Starting phenix.real_space_refine
on Wed Mar  4 12:51:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kfh_22853/03_2026/7kfh_22853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kfh_22853/03_2026/7kfh_22853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kfh_22853/03_2026/7kfh_22853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kfh_22853/03_2026/7kfh_22853.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kfh_22853/03_2026/7kfh_22853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kfh_22853/03_2026/7kfh_22853.map"
  }
  resolution = 3.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    8601      2.51       5
     N    2271      2.21       5
     O    2655      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13575
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1793
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 216}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "J"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 818
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 757
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 4, 'TRANS': 90}
    Chain: "G"
      Number of atoms: 1026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1026
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 5, 'TRANS': 127}
    Chain: "M"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "N"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    B, C, K, L, E, F, H, I, O, Q, P, R
  Time building chain proxies: 2.58, per 1000 atoms: 0.19
  Number of scatterers: 13575
  At special positions: 0
  Unit cell: (118.45, 123.6, 123.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    2655      8.00
     N    2271      7.00
     C    8601      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 108 " - pdb=" SG  CYS A 135 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 121 " - pdb=" SG  CYS A 147 " distance=2.02
    Simple disulfide: pdb=" SG  CYS J  23 " - pdb=" SG  CYS J  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 511 " - pdb=" SG  CYS D 556 " distance=2.05
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 108 " - pdb=" SG  CYS B 135 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 108 " - pdb=" SG  CYS C 135 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 147 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 121 " - pdb=" SG  CYS C 147 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 511 " - pdb=" SG  CYS E 556 " distance=2.05
    Simple disulfide: pdb=" SG  CYS F 511 " - pdb=" SG  CYS F 556 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " distance=2.02

  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
  Links applied
    ALPHA1-3
      " BMA N   3 " - " MAN N   4 "
      " BMA P   3 " - " MAN P   4 "
      " BMA R   3 " - " MAN R   4 "
    ALPHA1-6
      " BMA N   3 " - " MAN N   5 "
      " BMA P   3 " - " MAN P   5 "
      " BMA R   3 " - " MAN R   5 "
    BETA1-4
      " NAG M   1 " - " NAG M   2 "
      " NAG N   1 " - " NAG N   2 "
      " NAG N   2 " - " BMA N   3 "
      " NAG O   1 " - " NAG O   2 "
      " NAG P   1 " - " NAG P   2 "
      " NAG P   2 " - " BMA P   3 "
      " NAG Q   1 " - " NAG Q   2 "
      " NAG R   1 " - " NAG R   2 "
      " NAG R   2 " - " BMA R   3 "
    NAG-ASN
      " NAG A 401 " - " ASN A 238 "
      " NAG A 402 " - " ASN A 268 "
      " NAG A 403 " - " ASN A 228 "
      " NAG B 401 " - " ASN B 238 "
      " NAG B 402 " - " ASN B 268 "
      " NAG B 403 " - " ASN B 228 "
      " NAG C 401 " - " ASN C 238 "
      " NAG C 402 " - " ASN C 268 "
      " NAG C 403 " - " ASN C 228 "
      " NAG M   1 " - " ASN A 257 "
      " NAG N   1 " - " ASN D 563 "
      " NAG O   1 " - " ASN B 257 "
      " NAG P   1 " - " ASN E 563 "
      " NAG Q   1 " - " ASN C 257 "
      " NAG R   1 " - " ASN F 563 "
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 629.6 milliseconds
  

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3066

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 30 sheets defined
      17.3% alpha, 35.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 61
      No H-bonds generated for 'chain 'A' and resid 59 through 61'
    Processing helix  chain 'A' and resid 71 through 74
    Processing helix  chain 'A' and resid 78 through 83
    Processing helix  chain 'A' and resid 249 through 264
    Processing helix  chain 'A' and resid 278 through 282
      removed outlier: 4.481A  pdb=" N   ASP A 282 " --> pdb=" O   PRO A 279 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 29 through 32
    Processing helix  chain 'J' and resid 80 through 84
