Starting phenix.real_space_refine
on Tue Mar  3 17:54:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y9v_33693/03_2026/7y9v_33693_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y9v_33693/03_2026/7y9v_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y9v_33693/03_2026/7y9v_33693_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y9v_33693/03_2026/7y9v_33693_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y9v_33693/03_2026/7y9v_33693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y9v_33693/03_2026/7y9v_33693.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.25, per 1000 atoms: 0.29
  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: 0.76
  Conformation dependent library (CDL) restraints added in 334.5 milliseconds
  

  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: 0.25
  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: 1.18

  Time building geometry restraints manager: 1.02 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: 0.01
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:             1.020
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.820
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.500
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.013   0.001   ARG D 109 
 TYR   0.034   0.003   TYR A 617 
 PHE   0.021   0.003   PHE B  58 
 TRP   0.025   0.004   TRP B  31 
 HIS   0.006   0.002   HIS B 594 

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

*********************** 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  : 0.292 
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: 0.8458 (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: 0.7926 (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: 0.7903 (m170)
REVERT: B   29 LYS cc_start: 0.7516 (tppt) cc_final: 0.7223 (tppt)
REVERT: B   32 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8204 (mmtm)
REVERT: B  122 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8304 (mtpt)
REVERT: B  181 ILE cc_start: 0.8458 (mt) cc_final: 0.8235 (mt)
REVERT: B  201 LYS cc_start: 0.7210 (mttt) cc_final: 0.6782 (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: 0.8315 (mmmt)
REVERT: B  512 ASP cc_start: 0.8358 (m-30) cc_final: 0.7758 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1198
  time to fit residues: 28.6174
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  : 0.277 
-------------------------------------------------------------------------------
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 49 optimal weight:   10.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.171146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115562 restraints weight = 9069.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 1.93
r_work: 0.3122 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2229

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= 0.142
  Angle     :  0.634   6.695  10766  Z= 0.333
  Chirality :  0.044   0.153   1246
  Planarity :  0.006   0.046   1322
  Dihedral  :  6.809  82.715   1074
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.12 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.76 (0.23), residues: 976
  helix: -2.50 (0.18), residues: 544
  sheet: -2.38 (0.44), residues: 124
  loop : -2.01 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 207 
 TYR   0.013   0.001   TYR C  41 
 PHE   0.014   0.002   PHE D  72 
 TRP   0.014   0.002   TRP C  40 
 HIS   0.002   0.001   HIS A 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7916)
  covalent geometry    : angle       0.63378 (10762)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       0.39338 (    4)
  hydrogen bonds       : bond        0.04627 (  338)
  hydrogen bonds       : angle       5.98942 (  996)

