Starting phenix.real_space_refine
on Fri Jul 25 15:16:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y9v_33693/07_2025/7y9v_33693_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y9v_33693/07_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_33693/07_2025/7y9v_33693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y9v_33693/07_2025/7y9v_33693.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y9v_33693/07_2025/7y9v_33693_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y9v_33693/07_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-5711/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: 6.08, per 1000 atoms: 0.79
  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: 1.88
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      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: 0.84
  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: 2.00

  Time building geometry restraints manager: 2.21 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:             1.260
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.320
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.120
-------------------------------------------------------------------------------
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  : 0.879 
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: 0.2469
  time to fit residues: 58.7921
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  : 0.795 
-------------------------------------------------------------------------------
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 = 42)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116101 restraints weight = 8878.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.93
r_work: 0.3128 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.90 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       5.96219 (  996)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       0.37329 (    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  : 0.917 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5559 (ppp) cc_final: 0.5174 (ppp)
REVERT: A   21 MET cc_start: 0.9005 (ttp) cc_final: 0.8656 (ttt)
REVERT: A   29 LYS cc_start: 0.8199 (tppt) cc_final: 0.7913 (ttmt)
REVERT: A   32 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8413 (mmtt)
REVERT: A  208 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7722 (mmm-85)
REVERT: A  459 SER cc_start: 0.8569 (t) cc_final: 0.8342 (p)
REVERT: A  505 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8388 (mmmt)
REVERT: A  512 ASP cc_start: 0.8342 (m-30) cc_final: 0.7984 (m-30)
REVERT: A  517 MET cc_start: 0.9041 (mmm) cc_final: 0.8832 (mmm)
REVERT: A  554 VAL cc_start: 0.8729 (p) cc_final: 0.8509 (p)
REVERT: C   56 GLN cc_start: 0.7005 (pp30) cc_final: 0.6523 (pt0)
REVERT: B    1 MET cc_start: 0.5380 (ppp) cc_final: 0.4961 (ppp)
REVERT: B   21 MET cc_start: 0.8963 (ttp) cc_final: 0.8677 (ttt)
REVERT: B   32 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8313 (mmtt)
REVERT: B  131 ASP cc_start: 0.7972 (t70) cc_final: 0.7705 (m-30)
REVERT: B  173 VAL cc_start: 0.9006 (t) cc_final: 0.8722 (m)
REVERT: B  467 ILE cc_start: 0.9095 (mm) cc_final: 0.8735 (mt)
REVERT: B  505 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8458 (mmmt)
REVERT: B  512 ASP cc_start: 0.8401 (m-30) cc_final: 0.8074 (m-30)
REVERT: B  517 MET cc_start: 0.9037 (mmm) cc_final: 0.8811 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 159
  average time/residue: 0.2162
  time to fit residues: 46.5141
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  : 0.765 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 69 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.170420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.113549 restraints weight = 9039.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.90
r_work: 0.3096 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7918  Z= 0.141
  Angle     :  0.560   5.685  10766  Z= 0.293
  Chirality :  0.043   0.148   1246
  Planarity :  0.005   0.043   1322
  Dihedral  :  6.167  77.465   1072
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 10.84 %
    Favored  : 86.63 %
  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: -2.62 (0.25), residues: 976
  helix: -1.26 (0.21), residues: 540
  sheet: -2.37 (0.39), residues: 164
  loop : -1.81 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 488 
 HIS   0.006   0.001   HIS B  57 
 PHE   0.010   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        0.04222 (  338)
  hydrogen bonds       : angle       5.17096 (  996)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.55090 (    4)
  covalent geometry    : bond        0.00340 ( 7916)
  covalent geometry    : angle       0.56021 (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