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 553 through 575
      removed outlier: 4.739A  pdb=" N   GLN D 567 " --> pdb=" O   ASN D 563 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ALA D 568 " --> pdb=" O   GLU D 564 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 583 through 597
    Processing helix  chain 'G' and resid 62 through 65
    Processing helix  chain 'G' and resid 74 through 76
      No H-bonds generated for 'chain 'G' and resid 74 through 76'
    Processing helix  chain 'G' and resid 87 through 91
    Processing helix  chain 'B' and resid 59 through 61
      No H-bonds generated for 'chain 'B' and resid 59 through 61'
    Processing helix  chain 'B' and resid 71 through 74
    Processing helix  chain 'B' and resid 78 through 83
    Processing helix  chain 'B' and resid 249 through 264
    Processing helix  chain 'B' and resid 278 through 282
      removed outlier: 4.483A  pdb=" N   ASP B 282 " --> pdb=" O   PRO B 279 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 29 through 32
    Processing helix  chain 'K' and resid 80 through 84
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 553 through 575
      removed outlier: 4.739A  pdb=" N   GLN E 567 " --> pdb=" O   ASN E 563 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ALA E 568 " --> pdb=" O   GLU E 564 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 583 through 597
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'C' and resid 59 through 61
      No H-bonds generated for 'chain 'C' and resid 59 through 61'
    Processing helix  chain 'C' and resid 71 through 74
    Processing helix  chain 'C' and resid 78 through 83
    Processing helix  chain 'C' and resid 249 through 264
    Processing helix  chain 'C' and resid 278 through 282
      removed outlier: 4.482A  pdb=" N   ASP C 282 " --> pdb=" O   PRO C 279 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 29 through 32
    Processing helix  chain 'L' and resid 80 through 84
    Processing helix  chain 'F' and resid 538 through 542
    Processing helix  chain 'F' and resid 553 through 575
      removed outlier: 4.739A  pdb=" N   GLN F 567 " --> pdb=" O   ASN F 563 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ALA F 568 " --> pdb=" O   GLU F 564 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 583 through 597
    Processing helix  chain 'I' and resid 62 through 65
    Processing helix  chain 'I' and resid 74 through 76
      No H-bonds generated for 'chain 'I' and resid 74 through 76'
    Processing helix  chain 'I' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45
      removed outlier: 6.700A  pdb=" N   GLY A  36 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 544 through 549
      removed outlier: 6.313A  pdb=" N   ASN A  69 " --> pdb=" O   GLU A 103 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL A  96 " --> pdb=" O   THR D 581 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89
    Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 114
      removed outlier: 6.273A  pdb=" N   GLU A 106 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   HIS A 139 " --> pdb=" O   GLU A 106 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   CYS A 108 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   VAL A 141 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ASN A 110 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   GLY A 143 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   GLU A 112 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ARG A 136 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   ILE A 218 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL A 138 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   TYR A 220 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   LYS A 140 " --> pdb=" O   TYR A 220 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ALA A 222 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER A 142 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
      removed outlier: 14.147A  pdb=" N   THR A 217 " --> pdb=" O   ASP A 237 " (cutoff:3.500A)
      removed outlier: 10.057A  pdb=" N   ASP A 237 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ARG A 219 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   THR A 240 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   TYR A 241 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   SER G 112 " --> pdb=" O   GLY G 104 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 4 through 7
    Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 13
