Starting phenix.real_space_refine
on Thu Sep 18 14:37:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bao_44408/09_2025/9bao_44408_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bao_44408/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bao_44408/09_2025/9bao_44408_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bao_44408/09_2025/9bao_44408_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bao_44408/09_2025/9bao_44408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bao_44408/09_2025/9bao_44408.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: 4.00, per 1000 atoms: 0.23
  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: 1.55
  Conformation dependent library (CDL) restraints added in 575.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.53
  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: 3.91

  Time building geometry restraints manager: 2.11 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:             18.360
  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:             0.110
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.280
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.000
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG D 543 
 TYR   0.014   0.001   TYR F  49 
 PHE   0.009   0.001   PHE F 208 
 TRP   0.005   0.001   TRP D 494 
 HIS   0.003   0.001   HIS D 506 

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

*********************** 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  : 0.503 
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: 0.2807
  time to fit residues: 36.5303
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  : 0.517 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.0370
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.7262

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.135890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.106201 restraints weight = 30759.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.48
r_work: 0.3166 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    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 = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.0453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9079  Z= 0.105
  Angle     :  0.517   5.236  12379  Z= 0.275
  Chirality :  0.043   0.153   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.323  38.466   1262
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.26), residues: 1142
  helix:  2.28 (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
 ARG   0.003   0.000   ARG B 465 
 TYR   0.008   0.001   TYR H  49 
 PHE   0.009   0.001   PHE F 208 
 TRP   0.005   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9065)
  covalent geometry    : angle       0.51190 (12351)
  SS BOND              : bond        0.00583 (   14)
  SS BOND              : angle       1.67279 (   28)
  hydrogen bonds       : bond        0.03526 (  317)
  hydrogen bonds       : angle       4.47838 (  849)

*********************** 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
  107 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5816 (mp)
REVERT: F  205 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8204 (p)
REVERT: H  168 LYS cc_start: 0.7378 (mmmt) cc_final: 0.6909 (mmtt)
REVERT: H  184 GLU cc_start: 0.7762 (tp30) cc_final: 0.7481 (tp30)
REVERT: H  205 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8284 (p)
  outliers start: 14
  outliers final: 9
  residues processed: 105
  average time/residue: 0.2516
  time to fit residues: 35.7115
Evaluate side-chains
  101 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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 112 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0970
   chunk 0 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.121108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.088728 restraints weight = 33425.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.74
r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.0621

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= 0.126
  Angle     :  0.528   4.248  12379  Z= 0.283
  Chirality :  0.044   0.152   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.353  36.954   1262
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.11 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.26), residues: 1142
  helix:  2.41 (0.48), residues: 110
  sheet:  0.64 (0.25), residues: 508
  loop : -1.82 (0.26), residues: 524

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9065)
  covalent geometry    : angle       0.52160 (12351)
  SS BOND              : bond        0.00677 (   14)
  SS BOND              : angle       1.79228 (   28)
  hydrogen bonds       : bond        0.03722 (  317)
  hydrogen bonds       : angle       4.43740 (  849)

*********************** 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
  116 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5782 (mp)
REVERT: F  205 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8208 (p)
REVERT: H  168 LYS cc_start: 0.7355 (mmmt) cc_final: 0.6892 (mmtt)
REVERT: H  184 GLU cc_start: 0.7707 (tp30) cc_final: 0.7425 (tp30)
REVERT: H  205 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8271 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 116
  average time/residue: 0.2326
  time to fit residues: 37.1454
Evaluate side-chains
  108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
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  108 ASP
Chi-restraints excluded: chain E residue  185 SER
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 16 optimal weight:    0.0270
   chunk 78 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.7444

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.130920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.100278 restraints weight = 38054.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.73
r_work: 0.2953 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2775
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9079  Z= 0.166
  Angle     :  0.582   4.980  12379  Z= 0.313
  Chirality :  0.045   0.151   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.618  36.234   1262
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.26), residues: 1142
  helix:  2.21 (0.49), residues: 110
  sheet:  0.61 (0.25), residues: 508
  loop : -1.91 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  54 
 TYR   0.012   0.001   TYR H  92 
 PHE   0.012   0.002   PHE H  73 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.004   0.001   HIS D 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9065)
  covalent geometry    : angle       0.57383 (12351)
  SS BOND              : bond        0.00893 (   14)
  SS BOND              : angle       2.09648 (   28)
  hydrogen bonds       : bond        0.04356 (  317)
  hydrogen bonds       : angle       4.57759 (  849)

*********************** 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
  119 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5850 (mp)
REVERT: B  556 GLU cc_start: 0.7552 (tt0) cc_final: 0.7281 (tt0)
REVERT: F   91 ASP cc_start: 0.8422 (t0) cc_final: 0.8147 (t0)
REVERT: F  166 ASP cc_start: 0.8408 (t0) cc_final: 0.8182 (t0)
REVERT: F  205 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8287 (p)
REVERT: H  168 LYS cc_start: 0.7420 (mmmt) cc_final: 0.6949 (mmtt)
REVERT: H  184 GLU cc_start: 0.7815 (tp30) cc_final: 0.7563 (tp30)
REVERT: H  205 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8317 (p)
  outliers start: 29
  outliers final: 23
  residues processed: 118
  average time/residue: 0.2383
  time to fit residues: 38.5052
Evaluate side-chains
  110 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain C residue  427 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 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  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  103 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.121232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.087701 restraints weight = 40667.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.29
r_work: 0.3076 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.0992

