Starting phenix.real_space_refine
on Sun May 18 21:39:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bao_44408/05_2025/9bao_44408_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bao_44408/05_2025/9bao_44408.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bao_44408/05_2025/9bao_44408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bao_44408/05_2025/9bao_44408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bao_44408/05_2025/9bao_44408_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bao_44408/05_2025/9bao_44408_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5577      2.51       5
     N    1526      2.21       5
     O    1722      1.98       5
     H    8725      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 17594
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 867
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 5, 'TRANS': 50}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1546
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 102, 1527
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
      Conformer: "B"
        Number of residues, atoms: 102, 1527
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
          bond proxies already assigned to first conformer: 1521
    Chain: "C"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 879
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 5, 'TRANS': 50}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 1546
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 102, 1527
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
      Conformer: "B"
        Number of residues, atoms: 102, 1527
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
          bond proxies already assigned to first conformer: 1521
    Chain: "E"
      Number of atoms: 3141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3141
          Classifications: {'peptide': 212}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 3242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3242
          Classifications: {'peptide': 212}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202}
    Chain: "G"
      Number of atoms: 3131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3131
          Classifications: {'peptide': 212}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU%NH1NOTPRO:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "H"
      Number of atoms: 3242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3242
          Classifications: {'peptide': 212}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202}
  Time building chain proxies: 13.46, per 1000 atoms: 0.77
  Number of scatterers: 17594
  At special positions: 0
  Unit cell: (97.5415, 89.4505, 126.309, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     O    1722      8.00
     N    1526      7.00
     C    5577      6.00
     H    8725      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 462 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 488 " - pdb=" SG  CYS B 557 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 492 " - pdb=" SG  CYS B 559 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 462 " - pdb=" SG  CYS D 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 488 " - pdb=" SG  CYS D 557 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 492 " - pdb=" SG  CYS D 559 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 202 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 133 " - pdb=" SG  CYS F 193 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 147 " - pdb=" SG  CYS G 202 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 133 " - pdb=" SG  CYS H 193 " distance=2.04

  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: 4.51
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 26 sheets defined
      11.1% alpha, 35.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 290 through 302
    Processing helix  chain 'A' and resid 425 through 439
      removed outlier: 3.641A  pdb=" N   VAL A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ARG A 439 " --> pdb=" O   ARG A 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 517
      removed outlier: 3.780A  pdb=" N   GLY B 517 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 302
    Processing helix  chain 'C' and resid 424 through 439
      removed outlier: 3.984A  pdb=" N   LEU C 428 " --> pdb=" O   ALA C 424 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL C 436 " --> pdb=" O   GLN C 432 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG C 439 " --> pdb=" O   ARG C 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 504 through 517
      removed outlier: 3.747A  pdb=" N   GLY D 517 " --> pdb=" O   MET D 513 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.525A  pdb=" N   THR E  32 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 163 through 165
      No H-bonds generated for 'chain 'E' and resid 163 through 165'
    Processing helix  chain 'F' and resid 120 through 127
    Processing helix  chain 'F' and resid 182 through 188
      removed outlier: 3.813A  pdb=" N   HIS F 188 " --> pdb=" O   GLU F 184 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 32
      removed outlier: 3.554A  pdb=" N   THR G  32 " --> pdb=" O   ILE G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 163 through 165
      No H-bonds generated for 'chain 'G' and resid 163 through 165'
    Processing helix  chain 'H' and resid 120 through 127
    Processing helix  chain 'H' and resid 182 through 186
    Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AA2, first strand: chain 'B' and resid 463 through 465
    Processing sheet with id=AA3, first strand: chain 'B' and resid 477 through 479
      removed outlier: 6.136A  pdb=" N   ALA B 532 " --> pdb=" O   MET B 552 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   LYS B 534 " --> pdb=" O   PRO B 550 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   LEU B 536 " --> pdb=" O   HIS B 548 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   HIS B 548 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   SER B 538 " --> pdb=" O   ALA B 546 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   ALA B 546 " --> pdb=" O   SER B 538 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   SER B 540 " --> pdb=" O   ILE B 544 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 519 through 520
      removed outlier: 3.648A  pdb=" N   ALA G 106 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 520
      removed outlier: 3.648A  pdb=" N   ALA G 106 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLY G  49 " --> pdb=" O   TRP G  36 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LYS G  38 " --> pdb=" O   TRP G  47 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   TRP G  47 " --> pdb=" O   LYS G  38 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   ARG G  40 " --> pdb=" O   LEU G  45 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   LEU G  45 " --> pdb=" O   ARG G  40 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 525 through 528
      removed outlier: 3.672A  pdb=" N   VAL B 527 " --> pdb=" O   GLY B 558 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 314 through 315
    Processing sheet with id=AA8, first strand: chain 'D' and resid 463 through 465
    Processing sheet with id=AA9, first strand: chain 'D' and resid 477 through 479
      removed outlier: 6.142A  pdb=" N   ALA D 532 " --> pdb=" O   MET D 552 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LYS D 534 " --> pdb=" O   PRO D 550 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   LEU D 536 " --> pdb=" O   HIS D 548 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   HIS D 548 " --> pdb=" O   LEU D 536 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   SER D 538 " --> pdb=" O   ALA D 546 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   ALA D 546 " --> pdb=" O   SER D 538 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   SER D 540 " --> pdb=" O   ILE D 544 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ILE D 544 " --> pdb=" O   SER D 540 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 519 through 520
      removed outlier: 3.515A  pdb=" N   ALA D 519 " --> pdb=" O   ALA E 106 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA E 106 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 519 through 520
      removed outlier: 3.515A  pdb=" N   ALA D 519 " --> pdb=" O   ALA E 106 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA E 106 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LYS E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   TRP E  47 " --> pdb=" O   LYS E  38 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG E  40 " --> pdb=" O   LEU E  45 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   LEU E  45 " --> pdb=" O   ARG E  40 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 525 through 528
      removed outlier: 3.616A  pdb=" N   VAL D 527 " --> pdb=" O   GLY D 558 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 6
    Processing sheet with id=AB5, first strand: chain 'E' and resid 127 through 131
    Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161
    Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 7
      removed outlier: 3.789A  pdb=" N   PHE F  71 " --> pdb=" O   CYS F  23 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP F  70 " --> pdb=" O   TYR F  67 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 48
      removed outlier: 5.770A  pdb=" N   LEU F  46 " --> pdb=" O   GLN F  37 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   GLN F  37 " --> pdb=" O   LEU F  46 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE F  48 " --> pdb=" O   TRP F  35 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 113 through 117
    Processing sheet with id=AC1, first strand: chain 'F' and resid 153 through 154
      removed outlier: 3.675A  pdb=" N   ARG F 154 " --> pdb=" O   TRP F 147 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   TRP F 147 " --> pdb=" O   ARG F 154 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 5 through 6
    Processing sheet with id=AC3, first strand: chain 'G' and resid 127 through 131
    Processing sheet with id=AC4, first strand: chain 'G' and resid 158 through 161
    Processing sheet with id=AC5, first strand: chain 'H' and resid 4 through 7
      removed outlier: 3.702A  pdb=" N   PHE H  71 " --> pdb=" O   CYS H  23 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP H  70 " --> pdb=" O   TYR H  67 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 45 through 48
      removed outlier: 5.590A  pdb=" N   LEU H  46 " --> pdb=" O   GLN H  37 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   GLN H  37 " --> pdb=" O   LEU H  46 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'H' and resid 113 through 117
    Processing sheet with id=AC8, first strand: chain 'H' and resid 144 through 149

    326 hydrogen bonds defined for protein.
