 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  63 
 HIS   0.004   0.001   HIS A  57 
 PHE   0.008   0.001   PHE A 585 
 TYR   0.017   0.001   TYR B 617 
 ARG   0.004   0.000   ARG A 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03578 (  338)
  hydrogen bonds       : angle       4.66055 (  996)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       0.29614 (    4)
  covalent geometry    : bond        0.00324 ( 7916)
  covalent geometry    : angle       0.55306 (10762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4903.60 seconds
wall clock time: 85 minutes 13.16 seconds (5113.16 seconds total)