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5536 (ppp) cc_final: 0.5320 (ppp)
REVERT: A   21 MET cc_start: 0.8998 (ttp) cc_final: 0.8700 (ttt)
REVERT: A   29 LYS cc_start: 0.8197 (tppt) cc_final: 0.7920 (ttmt)
REVERT: A   32 LYS cc_start: 0.8866 (mtmm) cc_final: 0.8438 (mmtt)
REVERT: A  459 SER cc_start: 0.8630 (t) cc_final: 0.8396 (p)
REVERT: A  467 ILE cc_start: 0.9080 (mm) cc_final: 0.8699 (mt)
REVERT: A  505 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8425 (mmmt)
REVERT: A  512 ASP cc_start: 0.8397 (m-30) cc_final: 0.8131 (m-30)
REVERT: A  517 MET cc_start: 0.9036 (mmm) cc_final: 0.8818 (mmm)
REVERT: C   56 GLN cc_start: 0.6991 (pp30) cc_final: 0.6612 (pt0)
REVERT: D   56 GLN cc_start: 0.7162 (pt0) cc_final: 0.6835 (pt0)
REVERT: B    1 MET cc_start: 0.5502 (ppp) cc_final: 0.5172 (ppp)
REVERT: B   21 MET cc_start: 0.8964 (ttp) cc_final: 0.8678 (ttt)
REVERT: B   32 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8329 (mmtt)
REVERT: B  173 VAL cc_start: 0.9131 (t) cc_final: 0.8809 (m)
REVERT: B  201 LYS cc_start: 0.7213 (mttt) cc_final: 0.6749 (mmtt)
REVERT: B  467 ILE cc_start: 0.9078 (mm) cc_final: 0.8712 (mt)
REVERT: B  505 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8505 (mmmt)
REVERT: B  512 ASP cc_start: 0.8385 (m-30) cc_final: 0.8120 (m-30)
REVERT: B  517 MET cc_start: 0.9044 (mmm) cc_final: 0.8779 (mmm)
  outliers start: 21
  outliers final: 10
  residues processed: 150
  average time/residue: 0.1969
  time to fit residues: 39.5895
Evaluate side-chains
  140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
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 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:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0020
   chunk 19 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0670
   overall best weight:    0.4526

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 140 GLN
B 140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.172116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.115372 restraints weight = 9000.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.91
r_work: 0.3117 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7918  Z= 0.104
  Angle     :  0.518   5.602  10766  Z= 0.271
  Chirality :  0.042   0.148   1246
  Planarity :  0.004   0.042   1322
  Dihedral  :  5.796  76.086   1072
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.60 %
    Favored  : 87.23 %
  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: -1.80 (0.26), residues: 976
  helix: -0.62 (0.22), residues: 540
  sheet: -1.94 (0.42), residues: 156
  loop : -1.47 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  40 
 HIS   0.005   0.001   HIS B  57 
 PHE   0.012   0.001   PHE A 585 
 TYR   0.011   0.001   TYR D  41 
 ARG   0.003   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  338)
  hydrogen bonds       : angle       4.80764 (  996)
  SS BOND              : bond        0.00096 (    2)
  SS BOND              : angle       0.60478 (    4)
  covalent geometry    : bond        0.00240 ( 7916)
  covalent geometry    : angle       0.51756 (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
  162 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5613 (ppp) cc_final: 0.5369 (ppp)
REVERT: A   21 MET cc_start: 0.8948 (ttp) cc_final: 0.8657 (ttt)
REVERT: A   29 LYS cc_start: 0.8147 (tppt) cc_final: 0.7815 (ttmt)
REVERT: A   32 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8458 (mmtt)
REVERT: A  467 ILE cc_start: 0.9030 (mm) cc_final: 0.8641 (mt)
REVERT: A  505 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8386 (mmmt)
REVERT: A  512 ASP cc_start: 0.8347 (m-30) cc_final: 0.8114 (m-30)
REVERT: D   56 GLN cc_start: 0.7127 (pt0) cc_final: 0.6842 (pt0)
REVERT: B    1 MET cc_start: 0.5495 (ppp) cc_final: 0.5149 (ppp)
REVERT: B   21 MET cc_start: 0.8917 (ttp) cc_final: 0.8609 (ttt)
REVERT: B   32 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8281 (mmtt)
REVERT: B  173 VAL cc_start: 0.9132 (t) cc_final: 0.8824 (m)
REVERT: B  467 ILE cc_start: 0.9033 (mm) cc_final: 0.8652 (mt)
REVERT: B  505 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8383 (mmmt)
REVERT: B  512 ASP cc_start: 0.8320 (m-30) cc_final: 0.8095 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 158
  average time/residue: 0.2526
  time to fit residues: 53.2068
Evaluate side-chains
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 44 optimal weight:   30.0000
   chunk 86 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 50 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 58 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.169724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.112226 restraints weight = 8975.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.93
r_work: 0.3080 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7918  Z= 0.142