    849 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: 6.29

  Time building geometry restraints manager: 5.41 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 8727
        1.04 -     1.23: 252
        1.23 -     1.43: 3511
        1.43 -     1.63: 5244
        1.63 -     1.82: 58
  Bond restraints: 17792
  Sorted by residual:
  bond pdb=" N   GLU G   1 "
       pdb=" H1  GLU G   1 "
    ideal  model  delta    sigma   weight residual
    0.960  0.859  0.101 2.00e-02 2.50e+03 2.53e+01
  bond pdb=" N   GLU E   1 "
       pdb=" H3  GLU E   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.961 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" N   SER F   1 "
       pdb=" H2  SER F   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.961 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" N   SER H   1 "
       pdb=" H3  SER H   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" N   SER H   1 "
       pdb=" H2  SER H   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.22e+01
  ... (remaining 17787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.67: 32112
        6.67 -    13.33: 2
       13.33 -    20.00: 2
       20.00 -    26.66: 2
       26.66 -    33.33: 2
  Bond angle restraints: 32120
  Sorted by residual:
  angle pdb=" H1  SER F   1 "
        pdb=" N   SER F   1 "
        pdb=" H3  SER F   1 "
      ideal   model   delta    sigma   weight residual
     109.47   76.14   33.33 3.00e+00 1.11e-01 1.23e+02
  angle pdb=" H1  GLU E   1 "
        pdb=" N   GLU E   1 "
        pdb=" H2  GLU E   1 "
      ideal   model   delta    sigma   weight residual
     109.47   82.46   27.01 3.00e+00 1.11e-01 8.11e+01
  angle pdb=" H1  SER F   1 "
        pdb=" N   SER F   1 "
        pdb=" H2  SER F   1 "
      ideal   model   delta    sigma   weight residual
     109.47  131.08  -21.61 3.00e+00 1.11e-01 5.19e+01
  angle pdb=" H1  SER H   1 "
        pdb=" N   SER H   1 "
        pdb=" H3  SER H   1 "
      ideal   model   delta    sigma   weight residual
     109.47   88.76   20.71 3.00e+00 1.11e-01 4.77e+01
  angle pdb=" H1  GLU E   1 "
        pdb=" N   GLU E   1 "
        pdb=" H3  GLU E   1 "
      ideal   model   delta    sigma   weight residual
     109.47  127.45  -17.98 3.00e+00 1.11e-01 3.59e+01
  ... (remaining 32115 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 7539
       16.99 -    33.97: 738
       33.97 -    50.96: 201
       50.96 -    67.95: 51
       67.95 -    84.93: 18
  Dihedral angle restraints: 8547
    sinusoidal: 4639
      harmonic: 3908
  Sorted by residual:
  dihedral pdb=" CB  CYS B 488 "
           pdb=" SG  CYS B 488 "
           pdb=" SG  CYS B 557 "
           pdb=" CB  CYS B 557 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.64  -66.64     1      1.00e+01 1.00e-02 5.79e+01
  dihedral pdb=" CB  CYS G 147 "
           pdb=" SG  CYS G 147 "
           pdb=" SG  CYS G 202 "
           pdb=" CB  CYS G 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.47   33.53     1      1.00e+01 1.00e-02 1.60e+01
  dihedral pdb=" CA  LEU C 422 "
           pdb=" C   LEU C 422 "
           pdb=" N   ARG C 423 "
           pdb=" CA  ARG C 423 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 8544 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 870
       0.031 -    0.063: 376
       0.063 -    0.094: 83
       0.094 -    0.125: 76
       0.125 -    0.157: 20
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" CA  PRO A 317 "
            pdb=" N   PRO A 317 "
            pdb=" C   PRO A 317 "
            pdb=" CB  PRO A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.13e-01
  chirality pdb=" CA  ILE H  75 "
            pdb=" N   ILE H  75 "
            pdb=" C   ILE H  75 "
            pdb=" CB  ILE H  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.12e-01
  chirality pdb=" CA  ILE F  48 "
            pdb=" N   ILE F  48 "
            pdb=" C   ILE F  48 "
            pdb=" CB  ILE F  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 1422 not shown)

  Planarity restraints: 2663
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C 317 "    0.015 2.00e-02 2.50e+03   2.89e-02 8.37e+00
        pdb=" C   PRO C 317 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   PRO C 317 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP C 318 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 320 "   -0.013 2.00e-02 2.50e+03   2.44e-02 5.97e+00
        pdb=" N   ALA C 321 "    0.042 2.00e-02 2.50e+03
        pdb=" CA  ALA C 321 "   -0.011 2.00e-02 2.50e+03