      removed outlier: 6.217A  pdb=" N   LEU J  34 " --> pdb=" O   TYR J  50 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   TYR J  50 " --> pdb=" O   LEU J  34 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP J  36 " --> pdb=" O   LEU J  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 10 through 13
    Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 6
    Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 12
      removed outlier: 7.146A  pdb=" N   PHE G  34 " --> pdb=" O   GLY G  50 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   GLY G  50 " --> pdb=" O   PHE G  34 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   TRP G  36 " --> pdb=" O   MET G  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 12
    Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 45
      removed outlier: 6.701A  pdb=" N   GLY B  36 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 544 through 549
      removed outlier: 6.311A  pdb=" N   ASN B  69 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   VAL B  96 " --> pdb=" O   THR E 581 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 89
    Processing sheet with id=AB5, first strand: chain 'B' and resid 105 through 114
      removed outlier: 6.274A  pdb=" N   GLU B 106 " --> pdb=" O   TYR B 137 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   HIS B 139 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   CYS B 108 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   VAL B 141 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASN B 110 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   GLY B 143 " --> pdb=" O   ASN B 110 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU B 112 " --> pdb=" O   GLY B 143 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ARG B 136 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE B 218 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL B 138 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   TYR B 220 " --> pdb=" O   VAL B 138 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   LYS B 140 " --> pdb=" O   TYR B 220 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   ALA B 222 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER B 142 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
      removed outlier: 14.147A  pdb=" N   THR B 217 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 10.058A  pdb=" N   ASP B 237 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ARG B 219 " --> pdb=" O   GLU B 235 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   THR B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   SER H 112 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 7
    Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 13
      removed outlier: 6.217A  pdb=" N   LEU K  34 " --> pdb=" O   TYR K  50 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   TYR K  50 " --> pdb=" O   LEU K  34 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP K  36 " --> pdb=" O   LEU K  48 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'K' and resid 10 through 13
    Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 7.145A  pdb=" N   PHE H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   GLY H  50 " --> pdb=" O   PHE H  34 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 45
      removed outlier: 6.700A  pdb=" N   GLY C  36 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 544 through 549
      removed outlier: 6.313A  pdb=" N   ASN C  69 " --> pdb=" O   GLU C 103 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL C  96 " --> pdb=" O   THR F 581 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 86 through 89
    Processing sheet with id=AC6, first strand: chain 'C' and resid 105 through 114
      removed outlier: 6.273A  pdb=" N   GLU C 106 " --> pdb=" O   TYR C 137 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   HIS C 139 " --> pdb=" O   GLU C 106 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   CYS C 108 " --> pdb=" O   HIS C 139 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   VAL C 141 " --> pdb=" O   CYS C 108 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASN C 110 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   GLY C 143 " --> pdb=" O   ASN C 110 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   GLU C 112 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ARG C 136 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   ILE C 218 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL C 138 " --> pdb=" O   ILE C 218 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   TYR C 220 " --> pdb=" O   VAL C 138 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   LYS C 140 " --> pdb=" O   TYR C 220 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ALA C 222 " --> pdb=" O   LYS C 140 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER C 142 " --> pdb=" O   ALA C 222 " (cutoff:3.500A)