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= 0.112
  Angle     :  0.523   4.362  12379  Z= 0.278
  Chirality :  0.043   0.152   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.438  35.342   1262
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.92 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.26), residues: 1142
  helix:  2.48 (0.50), residues: 110
  sheet:  0.59 (0.25), residues: 508
  loop : -1.84 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.009   0.001   TYR H  49 
 PHE   0.010   0.001   PHE F 208 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9065)
  covalent geometry    : angle       0.51732 (12351)
  SS BOND              : bond        0.00668 (   14)
  SS BOND              : angle       1.63236 (   28)
  hydrogen bonds       : bond        0.03447 (  317)
  hydrogen bonds       : angle       4.45709 (  849)

*********************** 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
  116 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5918 (mp)
REVERT: B  556 GLU cc_start: 0.7404 (tt0) cc_final: 0.7143 (tt0)
REVERT: F  205 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8229 (p)
REVERT: H  168 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6982 (mmtt)
REVERT: H  184 GLU cc_start: 0.7839 (tp30) cc_final: 0.7592 (tp30)
REVERT: H  205 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8280 (p)
  outliers start: 23
  outliers final: 18
  residues processed: 114
  average time/residue: 0.2392
  time to fit residues: 37.4340
Evaluate side-chains
  114 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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   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  170 SER
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   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  190 SER
Chi-restraints excluded: chain H residue  192 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 4 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0670
   chunk 6 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.123998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.089922 restraints weight = 35645.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.97
r_work: 0.3133 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9079  Z= 0.089
  Angle     :  0.480   4.120  12379  Z= 0.254
  Chirality :  0.043   0.154   1425
  Planarity :  0.004   0.050   1577
  Dihedral  :  4.146  35.686   1262
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 18.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.26), residues: 1142
  helix:  2.88 (0.52), residues: 104
  sheet:  0.59 (0.24), residues: 514
  loop : -1.69 (0.27), residues: 524

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 9065)
  covalent geometry    : angle       0.47699 (12351)
  SS BOND              : bond        0.00505 (   14)
  SS BOND              : angle       1.30168 (   28)
  hydrogen bonds       : bond        0.02797 (  317)
  hydrogen bonds       : angle       4.24384 (  849)

*********************** 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
  111 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5877 (mp)
REVERT: F   91 ASP cc_start: 0.8452 (t0) cc_final: 0.8074 (t0)
REVERT: F  205 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8231 (p)
REVERT: H  168 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6933 (mmtt)
REVERT: H  184 GLU cc_start: 0.7830 (tp30) cc_final: 0.7589 (tp30)
REVERT: H  205 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8281 (p)
  outliers start: 18
  outliers final: 14
  residues processed: 111
  average time/residue: 0.2573
  time to fit residues: 38.6458
Evaluate side-chains
  106 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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   43 GLN
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  205 VAL
Chi-restraints excluded: chain G residue   11 LEU
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  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 59 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0040
   chunk 11 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.136652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.105756 restraints weight = 35608.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.70
r_work: 0.3161 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9079  Z= 0.097
  Angle     :  0.487   3.802  12379  Z= 0.258
  Chirality :  0.043   0.152   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.143  35.894   1262
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 2.05
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.26), residues: 1142
  helix:  2.89 (0.52), residues: 104
  sheet:  0.60 (0.24), residues: 504
  loop : -1.68 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.008   0.001   TYR H  49 
 PHE   0.009   0.001   PHE H  73 
 TRP   0.004   0.001   TRP D 494 
 HIS   0.002   0.001   HIS D 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9065)
  covalent geometry    : angle       0.48345 (12351)
  SS BOND              : bond        0.00557 (   14)
  SS BOND              : angle       1.39742 (   28)
  hydrogen bonds       : bond        0.02994 (  317)
  hydrogen bonds       : angle       4.19341 (  849)

*********************** 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
  111 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5904 (mp)
REVERT: F  205 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8194 (p)
REVERT: H  144 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6901 (t0)
REVERT: H  168 LYS cc_start: 0.7379 (mmmt) cc_final: 0.6893 (mmtt)
REVERT: H  184 GLU cc_start: 0.7748 (tp30) cc_final: 0.7498 (tp30)
REVERT: H  205 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8246 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 109
  average time/residue: 0.2172
  time to fit residues: 33.1823
Evaluate side-chains
  106 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
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  185 SER
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  103 LEU
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  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:    0.1980
   chunk 112 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.121269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.087472 restraints weight = 40327.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 3.37
r_work: 0.3005 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9079  Z= 0.125
  Angle     :  0.521   4.185  12379  Z= 0.278
  Chirality :  0.044   0.150   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.294  34.812   1262
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.26), residues: 1142
  helix:  2.58 (0.50), residues: 110
  sheet:  0.61 (0.25), residues: 498
  loop : -1.72 (0.26), residues: 534