        pdb=" H   ALA C 321 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 316 "    0.012 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" C   ASP A 316 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ASP A 316 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO A 317 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2660 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 3495
        2.30 -     2.87: 37601
        2.87 -     3.45: 37629
        3.45 -     4.02: 55028
        4.02 -     4.60: 81768
  Nonbonded interactions: 215521
  Sorted by model distance:
  nonbonded pdb=" HZ2 LYS F  24 "
            pdb=" OD2 ASP F  70 "
     model   vdw
     1.720 2.450
  nonbonded pdb=" HZ2 LYS H  24 "
            pdb=" OD2 ASP H  70 "
     model   vdw
     1.723 2.450
  nonbonded pdb=" OD1 ASP F 183 "
            pdb=" H   GLU F 184 "
     model   vdw
     1.731 2.450
  nonbonded pdb=" O   PHE A 290 "
            pdb=" HG1 THR A 293 "
     model   vdw
     1.736 2.450
  nonbonded pdb=" OD1 ASP H 183 "
            pdb=" H   GLU H 184 "
     model   vdw
     1.737 2.450
  ... (remaining 215516 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and (resid 289 through 424 or (resid 425 and (name N or name CA or na \ 
me C or name O or name CB or name H or name HA )) or resid 426 through 440))
}
ncs_group {
  reference = (chain 'B' and (resid 459 through 501 or resid 503 through 560))
  selection = (chain 'D' and (resid 459 through 501 or resid 503 through 560))
}
ncs_group {
  reference = (chain 'E' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ 
r name H1 or name HA )) or resid 2 through 219))
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

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=0.48 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:             21.030
  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:             0.300
  Extract box with map and model:          0.780
  Check model and map are aligned:         0.130
  Set scattering table:                    0.150
  Process input model:                     44.060
  Find NCS groups from input model:        0.640
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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      :  0.003   0.050   9079  Z= 0.154
  Angle     :  0.602   7.089  12379  Z= 0.337
  Chirality :  0.044   0.157   1425
  Planarity :  0.004   0.051   1577
  Dihedral  : 14.819  82.588   3267
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 19.45 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.26), residues: 1142
  helix:  2.06 (0.50), residues: 110
  sheet:  0.57 (0.24), residues: 516
  loop : -1.95 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.003   0.001   HIS D 506 
 PHE   0.009   0.001   PHE F 208 
 TYR   0.014   0.001   TYR F  49 
 ARG   0.002   0.000   ARG D 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09755 (  317)
  hydrogen bonds       : angle       4.99701 (  849)
  SS BOND              : bond        0.00591 (   14)
  SS BOND              : angle       1.90848 (   28)
  covalent geometry    : bond        0.00317 ( 9065)
  covalent geometry    : angle       0.59619 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  168 LYS cc_start: 0.7218 (mmmt) cc_final: 0.6723 (mmtt)
REVERT: H  184 GLU cc_start: 0.7236 (tp30) cc_final: 0.6746 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.5317
  time to fit residues: 70.5243
Evaluate side-chains
  90 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0030
   chunk 89 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
G  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.135738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.105086 restraints weight = 36628.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.70
r_work: 0.3145 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.0485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9079  Z= 0.106
  Angle     :  0.519   5.087  12379  Z= 0.275
  Chirality :  0.043   0.154   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.331  37.988   1262
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 18.13 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.26), residues: 1142
  helix:  2.24 (0.49), residues: 110
  sheet:  0.63 (0.25), residues: 508
  loop : -1.85 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 
 PHE   0.009   0.001   PHE F 208 
 TYR   0.008   0.001   TYR H  49 
 ARG   0.003   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03451 (  317)
  hydrogen bonds       : angle       4.46533 (  849)
  SS BOND              : bond        0.00577 (   14)
  SS BOND              : angle       1.67013 (   28)