*********************** 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
  161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5385 (ppp) cc_final: 0.5045 (ppp)
REVERT: A   21 MET cc_start: 0.9006 (ttp) cc_final: 0.8652 (ttt)
REVERT: A   29 LYS cc_start: 0.8194 (tppt) cc_final: 0.7912 (ttmt)
REVERT: A   32 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8416 (mmtt)
REVERT: A  459 SER cc_start: 0.8554 (t) cc_final: 0.8343 (p)
REVERT: A  502 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8179 (tt)
REVERT: A  505 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8385 (mmmt)
REVERT: A  512 ASP cc_start: 0.8338 (m-30) cc_final: 0.7979 (m-30)
REVERT: C   56 GLN cc_start: 0.7193 (pp30) cc_final: 0.6698 (pt0)
REVERT: D   56 GLN cc_start: 0.7624 (pp30) cc_final: 0.7413 (pt0)
REVERT: B    1 MET cc_start: 0.5493 (ppp) cc_final: 0.5083 (ppp)
REVERT: B   21 MET cc_start: 0.8965 (ttp) cc_final: 0.8673 (ttt)
REVERT: B   32 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8327 (mmtt)
REVERT: B  131 ASP cc_start: 0.7901 (t70) cc_final: 0.7651 (m-30)
REVERT: B  173 VAL cc_start: 0.9009 (t) cc_final: 0.8712 (m)
REVERT: B  201 LYS cc_start: 0.7084 (mttt) cc_final: 0.6605 (mmtt)
REVERT: B  467 ILE cc_start: 0.9097 (mm) cc_final: 0.8735 (mt)
REVERT: B  505 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8460 (mmmt)
REVERT: B  512 ASP cc_start: 0.8433 (m-30) cc_final: 0.8117 (m-30)
REVERT: B  517 MET cc_start: 0.9050 (mmm) cc_final: 0.8386 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 159
  average time/residue: 0.0938
  time to fit residues: 19.8497
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  : 0.189 
-------------------------------------------------------------------------------
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 81 optimal weight:    0.0970
   chunk 63 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 85 optimal weight:    0.0770
   chunk 25 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.173198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.116739 restraints weight = 8947.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.92
r_work: 0.3142 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7918  Z= 0.103
  Angle     :  0.524   5.696  10766  Z= 0.276
  Chirality :  0.041   0.131   1246
  Planarity :  0.005   0.042   1322
  Dihedral  :  5.975  75.197   1072
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 10.36 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.26), residues: 976
  helix: -1.18 (0.21), residues: 540
  sheet: -2.32 (0.40), residues: 164
  loop : -1.74 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 208 
 TYR   0.013   0.001   TYR C  41 
 PHE   0.013   0.001   PHE A 585 
 TRP   0.010   0.001   TRP C  40 
 HIS   0.005   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7916)
  covalent geometry    : angle       0.52363 (10762)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       0.58505 (    4)
  hydrogen bonds       : bond        0.03773 (  338)
  hydrogen bonds       : angle       5.02999 (  996)

*********************** 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
  171 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5490 (ppp) cc_final: 0.5239 (ppp)
REVERT: A   21 MET cc_start: 0.8975 (ttp) cc_final: 0.8675 (ttt)
REVERT: A   29 LYS cc_start: 0.8190 (tppt) cc_final: 0.7900 (ttmt)
REVERT: A   32 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8491 (mmtt)
REVERT: A  467 ILE cc_start: 0.9063 (mm) cc_final: 0.8705 (mt)
REVERT: A  505 LYS cc_start: 0.8732 (mmtp) cc_final: 0.8390 (mmmt)
REVERT: C   56 GLN cc_start: 0.7036 (pp30) cc_final: 0.6715 (pt0)
REVERT: D   56 GLN cc_start: 0.7481 (pp30) cc_final: 0.7198 (pt0)
REVERT: B    1 MET cc_start: 0.5675 (ppp) cc_final: 0.5309 (ppp)
REVERT: B   32 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8283 (mmtt)
REVERT: B  173 VAL cc_start: 0.9064 (t) cc_final: 0.8787 (m)
REVERT: B  201 LYS cc_start: 0.7176 (mttt) cc_final: 0.6672 (mmtt)
REVERT: B  467 ILE cc_start: 0.9076 (mm) cc_final: 0.8721 (mt)
REVERT: B  505 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8501 (mmmt)
REVERT: B  512 ASP cc_start: 0.8299 (m-30) cc_final: 0.8077 (m-30)
REVERT: B  517 MET cc_start: 0.8983 (mmm) cc_final: 0.8665 (mmm)
  outliers start: 21
  outliers final: 11
  residues processed: 166
  average time/residue: 0.0884
  time to fit residues: 20.1375
Evaluate side-chains
  148 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  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   97 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 88 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0270
   chunk 54 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7238

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.171324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.114162 restraints weight = 9099.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.95
r_work: 0.3110 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3045

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= 0.127
  Angle     :  0.532   5.616  10766  Z= 0.278
  Chirality :  0.043   0.145   1246
  Planarity :  0.004   0.042   1322
  Dihedral  :  5.815  76.191   1072
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 11.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.26), residues: 976
  helix: -0.67 (0.22), residues: 540
  sheet: -1.87 (0.43), residues: 154
  loop : -1.36 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 207 
 TYR   0.017   0.001   TYR B 617 
 PHE   0.009   0.001   PHE A 585 
 TRP   0.010   0.001   TRP B 488 
 HIS   0.004   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7916)
  covalent geometry    : angle       0.53236 (10762)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.51307 (    4)
  hydrogen bonds       : bond        0.03721 (  338)
  hydrogen bonds       : angle       4.84678 (  996)