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9065)
  covalent geometry    : angle       0.51547 (12351)
  SS BOND              : bond        0.00694 (   14)
  SS BOND              : angle       1.69371 (   28)
  hydrogen bonds       : bond        0.03563 (  317)
  hydrogen bonds       : angle       4.28689 (  849)

*********************** 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
  111 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.6034 (mp)
REVERT: B  556 GLU cc_start: 0.7427 (tt0) cc_final: 0.7107 (tt0)
REVERT: F   91 ASP cc_start: 0.8372 (t0) cc_final: 0.8028 (t0)
REVERT: F  205 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8257 (p)
REVERT: H  168 LYS cc_start: 0.7466 (mmmt) cc_final: 0.6969 (mmtt)
REVERT: H  184 GLU cc_start: 0.7875 (tp30) cc_final: 0.7629 (tp30)
REVERT: H  205 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8287 (p)
  outliers start: 24
  outliers final: 15
  residues processed: 109
  average time/residue: 0.2012
  time to fit residues: 31.1106
Evaluate side-chains
  105 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
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  205 VAL
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  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 90 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3362 r_free = 0.3362 target = 0.122022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.088084 restraints weight = 36048.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.97
r_work: 0.3088 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    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 = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1234

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= 0.108
  Angle     :  0.505   3.947  12379  Z= 0.268
  Chirality :  0.043   0.151   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.264  34.918   1262
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.26), residues: 1142
  helix:  2.64 (0.50), residues: 110
  sheet:  0.65 (0.25), residues: 496
  loop : -1.71 (0.26), residues: 536

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9065)
  covalent geometry    : angle       0.50004 (12351)
  SS BOND              : bond        0.00640 (   14)
  SS BOND              : angle       1.54208 (   28)
  hydrogen bonds       : bond        0.03285 (  317)
  hydrogen bonds       : angle       4.26100 (  849)

*********************** 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
  106 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5986 (mp)
REVERT: B  556 GLU cc_start: 0.7513 (tt0) cc_final: 0.7186 (tt0)
REVERT: F  205 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8271 (p)
REVERT: H  168 LYS cc_start: 0.7427 (mmmt) cc_final: 0.6923 (mmtt)
REVERT: H  184 GLU cc_start: 0.7856 (tp30) cc_final: 0.7618 (tp30)
REVERT: H  205 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8297 (p)
  outliers start: 17
  outliers final: 13
  residues processed: 104
  average time/residue: 0.2090
  time to fit residues: 30.6656
Evaluate side-chains
  105 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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  205 VAL
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  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 36 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 113 optimal weight:    0.3980
   chunk 47 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0670
   chunk 92 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.0322

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.121502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.087293 restraints weight = 40268.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.09
r_work: 0.3052 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    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 = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1276

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= 0.115
  Angle     :  0.512   4.050  12379  Z= 0.273
  Chirality :  0.043   0.150   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.296  35.851   1262
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.26), residues: 1142
  helix:  2.62 (0.50), residues: 110
  sheet:  0.65 (0.25), residues: 496
  loop : -1.73 (0.26), residues: 536

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9065)
  covalent geometry    : angle       0.50706 (12351)
  SS BOND              : bond        0.00675 (   14)
  SS BOND              : angle       1.59593 (   28)
  hydrogen bonds       : bond        0.03403 (  317)
  hydrogen bonds       : angle       4.26662 (  849)

********************** 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
  109 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: B  556 GLU cc_start: 0.7571 (tt0) cc_final: 0.7268 (tt0)
REVERT: F  205 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8301 (p)
REVERT: H  168 LYS cc_start: 0.7440 (mmmt) cc_final: 0.6931 (mmtt)
REVERT: H  184 GLU cc_start: 0.7880 (tp30) cc_final: 0.7645 (tp30)
REVERT: H  205 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8324 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 107
  average time/residue: 0.1785
  time to fit residues: 27.0576
Evaluate side-chains
  103 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 LEU
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 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   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 46 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.132124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.102339 restraints weight = 31836.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.51
r_work: 0.2981 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9079  Z= 0.146
  Angle     :  0.551   4.661  12379  Z= 0.295
  Chirality :  0.044   0.150   1425
  Planarity :  0.004   0.051   1577
  Dihedral  :  4.322  15.941   1260
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.26), residues: 1142
  helix:  2.42 (0.50), residues: 110
  sheet:  0.57 (0.25), residues: 498
  loop : -1.79 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 187 
 TYR   0.010   0.001   TYR H  49 
 PHE   0.012   0.002   PHE H  73 
 TRP   0.005   0.001   TRP D 494 
 HIS   0.003   0.001   HIS G 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9065)
  covalent geometry    : angle       0.54390 (12351)
  SS BOND              : bond        0.00816 (   14)
  SS BOND              : angle       1.88720 (   28)
  hydrogen bonds       : bond        0.03992 (  317)
  hydrogen bonds       : angle       4.37431 (  849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6482.35 seconds
wall clock time: 110 minutes 29.57 seconds (6629.57 seconds total)