  Angle     :  0.553   5.755  10766  Z= 0.285
  Chirality :  0.043   0.148   1246
  Planarity :  0.004   0.044   1322
  Dihedral  :  5.823  79.452   1072
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 10.12 %
    Favored  : 86.14 %
  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: -1.48 (0.27), residues: 976
  helix: -0.35 (0.22), residues: 542
  sheet: -1.76 (0.43), residues: 156
  loop : -1.42 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 488 
 HIS   0.005   0.001   HIS B  57 
 PHE   0.009   0.001   PHE A 585 
 TYR   0.010   0.001   TYR C  61 
 ARG   0.004   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  338)
  hydrogen bonds       : angle       4.78332 (  996)
  SS BOND              : bond        0.00101 (    2)
  SS BOND              : angle       0.47079 (    4)
  covalent geometry    : bond        0.00351 ( 7916)
  covalent geometry    : angle       0.55302 (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
  163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.894 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5706 (ppp) cc_final: 0.5483 (ppp)
REVERT: A   32 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8411 (mmtt)
REVERT: A  467 ILE cc_start: 0.9073 (mm) cc_final: 0.8694 (mt)
REVERT: A  505 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8475 (mmmt)
REVERT: A  512 ASP cc_start: 0.8366 (m-30) cc_final: 0.8106 (m-30)
REVERT: A  517 MET cc_start: 0.9107 (mmm) cc_final: 0.8851 (mmm)
REVERT: A  547 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8316 (tpt90)
REVERT: D   56 GLN cc_start: 0.7089 (pt0) cc_final: 0.6713 (pt0)
REVERT: B    1 MET cc_start: 0.5523 (ppp) cc_final: 0.5228 (ppp)
REVERT: B   21 MET cc_start: 0.8960 (ttp) cc_final: 0.8654 (ttt)
REVERT: B   32 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8373 (mmtt)
REVERT: B  208 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7795 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9075 (mm) cc_final: 0.8703 (mt)
REVERT: B  505 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8460 (mmmt)
REVERT: B  512 ASP cc_start: 0.8366 (m-30) cc_final: 0.8106 (m-30)
REVERT: B  517 MET cc_start: 0.9094 (mmm) cc_final: 0.8825 (mmm)
  outliers start: 31
  outliers final: 20
  residues processed: 155
  average time/residue: 0.2593
  time to fit residues: 52.4673
Evaluate side-chains
  153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 1.912 
-------------------------------------------------------------------------------
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  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  589 LYS
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   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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0060
   chunk 7 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   chunk 91 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5596

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.186042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.128067 restraints weight = 8807.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.83
r_work: 0.3049 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3440

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= 0.107
  Angle     :  0.508   5.713  10766  Z= 0.264
  Chirality :  0.042   0.134   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.565  76.439   1072
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.27), residues: 976
  helix:  0.04 (0.22), residues: 542
  sheet: -1.62 (0.43), residues: 156
  loop : -1.31 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  37 
 HIS   0.005   0.001   HIS B  57 
 PHE   0.011   0.001   PHE A 585 
 TYR   0.010   0.001   TYR C  61 
 ARG   0.004   0.000   ARG A 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03326 (  338)
  hydrogen bonds       : angle       4.59846 (  996)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       0.49402 (    4)
  covalent geometry    : bond        0.00254 ( 7916)
  covalent geometry    : angle       0.50797 (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
  159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5686 (ppp) cc_final: 0.5455 (ppp)
REVERT: A   32 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8400 (mmtt)
REVERT: A  208 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7915 (mmm-85)
REVERT: A  461 MET cc_start: 0.8411 (mmm) cc_final: 0.8149 (tpp)
REVERT: A  467 ILE cc_start: 0.9003 (mm) cc_final: 0.8624 (mt)
REVERT: A  505 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8459 (mmmt)
REVERT: A  512 ASP cc_start: 0.8411 (m-30) cc_final: 0.8198 (m-30)
REVERT: A  547 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8432 (tpt90)
REVERT: D   56 GLN cc_start: 0.6955 (pt0) cc_final: 0.6633 (pt0)
REVERT: B   21 MET cc_start: 0.8923 (ttp) cc_final: 0.8608 (ttt)