  covalent geometry    : bond        0.00251 ( 9065)
  covalent geometry    : angle       0.51383 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  106 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5808 (mp)
REVERT: F  205 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8218 (p)
REVERT: H  168 LYS cc_start: 0.7380 (mmmt) cc_final: 0.6909 (mmtt)
REVERT: H  184 GLU cc_start: 0.7784 (tp30) cc_final: 0.7506 (tp30)
REVERT: H  205 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8288 (p)
  outliers start: 15
  outliers final: 9
  residues processed: 104
  average time/residue: 0.4729
  time to fit residues: 67.1047
Evaluate side-chains
  99 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue   55 ASN
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
E  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.120009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.087435 restraints weight = 34679.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.80
r_work: 0.3064 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.0689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9079  Z= 0.138
  Angle     :  0.543   4.441  12379  Z= 0.291
  Chirality :  0.044   0.152   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.416  36.668   1262
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.52 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.26), residues: 1142
  helix:  2.38 (0.48), residues: 110
  sheet:  0.64 (0.25), residues: 508
  loop : -1.86 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.003   0.001   HIS D 506 
 PHE   0.011   0.001   PHE H  73 
 TYR   0.010   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  317)
  hydrogen bonds       : angle       4.46621 (  849)
  SS BOND              : bond        0.00735 (   14)
  SS BOND              : angle       1.89027 (   28)
  covalent geometry    : bond        0.00341 ( 9065)
  covalent geometry    : angle       0.53639 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5835 (mp)
REVERT: F  205 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8257 (p)
REVERT: H  168 LYS cc_start: 0.7406 (mmmt) cc_final: 0.6907 (mmtt)
REVERT: H  184 GLU cc_start: 0.7801 (tp30) cc_final: 0.7529 (tp30)
REVERT: H  205 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8317 (p)
  outliers start: 23
  outliers final: 17
  residues processed: 114
  average time/residue: 0.4430
  time to fit residues: 69.2947
Evaluate side-chains
  114 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain G residue  194 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 103 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 43 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
F 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.122320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.088633 restraints weight = 34005.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.87
r_work: 0.3112 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.0782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9079  Z= 0.109
  Angle     :  0.510   4.032  12379  Z= 0.272
  Chirality :  0.043   0.152   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.333  36.938   1262
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.41 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.26), residues: 1142
  helix:  2.59 (0.50), residues: 110
  sheet:  0.63 (0.25), residues: 508
  loop : -1.79 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 
 PHE   0.010   0.001   PHE F 208 
 TYR   0.009   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  317)
  hydrogen bonds       : angle       4.39720 (  849)
  SS BOND              : bond        0.00634 (   14)
  SS BOND              : angle       1.60778 (   28)
  covalent geometry    : bond        0.00263 ( 9065)
  covalent geometry    : angle       0.50468 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5826 (mp)
REVERT: F  205 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8239 (p)
REVERT: H  168 LYS cc_start: 0.7382 (mmmt) cc_final: 0.6924 (mmtt)
REVERT: H  184 GLU cc_start: 0.7797 (tp30) cc_final: 0.7533 (tp30)
REVERT: H  205 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8298 (p)
  outliers start: 24
  outliers final: 18
  residues processed: 117
  average time/residue: 0.4364
  time to fit residues: 70.5563
Evaluate side-chains
  109 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   32 THR
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3309 r_free = 0.3309 target = 0.117820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.082924 restraints weight = 40372.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 3.13