*********************** 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
  161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5568 (ppp) cc_final: 0.5346 (ppp)
REVERT: A   29 LYS cc_start: 0.8181 (tppt) cc_final: 0.7880 (ttmt)
REVERT: A   32 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8473 (mmtt)
REVERT: A  467 ILE cc_start: 0.9037 (mm) cc_final: 0.8663 (mt)
REVERT: A  505 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8372 (mmmt)
REVERT: B    1 MET cc_start: 0.5532 (ppp) cc_final: 0.5249 (ppp)
REVERT: B   32 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8365 (mmtt)
REVERT: B  173 VAL cc_start: 0.9132 (t) cc_final: 0.8832 (m)
REVERT: B  180 ASP cc_start: 0.8470 (t0) cc_final: 0.8249 (t0)
REVERT: B  208 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7771 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9040 (mm) cc_final: 0.8665 (mt)
REVERT: B  505 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8393 (mmmt)
REVERT: B  512 ASP cc_start: 0.8398 (m-30) cc_final: 0.8171 (m-30)
REVERT: B  517 MET cc_start: 0.8990 (mmm) cc_final: 0.8683 (mmm)
  outliers start: 24
  outliers final: 14
  residues processed: 155
  average time/residue: 0.0914
  time to fit residues: 19.3500
Evaluate side-chains
  145 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
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  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 D residue   97 VAL
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  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 58 optimal weight:    6.9990
   chunk 95 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 49 optimal weight:   40.0000
   chunk 54 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
C  56 GLN
D  56 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.170807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.113514 restraints weight = 8962.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.93
r_work: 0.3085 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7918  Z= 0.124
  Angle     :  0.530   5.896  10766  Z= 0.274
  Chirality :  0.043   0.141   1246
  Planarity :  0.004   0.042   1322
  Dihedral  :  5.651  75.275   1072
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 11.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.27), residues: 976
  helix: -0.25 (0.22), residues: 540
  sheet: -1.69 (0.43), residues: 154
  loop : -1.28 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 207 
 TYR   0.011   0.001   TYR D  61 
 PHE   0.010   0.001   PHE A 585 
 TRP   0.009   0.001   TRP A 488 
 HIS   0.005   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7916)
  covalent geometry    : angle       0.52984 (10762)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       0.45056 (    4)
  hydrogen bonds       : bond        0.03612 (  338)
  hydrogen bonds       : angle       4.72514 (  996)

*********************** 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
  161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8485 (mmtt)
REVERT: A  180 ASP cc_start: 0.8470 (t0) cc_final: 0.8258 (t0)
REVERT: A  208 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7921 (mmm-85)
REVERT: A  467 ILE cc_start: 0.9076 (mm) cc_final: 0.8702 (mt)
REVERT: A  505 LYS cc_start: 0.8774 (mmtp) cc_final: 0.8446 (mmmt)
REVERT: A  547 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8186 (tpt90)
REVERT: B    1 MET cc_start: 0.5542 (ppp) cc_final: 0.5289 (ppp)
REVERT: B   32 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8361 (mmtt)
REVERT: B  173 VAL cc_start: 0.9128 (t) cc_final: 0.8825 (m)
REVERT: B  180 ASP cc_start: 0.8407 (t0) cc_final: 0.8163 (t0)
REVERT: B  208 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7787 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9071 (mm) cc_final: 0.8697 (mt)
REVERT: B  505 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8457 (mmmt)
REVERT: B  512 ASP cc_start: 0.8394 (m-30) cc_final: 0.8176 (m-30)
REVERT: B  547 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8470 (tpt90)
  outliers start: 30
  outliers final: 20
  residues processed: 154
  average time/residue: 0.0990
  time to fit residues: 20.3267
Evaluate side-chains
  151 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   97 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  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 30 optimal weight:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0670
   chunk 15 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.5518

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.185890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.128148 restraints weight = 8868.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.82
r_work: 0.3191 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3449