REVERT: B   32 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8341 (mmtt)
REVERT: B  131 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7469 (m-30)
REVERT: B  208 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7835 (mmm-85)
REVERT: B  461 MET cc_start: 0.8396 (mmm) cc_final: 0.8162 (tpp)
REVERT: B  467 ILE cc_start: 0.9000 (mm) cc_final: 0.8626 (mt)
REVERT: B  505 LYS cc_start: 0.8799 (mmtp) cc_final: 0.8463 (mmmt)
REVERT: B  512 ASP cc_start: 0.8372 (m-30) cc_final: 0.8166 (m-30)
  outliers start: 23
  outliers final: 19
  residues processed: 152
  average time/residue: 0.2316
  time to fit residues: 45.8244
Evaluate side-chains
  151 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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   99 ASP
Chi-restraints excluded: chain A residue  113 THR
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 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   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:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.182182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.127567 restraints weight = 8915.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.33
r_work: 0.3195 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7918  Z= 0.185
  Angle     :  0.589   8.812  10766  Z= 0.299
  Chirality :  0.045   0.154   1246
  Planarity :  0.004   0.044   1322
  Dihedral  :  5.743  79.405   1072
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.69 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.27), residues: 976
  helix: -0.00 (0.22), residues: 542
  sheet: -1.58 (0.43), residues: 156
  loop : -1.32 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  37 
 HIS   0.004   0.001   HIS B  57 
 PHE   0.008   0.002   PHE B 493 
 TYR   0.015   0.001   TYR B 617 
 ARG   0.003   0.000   ARG C 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  338)
  hydrogen bonds       : angle       4.79303 (  996)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.41276 (    4)
  covalent geometry    : bond        0.00463 ( 7916)
  covalent geometry    : angle       0.58920 (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
  152 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5778 (ppp) cc_final: 0.5560 (ppp)
REVERT: A   32 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8478 (mmtm)
REVERT: A  208 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7947 (mmm-85)
REVERT: A  467 ILE cc_start: 0.9085 (mm) cc_final: 0.8718 (mt)
REVERT: A  505 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8654 (mmmt)
REVERT: A  512 ASP cc_start: 0.8531 (m-30) cc_final: 0.8279 (m-30)
REVERT: A  517 MET cc_start: 0.9070 (mmm) cc_final: 0.8849 (mmm)
REVERT: A  547 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8405 (tpt90)
REVERT: D   56 GLN cc_start: 0.7142 (pt0) cc_final: 0.6787 (pt0)
REVERT: B   21 MET cc_start: 0.8992 (ttp) cc_final: 0.8724 (ttt)
REVERT: B   32 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8509 (mmtt)
REVERT: B  131 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7554 (m-30)
REVERT: B  201 LYS cc_start: 0.7372 (mttt) cc_final: 0.6969 (mmtt)
REVERT: B  208 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7930 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9084 (mm) cc_final: 0.8721 (mt)
REVERT: B  505 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8648 (mmmt)
REVERT: B  512 ASP cc_start: 0.8538 (m-30) cc_final: 0.8306 (m-30)
  outliers start: 25
  outliers final: 17
  residues processed: 146
  average time/residue: 0.2555
  time to fit residues: 47.8627
Evaluate side-chains
  146 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
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  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 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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 40 optimal weight:    0.1980
   chunk 78 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0370
   chunk 45 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 30 optimal weight:    0.5980
   chunk 80 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.186151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.133782 restraints weight = 8914.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.59
r_work: 0.2985 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7918  Z= 0.102
  Angle     :  0.516   8.161  10766  Z= 0.263
  Chirality :  0.041   0.132   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.466  75.957   1072
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.77 %
    Favored  : 84.94 %
  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: -0.66 (0.27), residues: 976
  helix:  0.36 (0.22), residues: 542
  sheet: -1.46 (0.43), residues: 154
  loop : -1.15 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 488 