r_work: 0.3028 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   9079  Z= 0.206
  Angle     :  0.627   5.510  12379  Z= 0.339
  Chirality :  0.047   0.154   1425
  Planarity :  0.005   0.050   1577
  Dihedral  :  4.814  35.010   1262
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.41 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.26), residues: 1142
  helix:  2.05 (0.49), residues: 110
  sheet:  0.55 (0.25), residues: 508
  loop : -2.00 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 494 
 HIS   0.004   0.001   HIS D 506 
 PHE   0.015   0.002   PHE H  73 
 TYR   0.012   0.002   TYR H  49 
 ARG   0.003   0.000   ARG F  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04973 (  317)
  hydrogen bonds       : angle       4.67578 (  849)
  SS BOND              : bond        0.01015 (   14)
  SS BOND              : angle       2.29640 (   28)
  covalent geometry    : bond        0.00519 ( 9065)
  covalent geometry    : angle       0.61814 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5988 (mp)
REVERT: B  556 GLU cc_start: 0.7637 (tt0) cc_final: 0.7384 (tt0)
REVERT: E   43 GLN cc_start: 0.7127 (mp10) cc_final: 0.6873 (mp10)
REVERT: F  205 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (p)
REVERT: H   91 ASP cc_start: 0.8583 (t0) cc_final: 0.8300 (t0)
REVERT: H  168 LYS cc_start: 0.7489 (mmmt) cc_final: 0.6955 (mmtt)
REVERT: H  184 GLU cc_start: 0.7853 (tp30) cc_final: 0.7601 (tp30)
REVERT: H  205 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8355 (p)
  outliers start: 29
  outliers final: 21
  residues processed: 111
  average time/residue: 0.4113
  time to fit residues: 64.4494
Evaluate side-chains
  104 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  115 SER
Chi-restraints excluded: chain F residue  170 SER
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain G residue  194 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  115 SER
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  196 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 86 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.120338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.086977 restraints weight = 32509.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.81
r_work: 0.3093 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9079  Z= 0.118
  Angle     :  0.530   4.507  12379  Z= 0.283
  Chirality :  0.044   0.153   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.541  35.840   1262
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.23 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.26), residues: 1142
  helix:  2.36 (0.50), residues: 110
  sheet:  0.53 (0.25), residues: 508
  loop : -1.90 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 
 PHE   0.010   0.001   PHE F 208 
 TYR   0.010   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  317)
  hydrogen bonds       : angle       4.49060 (  849)
  SS BOND              : bond        0.00706 (   14)
  SS BOND              : angle       1.66529 (   28)
  covalent geometry    : bond        0.00287 ( 9065)
  covalent geometry    : angle       0.52485 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5980 (mp)
REVERT: B  556 GLU cc_start: 0.7487 (tt0) cc_final: 0.7145 (tt0)
REVERT: E   43 GLN cc_start: 0.7037 (mp10) cc_final: 0.6786 (mp10)
REVERT: F   91 ASP cc_start: 0.8419 (t0) cc_final: 0.8089 (t0)
REVERT: F  205 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8267 (p)
REVERT: H   91 ASP cc_start: 0.8457 (t0) cc_final: 0.8119 (t0)
REVERT: H  168 LYS cc_start: 0.7438 (mmmt) cc_final: 0.6938 (mmtt)
REVERT: H  184 GLU cc_start: 0.7865 (tp30) cc_final: 0.7640 (tp30)
REVERT: H  205 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8299 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 104
  average time/residue: 0.4753
  time to fit residues: 67.2241
Evaluate side-chains
  103 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 108 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.121773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.087415 restraints weight = 38310.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 3.06
r_work: 0.3028 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9079  Z= 0.105
  Angle     :  0.504   3.997  12379  Z= 0.268
  Chirality :  0.043   0.154   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.315  35.826   1262
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.82 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.26), residues: 1142