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     :  0.517   8.411  10766  Z= 0.265
  Chirality :  0.042   0.134   1246
  Planarity :  0.004   0.042   1322
  Dihedral  :  5.466  74.060   1072
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.53 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.27), residues: 976
  helix:  0.05 (0.22), residues: 540
  sheet: -1.56 (0.43), residues: 154
  loop : -1.15 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 207 
 TYR   0.012   0.001   TYR B 617 
 PHE   0.010   0.001   PHE A 585 
 TRP   0.011   0.001   TRP D  37 
 HIS   0.004   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7916)
  covalent geometry    : angle       0.51694 (10762)
  SS BOND              : bond        0.00061 (    2)
  SS BOND              : angle       0.48514 (    4)
  hydrogen bonds       : bond        0.03368 (  338)
  hydrogen bonds       : angle       4.59617 (  996)

*********************** 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
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8452 (mmtt)
REVERT: A  180 ASP cc_start: 0.8473 (t0) cc_final: 0.8243 (t0)
REVERT: A  208 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7797 (mmm-85)
REVERT: A  461 MET cc_start: 0.8402 (mmm) cc_final: 0.8143 (tpp)
REVERT: A  467 ILE cc_start: 0.9038 (mm) cc_final: 0.8662 (mt)
REVERT: A  505 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8499 (mmmt)
REVERT: A  547 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8206 (tpt90)
REVERT: B   32 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8380 (mmtt)
REVERT: B  173 VAL cc_start: 0.9107 (t) cc_final: 0.8796 (m)
REVERT: B  180 ASP cc_start: 0.8361 (t0) cc_final: 0.8113 (t0)
REVERT: B  208 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7753 (mmm-85)
REVERT: B  461 MET cc_start: 0.8403 (mmm) cc_final: 0.8152 (tpp)
REVERT: B  467 ILE cc_start: 0.9038 (mm) cc_final: 0.8664 (mt)
REVERT: B  505 LYS cc_start: 0.8832 (mmtp) cc_final: 0.8510 (mmmt)
REVERT: B  512 ASP cc_start: 0.8431 (m-30) cc_final: 0.8231 (m-30)
REVERT: B  547 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8411 (tpt90)
  outliers start: 25
  outliers final: 21
  residues processed: 152
  average time/residue: 0.1082
  time to fit residues: 21.4837
Evaluate side-chains
  155 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  592 ASN
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue   87 MET
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  102 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0980
   chunk 43 optimal weight:    0.0270
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.5038

-------------------------------------------------------------------------------
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 = 0.4110 r_free = 0.4110 target = 0.186594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.128821 restraints weight = 8881.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.83
r_work: 0.3054 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3602

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= 0.102
  Angle     :  0.525  10.590  10766  Z= 0.264
  Chirality :  0.042   0.133   1246
  Planarity :  0.004   0.042   1322
  Dihedral  :  5.326  72.488   1072
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.81 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.27), residues: 976
  helix:  0.34 (0.23), residues: 542
  sheet: -1.47 (0.43), residues: 154
  loop : -1.10 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 207 
 TYR   0.010   0.001   TYR A 617 
 PHE   0.010   0.001   PHE A 585 
 TRP   0.008   0.001   TRP A 488 
 HIS   0.004   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7916)
  covalent geometry    : angle       0.52500 (10762)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       0.47707 (    4)
  hydrogen bonds       : bond        0.03263 (  338)
  hydrogen bonds       : angle       4.52603 (  996)