 HIS   0.004   0.001   HIS B  57 
 PHE   0.011   0.001   PHE A 585 
 TYR   0.009   0.001   TYR C  99 
 ARG   0.004   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03225 (  338)
  hydrogen bonds       : angle       4.56485 (  996)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.42535 (    4)
  covalent geometry    : bond        0.00237 ( 7916)
  covalent geometry    : angle       0.51597 (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
  159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 1.090 
Fit side-chains
REVERT: A   11 MET cc_start: 0.8834 (mmm) cc_final: 0.8622 (mmm)
REVERT: A   32 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8423 (mmtt)
REVERT: A  131 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7285 (m-30)
REVERT: A  208 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7877 (mmm-85)
REVERT: A  467 ILE cc_start: 0.9023 (mm) cc_final: 0.8651 (mt)
REVERT: A  505 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8561 (mmmt)
REVERT: A  512 ASP cc_start: 0.8354 (m-30) cc_final: 0.8149 (m-30)
REVERT: D   56 GLN cc_start: 0.7063 (pt0) cc_final: 0.6849 (pt0)
REVERT: B    1 MET cc_start: 0.5490 (ppp) cc_final: 0.5204 (ppp)
REVERT: B   21 MET cc_start: 0.8924 (ttp) cc_final: 0.8624 (ttt)
REVERT: B   32 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8364 (mmtm)
REVERT: B  131 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7332 (m-30)
REVERT: B  208 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7841 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9027 (mm) cc_final: 0.8661 (mt)
REVERT: B  505 LYS cc_start: 0.8840 (mmtp) cc_final: 0.8524 (mmmt)
REVERT: B  512 ASP cc_start: 0.8347 (m-30) cc_final: 0.8139 (m-30)
REVERT: B  517 MET cc_start: 0.9001 (mmm) cc_final: 0.8711 (mmm)
  outliers start: 19
  outliers final: 15
  residues processed: 152
  average time/residue: 0.4213
  time to fit residues: 83.3099
Evaluate side-chains
  153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
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 A residue  547 ARG
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   72 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0980
   chunk 22 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 25 optimal weight:    0.3980
   chunk 87 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0170
   overall best weight:    0.3818

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.187359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.128919 restraints weight = 8892.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.84
r_work: 0.3054 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7918  Z= 0.097
  Angle     :  0.525  10.550  10766  Z= 0.266
  Chirality :  0.041   0.134   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.336  75.315   1072
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.41 %
    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: -0.34 (0.27), residues: 976
  helix:  0.60 (0.23), residues: 540
  sheet: -1.38 (0.43), residues: 154
  loop : -0.89 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  63 
 HIS   0.004   0.001   HIS B  57 
 PHE   0.011   0.001   PHE A 585 
 TYR   0.009   0.001   TYR B 617 
 ARG   0.004   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03128 (  338)
  hydrogen bonds       : angle       4.49511 (  996)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.39122 (    4)
  covalent geometry    : bond        0.00226 ( 7916)
  covalent geometry    : angle       0.52487 (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
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A   11 MET cc_start: 0.8822 (mmm) cc_final: 0.8601 (mmm)
REVERT: A   32 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8355 (mmtt)
REVERT: A  131 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7254 (m-30)
REVERT: A  467 ILE cc_start: 0.9003 (mm) cc_final: 0.8631 (mt)
REVERT: A  505 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8528 (mmmt)
REVERT: A  521 SER cc_start: 0.8558 (t) cc_final: 0.8231 (m)
REVERT: A  547 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8535 (tpt90)
REVERT: D   56 GLN cc_start: 0.6994 (pt0) cc_final: 0.6686 (pt0)
REVERT: B    1 MET cc_start: 0.5410 (ppp) cc_final: 0.5144 (ppp)
REVERT: B   21 MET cc_start: 0.8902 (ttp) cc_final: 0.8592 (ttt)
REVERT: B   32 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8367 (mmtt)
REVERT: B  131 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7511 (m-30)
REVERT: B  467 ILE cc_start: 0.8998 (mm) cc_final: 0.8636 (mt)
REVERT: B  505 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8504 (mmmt)
REVERT: B  517 MET cc_start: 0.8986 (mmm) cc_final: 0.8700 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 151
  average time/residue: 0.2843
  time to fit residues: 55.5892
Evaluate side-chains