  helix:  2.55 (0.51), residues: 110
  sheet:  0.55 (0.25), residues: 508
  loop : -1.79 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 
 PHE   0.010   0.001   PHE H  73 
 TYR   0.010   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03240 (  317)
  hydrogen bonds       : angle       4.33856 (  849)
  SS BOND              : bond        0.00620 (   14)
  SS BOND              : angle       1.49685 (   28)
  covalent geometry    : bond        0.00257 ( 9065)
  covalent geometry    : angle       0.49938 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5935 (mp)
REVERT: F   91 ASP cc_start: 0.8458 (t0) cc_final: 0.8139 (t0)
REVERT: F  205 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (p)
REVERT: H   91 ASP cc_start: 0.8466 (t0) cc_final: 0.8130 (t0)
REVERT: H  144 ASN cc_start: 0.7136 (OUTLIER) cc_final: 0.6933 (t0)
REVERT: H  168 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6861 (mmtt)
REVERT: H  184 GLU cc_start: 0.7769 (tp30) cc_final: 0.7541 (tp30)
REVERT: H  205 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8262 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 109
  average time/residue: 0.4722
  time to fit residues: 70.7135
Evaluate side-chains
  102 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  144 ASN
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3361 r_free = 0.3361 target = 0.121998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.087873 restraints weight = 36396.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.99
r_work: 0.3065 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2785
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2785
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9079  Z= 0.105
  Angle     :  0.501   3.946  12379  Z= 0.266
  Chirality :  0.043   0.152   1425
  Planarity :  0.004   0.052   1577
  Dihedral  :  4.267  35.788   1262
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.92 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.26), residues: 1142
  helix:  2.59 (0.51), residues: 110
  sheet:  0.58 (0.25), residues: 496
  loop : -1.80 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 
 PHE   0.010   0.001   PHE H  73 
 TYR   0.009   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03214 (  317)
  hydrogen bonds       : angle       4.29832 (  849)
  SS BOND              : bond        0.00627 (   14)
  SS BOND              : angle       1.49212 (   28)
  covalent geometry    : bond        0.00256 ( 9065)
  covalent geometry    : angle       0.49607 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  106 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 1.394 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.6034 (mp)
REVERT: F   91 ASP cc_start: 0.8463 (t0) cc_final: 0.8132 (t0)
REVERT: F  205 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8296 (p)
REVERT: H   91 ASP cc_start: 0.8460 (t0) cc_final: 0.8122 (t0)
REVERT: H  168 LYS cc_start: 0.7434 (mmmt) cc_final: 0.6924 (mmtt)
REVERT: H  184 GLU cc_start: 0.7873 (tp30) cc_final: 0.7648 (tp30)
REVERT: H  205 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8303 (p)
  outliers start: 24
  outliers final: 16
  residues processed: 103
  average time/residue: 0.4292
  time to fit residues: 62.4284
Evaluate side-chains
  101 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.135850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.104341 restraints weight = 38596.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.83
r_work: 0.3111 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9079  Z= 0.098
  Angle     :  0.489   3.924  12379  Z= 0.260
  Chirality :  0.043   0.152   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.178  35.691   1262
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.92 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.26), residues: 1142
  helix:  2.68 (0.51), residues: 110
  sheet:  0.54 (0.25), residues: 504
  loop : -1.78 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 
 PHE   0.009   0.001   PHE H  73 
 TYR   0.009   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03036 (  317)
  hydrogen bonds       : angle       4.24646 (  849)
  SS BOND              : bond        0.00581 (   14)
  SS BOND              : angle       1.40889 (   28)
  covalent geometry    : bond        0.00238 ( 9065)
  covalent geometry    : angle       0.48526 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.6072 (mp)
REVERT: F   91 ASP cc_start: 0.8457 (t0) cc_final: 0.8130 (t0)
REVERT: F  144 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.7077 (t0)
REVERT: F  205 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8289 (p)