*********************** 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
  165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8831 (mtmm) cc_final: 0.8414 (mmtt)
REVERT: A  180 ASP cc_start: 0.8481 (t0) cc_final: 0.8049 (t0)
REVERT: A  208 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7771 (mmm-85)
REVERT: A  461 MET cc_start: 0.8440 (mmm) cc_final: 0.8222 (tpp)
REVERT: A  467 ILE cc_start: 0.9010 (mm) cc_final: 0.8641 (mt)
REVERT: A  505 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8469 (mmmt)
REVERT: A  547 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8168 (tpt90)
REVERT: B   32 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8337 (mmtt)
REVERT: B  173 VAL cc_start: 0.9118 (t) cc_final: 0.8790 (m)
REVERT: B  180 ASP cc_start: 0.8390 (t0) cc_final: 0.8080 (t0)
REVERT: B  208 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7696 (mmm-85)
REVERT: B  461 MET cc_start: 0.8446 (mmm) cc_final: 0.8231 (tpp)
REVERT: B  467 ILE cc_start: 0.9002 (mm) cc_final: 0.8636 (mt)
REVERT: B  505 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8477 (mmmt)
REVERT: B  547 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8473 (tpt90)
  outliers start: 25
  outliers final: 20
  residues processed: 159
  average time/residue: 0.1156
  time to fit residues: 23.7612
Evaluate side-chains
  158 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  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   90 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  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 40 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 91 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.185217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.127290 restraints weight = 8867.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.82
r_work: 0.3323 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7918  Z= 0.122
  Angle     :  0.546   9.916  10766  Z= 0.273
  Chirality :  0.042   0.142   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.324  72.918   1072
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.05 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.27), residues: 976
  helix:  0.45 (0.22), residues: 542
  sheet: -1.38 (0.44), residues: 154
  loop : -1.07 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 475 
 TYR   0.013   0.001   TYR D  99 
 PHE   0.009   0.001   PHE A 585 
 TRP   0.022   0.001   TRP C  63 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7916)
  covalent geometry    : angle       0.54609 (10762)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       0.34456 (    4)
  hydrogen bonds       : bond        0.03453 (  338)
  hydrogen bonds       : angle       4.55849 (  996)

*********************** 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
  155 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8528 (mmtt)
REVERT: A  182 MET cc_start: 0.7686 (mmm) cc_final: 0.7425 (mmt)
REVERT: A  208 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7812 (mmm-85)
REVERT: A  467 ILE cc_start: 0.9099 (mm) cc_final: 0.8731 (mt)
REVERT: A  505 LYS cc_start: 0.9012 (mmtp) cc_final: 0.8750 (mmmt)
REVERT: B    1 MET cc_start: 0.5577 (ppp) cc_final: 0.5320 (ppp)
REVERT: B   32 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8485 (mmtt)
REVERT: B  131 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7446 (m-30)
REVERT: B  180 ASP cc_start: 0.8411 (t0) cc_final: 0.8059 (t0)
REVERT: B  208 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7732 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9085 (mm) cc_final: 0.8728 (mt)
REVERT: B  505 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8687 (mmmt)
REVERT: B  547 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8480 (tpt90)
  outliers start: 23
  outliers final: 19
  residues processed: 149
  average time/residue: 0.1098
  time to fit residues: 21.4023
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  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0980
   chunk 10 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0570
   chunk 68 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.4098

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.187575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.129373 restraints weight = 8883.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.84
r_work: 0.3088 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7918  Z= 0.097
  Angle     :  0.531   9.217  10766  Z= 0.264
  Chirality :  0.041   0.131   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.159  69.979   1072
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.41 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.27), residues: 976
  helix:  0.74 (0.23), residues: 536
  sheet: -1.33 (0.43), residues: 156
  loop : -0.89 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 475 
 TYR   0.008   0.001   TYR A 617 
 PHE   0.010   0.001   PHE A 585 
 TRP   0.018   0.001   TRP C  63 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7916)
  covalent geometry    : angle       0.53089 (10762)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.36612 (    4)
  hydrogen bonds       : bond        0.03164 (  338)
  hydrogen bonds       : angle       4.45536 (  996)