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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  113 THR
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 A residue  547 ARG
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   99 TYR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
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  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    0.0970
   chunk 85 optimal weight:    0.9980
   chunk 94 optimal weight:    0.2980
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.4113 r_free = 0.4113 target = 0.187082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.131879 restraints weight = 8872.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.95
r_work: 0.3014 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7918  Z= 0.105
  Angle     :  0.540  10.524  10766  Z= 0.270
  Chirality :  0.042   0.138   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.318  75.537   1072
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.13 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.27), residues: 976
  helix:  0.72 (0.23), residues: 540
  sheet: -1.37 (0.43), residues: 156
  loop : -0.87 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  63 
 HIS   0.004   0.001   HIS B  57 
 PHE   0.010   0.001   PHE A 585 
 TYR   0.010   0.001   TYR B 617 
 ARG   0.003   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03193 (  338)
  hydrogen bonds       : angle       4.51354 (  996)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       0.34489 (    4)
  covalent geometry    : bond        0.00250 ( 7916)
  covalent geometry    : angle       0.54036 (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
  151 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 1.183 
Fit side-chains
REVERT: A   11 MET cc_start: 0.8840 (mmm) cc_final: 0.8628 (mmm)
REVERT: A   32 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8379 (mmtt)
REVERT: A  131 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7290 (m-30)
REVERT: A  467 ILE cc_start: 0.9023 (mm) cc_final: 0.8658 (mt)
REVERT: A  505 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8626 (mmmt)
REVERT: A  521 SER cc_start: 0.8572 (t) cc_final: 0.8254 (m)
REVERT: A  547 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8515 (tpt90)
REVERT: D   56 GLN cc_start: 0.6964 (pt0) cc_final: 0.6664 (pt0)
REVERT: B   21 MET cc_start: 0.8929 (ttp) cc_final: 0.8626 (ttt)
REVERT: B   32 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8393 (mmtt)
REVERT: B  131 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7485 (m-30)
REVERT: B  467 ILE cc_start: 0.9023 (mm) cc_final: 0.8670 (mt)
REVERT: B  505 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8501 (mmmt)
REVERT: B  517 MET cc_start: 0.8996 (mmm) cc_final: 0.8711 (mmm)
  outliers start: 20
  outliers final: 17
  residues processed: 147
  average time/residue: 0.2916
  time to fit residues: 57.0443
Evaluate side-chains
  151 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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  113 THR
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 A residue  547 ARG
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   99 TYR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
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  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 10 optimal weight:    0.1980
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.1986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.180944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.128208 restraints weight = 8858.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.24
r_work: 0.3038 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.3807

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= 0.175
  Angle     :  0.603  11.380  10766  Z= 0.300
  Chirality :  0.044   0.155   1246
  Planarity :  0.004   0.041   1322
  Dihedral  :  5.540  78.532   1072
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.65 %
    Favored  : 84.58 %
  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: -0.23 (0.27), residues: 976
  helix:  0.66 (0.22), residues: 536
  sheet: -1.32 (0.43), residues: 154
  loop : -0.77 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C  63 
 HIS   0.005   0.001   HIS B  57 
 PHE   0.008   0.002   PHE B 493 
 TYR   0.015   0.001   TYR C  99 
 ARG   0.003   0.000   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  338)
  hydrogen bonds       : angle       4.71224 (  996)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       0.32541 (    4)
  covalent geometry    : bond        0.00439 ( 7916)
  covalent geometry    : angle       0.60299 (10762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5652.12 seconds
wall clock time: 101 minutes 51.21 seconds (6111.21 seconds total)