REVERT: H   91 ASP cc_start: 0.8447 (t0) cc_final: 0.8114 (t0)
REVERT: H  168 LYS cc_start: 0.7456 (mmmt) cc_final: 0.6948 (mmtt)
REVERT: H  184 GLU cc_start: 0.7922 (tp30) cc_final: 0.7701 (tp30)
REVERT: H  205 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8306 (p)
  outliers start: 22
  outliers final: 17
  residues processed: 101
  average time/residue: 0.4544
  time to fit residues: 65.7733
Evaluate side-chains
  102 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  144 ASN
Chi-restraints excluded: chain F residue  155 GLN
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue   55 ASN
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0020
   chunk 83 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.9994

-------------------------------------------------------------------------------
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 = 0.3358 r_free = 0.3358 target = 0.121736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.088136 restraints weight = 33577.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.87
r_work: 0.3122 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9079  Z= 0.113
  Angle     :  0.507   4.068  12379  Z= 0.269
  Chirality :  0.043   0.150   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.231  35.586   1262
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.92 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1142
  helix:  2.65 (0.51), residues: 110
  sheet:  0.61 (0.25), residues: 496
  loop : -1.77 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 494 
 HIS   0.003   0.001   HIS D 506 
 PHE   0.010   0.001   PHE H  73 
 TYR   0.010   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  317)
  hydrogen bonds       : angle       4.28155 (  849)
  SS BOND              : bond        0.00665 (   14)
  SS BOND              : angle       1.55005 (   28)
  covalent geometry    : bond        0.00276 ( 9065)
  covalent geometry    : angle       0.50168 (12351)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue LEU  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 1.434 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6094 (mp)
REVERT: F   91 ASP cc_start: 0.8477 (t0) cc_final: 0.8146 (t0)
REVERT: F  144 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.7097 (t0)
REVERT: F  205 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8285 (p)
REVERT: H   91 ASP cc_start: 0.8475 (t0) cc_final: 0.8150 (t0)
REVERT: H  168 LYS cc_start: 0.7449 (mmmt) cc_final: 0.6938 (mmtt)
REVERT: H  184 GLU cc_start: 0.7912 (tp30) cc_final: 0.7682 (tp30)
REVERT: H  205 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8300 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 98
  average time/residue: 0.4566
  time to fit residues: 62.8926
Evaluate side-chains
  99 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  144 ASN
Chi-restraints excluded: chain F residue  155 GLN
Chi-restraints excluded: chain F residue  205 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 THR
Chi-restraints excluded: chain G residue   55 ASN
Chi-restraints excluded: chain G residue  108 ASP
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 112 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 111 optimal weight:    0.1980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.123572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.089915 restraints weight = 39356.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 3.26
r_work: 0.3107 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9079  Z= 0.092
  Angle     :  0.482   3.930  12379  Z= 0.255
  Chirality :  0.043   0.153   1425
  Planarity :  0.004   0.052   1577
  Dihedral  :  4.130  35.650   1262
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.82 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.26), residues: 1142
  helix:  2.78 (0.51), residues: 110
  sheet:  0.57 (0.24), residues: 504
  loop : -1.72 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP D 494 
 HIS   0.002   0.000   HIS D 506 
 PHE   0.009   0.001   PHE H  73 
 TYR   0.008   0.001   TYR H  49 
 ARG   0.002   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02888 (  317)
  hydrogen bonds       : angle       4.21446 (  849)
  SS BOND              : bond        0.00546 (   14)
  SS BOND              : angle       1.31666 (   28)
  covalent geometry    : bond        0.00222 ( 9065)
  covalent geometry    : angle       0.47810 (12351)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12280.81 seconds
wall clock time: 212 minutes 20.05 seconds (12740.05 seconds total)