*********************** 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
  157 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8379 (mmtt)
REVERT: A  182 MET cc_start: 0.7647 (mmm) cc_final: 0.7318 (mmt)
REVERT: A  461 MET cc_start: 0.8086 (tpp) cc_final: 0.7672 (mmt)
REVERT: A  467 ILE cc_start: 0.9014 (mm) cc_final: 0.8650 (mt)
REVERT: A  505 LYS cc_start: 0.8847 (mmtp) cc_final: 0.8548 (mmmt)
REVERT: A  521 SER cc_start: 0.8597 (t) cc_final: 0.8337 (m)
REVERT: A  547 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8645 (tpm170)
REVERT: B   32 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8353 (mmtt)
REVERT: B  173 VAL cc_start: 0.9136 (t) cc_final: 0.8806 (m)
REVERT: B  180 ASP cc_start: 0.8358 (t0) cc_final: 0.8104 (t0)
REVERT: B  208 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7676 (mmm-85)
REVERT: B  467 ILE cc_start: 0.9001 (mm) cc_final: 0.8645 (mt)
REVERT: B  505 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8498 (mmmt)
REVERT: B  521 SER cc_start: 0.8725 (t) cc_final: 0.8503 (m)
  outliers start: 19
  outliers final: 17
  residues processed: 153
  average time/residue: 0.1133
  time to fit residues: 22.5594
Evaluate side-chains
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  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 C residue  118 SER
Chi-restraints excluded: chain D residue    9 VAL
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0010
   chunk 9 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 91 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
D  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.184482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.127698 restraints weight = 8809.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.78
r_work: 0.3090 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7918  Z= 0.105
  Angle     :  0.547  11.261  10766  Z= 0.270
  Chirality :  0.042   0.135   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.117  69.242   1072
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.53 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.27), residues: 976
  helix:  0.84 (0.23), residues: 538
  sheet: -1.28 (0.44), residues: 156
  loop : -0.82 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 207 
 TYR   0.010   0.001   TYR A 617 
 PHE   0.009   0.001   PHE A 585 
 TRP   0.016   0.001   TRP C  63 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7916)
  covalent geometry    : angle       0.54706 (10762)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       0.33339 (    4)
  hydrogen bonds       : bond        0.03230 (  338)
  hydrogen bonds       : angle       4.47292 (  996)

********************** 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
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   11 MET cc_start: 0.8816 (mmm) cc_final: 0.8604 (mmm)
REVERT: A   32 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8357 (mmtt)
REVERT: A  182 MET cc_start: 0.7567 (mmm) cc_final: 0.7111 (mmt)
REVERT: A  467 ILE cc_start: 0.8993 (mm) cc_final: 0.8631 (mt)
REVERT: A  505 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8591 (mmmt)
REVERT: A  521 SER cc_start: 0.8562 (t) cc_final: 0.8260 (m)
REVERT: A  547 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8619 (tpm170)
REVERT: B   32 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8331 (mmtt)
REVERT: B  173 VAL cc_start: 0.9159 (t) cc_final: 0.8817 (m)
REVERT: B  180 ASP cc_start: 0.8363 (t0) cc_final: 0.8024 (t0)
REVERT: B  208 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7669 (mmm-85)
REVERT: B  467 ILE cc_start: 0.8993 (mm) cc_final: 0.8630 (mt)
REVERT: B  505 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8512 (mmmt)
REVERT: B  521 SER cc_start: 0.8624 (t) cc_final: 0.8353 (m)
REVERT: B  547 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8619 (tpm170)
  outliers start: 17
  outliers final: 15
  residues processed: 147
  average time/residue: 0.1098
  time to fit residues: 21.0711
Evaluate side-chains
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
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  113 THR
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  102 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  455 MET
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  547 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0870
   chunk 79 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.7360

-------------------------------------------------------------------------------
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 = 0.4073 r_free = 0.4073 target = 0.183224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.130905 restraints weight = 8813.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.30
r_work: 0.2972 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7918  Z= 0.124
  Angle     :  0.562  11.259  10766  Z= 0.277
  Chirality :  0.043   0.144   1246
  Planarity :  0.004   0.043   1322
  Dihedral  :  5.175  69.734   1072
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.41 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.28), residues: 976
  helix:  0.87 (0.23), residues: 538
  sheet: -1.26 (0.44), residues: 156
  loop : -0.76 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 207 
 TYR   0.013   0.001   TYR B 617 
 PHE   0.008   0.001   PHE A 585 
 TRP   0.014   0.001   TRP C  63 
 HIS   0.004   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7916)
  covalent geometry    : angle       0.56186 (10762)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.27389 (    4)
  hydrogen bonds       : bond        0.03439 (  338)
  hydrogen bonds       : angle       4.56225 (  996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2464.18 seconds
wall clock time: 42 minutes 41.47 seconds (2561.47 seconds total)