      removed outlier: 14.147A  pdb=" N   THR C 217 " --> pdb=" O   ASP C 237 " (cutoff:3.500A)
      removed outlier: 10.059A  pdb=" N   ASP C 237 " --> pdb=" O   THR C 217 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ARG C 219 " --> pdb=" O   GLU C 235 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   THR C 240 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   SER I 112 " --> pdb=" O   GLY I 104 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.216A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12
      removed outlier: 7.146A  pdb=" N   PHE I  34 " --> pdb=" O   GLY I  50 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   GLY I  50 " --> pdb=" O   PHE I  34 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   TRP I  36 " --> pdb=" O   MET I  48 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 12

    549 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2776
        1.32 -     1.45: 4283
        1.45 -     1.59: 6703
        1.59 -     1.72: 62
        1.72 -     1.85: 60
  Bond restraints: 13884
  Sorted by residual:
  bond pdb=" CB  HIS D 549 "
       pdb=" CG  HIS D 549 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.11e+01
  bond pdb=" CB  HIS F 549 "
       pdb=" CG  HIS F 549 "
    ideal  model  delta    sigma   weight residual
    1.497  1.398  0.099 1.40e-02 5.10e+03 5.02e+01
  bond pdb=" CB  HIS E 549 "
       pdb=" CG  HIS E 549 "
    ideal  model  delta    sigma   weight residual
    1.497  1.398  0.099 1.40e-02 5.10e+03 4.95e+01
  bond pdb=" CZ2 TRP F 597 "
       pdb=" CH2 TRP F 597 "
    ideal  model  delta    sigma   weight residual
    1.368  1.490 -0.122 1.90e-02 2.77e+03 4.11e+01
  bond pdb=" CZ2 TRP E 597 "
       pdb=" CH2 TRP E 597 "
    ideal  model  delta    sigma   weight residual
    1.368  1.489 -0.121 1.90e-02 2.77e+03 4.08e+01
  ... (remaining 13879 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 16173
        2.38 -     4.76: 2247
        4.76 -     7.14: 363
        7.14 -     9.52: 54
        9.52 -    11.90: 9
  Bond angle restraints: 18846
  Sorted by residual:
  angle pdb=" N   PHE I  55 "
        pdb=" CA  PHE I  55 "
        pdb=" C   PHE I  55 "
      ideal   model   delta    sigma   weight residual
     113.97  102.49   11.48 1.28e+00 6.10e-01 8.04e+01
  angle pdb=" N   PHE G  55 "
        pdb=" CA  PHE G  55 "
        pdb=" C   PHE G  55 "
      ideal   model   delta    sigma   weight residual
     113.97  102.56   11.41 1.28e+00 6.10e-01 7.95e+01
  angle pdb=" N   PHE H  55 "
        pdb=" CA  PHE H  55 "
        pdb=" C   PHE H  55 "
      ideal   model   delta    sigma   weight residual
     113.97  102.60   11.37 1.28e+00 6.10e-01 7.89e+01
  angle pdb=" N   SER A  41 "
        pdb=" CA  SER A  41 "
        pdb=" C   SER A  41 "
      ideal   model   delta    sigma   weight residual
     114.12  102.22   11.90 1.39e+00 5.18e-01 7.33e+01
  angle pdb=" N   SER C  41 "
        pdb=" CA  SER C  41 "
        pdb=" C   SER C  41 "
      ideal   model   delta    sigma   weight residual
     114.12  102.24   11.88 1.39e+00 5.18e-01 7.30e+01
  ... (remaining 18841 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.15: 8313
       21.15 -    42.30: 150
       42.30 -    63.45: 63
       63.45 -    84.60: 35
       84.60 -   105.75: 16
  Dihedral angle restraints: 8577
    sinusoidal: 3756
      harmonic: 4821
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   PRO H 101 "
           pdb=" CA  PRO H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.42   18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  PRO G 100 "
           pdb=" C   PRO G 100 "
           pdb=" N   PRO G 101 "
           pdb=" CA  PRO G 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  PRO I 100 "
           pdb=" C   PRO I 100 "
           pdb=" N   PRO I 101 "
           pdb=" CA  PRO I 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.44   18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 8574 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1667
       0.113 -    0.225: 378
       0.225 -    0.338: 64
       0.338 -    0.451: 39
       0.451 -    0.563: 9
  Chirality restraints: 2157
  Sorted by residual:
  chirality pdb=" C1  NAG Q   2 "
            pdb=" O4  NAG Q   1 "
            pdb=" C2  NAG Q   2 "
            pdb=" O5  NAG Q   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.62    0.22 2.00e-02 2.50e+03 1.16e+02
  chirality pdb=" C1  NAG O   2 "
            pdb=" O4  NAG O   1 "
            pdb=" C2  NAG O   2 "
            pdb=" O5  NAG O   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.61    0.21 2.00e-02 2.50e+03 1.10e+02
  chirality pdb=" C1  NAG M   2 "
            pdb=" O4  NAG M   1 "
            pdb=" C2  NAG M   2 "
            pdb=" O5  NAG M   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.61    0.21 2.00e-02 2.50e+03 1.10e+02
  ... (remaining 2154 not shown)

  Planarity restraints: 2400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 238 "    0.096 2.00e-02 2.50e+03   1.02e-01 1.30e+02
        pdb=" CG  ASN B 238 "   -0.041 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 238 "   -0.018 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 238 "   -0.160 2.00e-02 2.50e+03
        pdb=" C1  NAG B 401 "    0.122 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 238 "   -0.096 2.00e-02 2.50e+03   1.02e-01 1.29e+02
        pdb=" CG  ASN A 238 "    0.041 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 238 "    0.018 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 238 "    0.160 2.00e-02 2.50e+03
        pdb=" C1  NAG A 401 "   -0.122 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 238 "   -0.096 2.00e-02 2.50e+03   1.01e-01 1.29e+02
        pdb=" CG  ASN C 238 "    0.039 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 238 "    0.018 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 238 "    0.160 2.00e-02 2.50e+03
        pdb=" C1  NAG C 401 "   -0.122 2.00e-02 2.50e+03
  ... (remaining 2397 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 4601
        2.87 -     3.38: 11831
        3.38 -     3.88: 22877
        3.88 -     4.39: 26253
        4.39 -     4.90: 43569
  Nonbonded interactions: 109131
  Sorted by model distance:
  nonbonded pdb=" N   SER C  41 "
            pdb=" N   THR C  42 "
     model   vdw
     2.360 2.560
  nonbonded pdb=" N   SER B  41 "
            pdb=" N   THR B  42 "
     model   vdw
     2.362 2.560
  nonbonded pdb=" N   SER A  41 "
            pdb=" N   THR A  42 "
     model   vdw
     2.362 2.560
  nonbonded pdb=" N   PHE I  55 "
            pdb=" N   GLY I  56 "
     model   vdw
     2.411 2.560
  nonbonded pdb=" N   PHE H  55 "
            pdb=" N   GLY H  56 "
     model   vdw
     2.412 2.560
  ... (remaining 109126 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'O'
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.280
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.070
  Process input model:                     13.910
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
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      :  0.021   0.122  13929  Z= 1.103
  Angle     :  1.776  11.901  18966  Z= 1.166
  Chirality :  0.114   0.563   2157
  Planarity :  0.008   0.045   2385
  Dihedral  : 11.997 105.755   5466
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  1.80 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.99 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.20), residues: 1665
  helix:  1.13 (0.31), residues: 159
  sheet:  0.97 (0.21), residues: 594
  loop :  0.65 (0.20), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  46 
 TYR   0.060   0.009   TYR H  60 
 PHE   0.026   0.006   PHE J  84 
 TRP   0.046   0.009   TRP L  36 
 HIS   0.005   0.002   HIS F 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.02117 (13884)
  covalent geometry    : angle       1.75667 (18846)
  SS BOND              : bond        0.01232 (   15)
  SS BOND              : angle       1.87656 (   30)
  hydrogen bonds       : bond        0.15850 (  513)
  hydrogen bonds       : angle       7.44945 ( 1296)
  link_ALPHA1-3        : bond        0.08200 (    3)
  link_ALPHA1-3        : angle       4.23005 (    9)
  link_ALPHA1-6        : bond        0.06335 (    3)
  link_ALPHA1-6        : angle       3.87776 (    9)
  link_BETA1-4         : bond        0.06563 (    9)
  link_BETA1-4         : angle       5.87401 (   27)
  link_NAG-ASN         : bond        0.07581 (   15)
  link_NAG-ASN         : angle       2.60121 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 383
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8153 (m-30) cc_final: 0.7343 (m-30)
REVERT: A  258 GLU cc_start: 0.7972 (tp30) cc_final: 0.7394 (tp30)
REVERT: D  549 HIS cc_start: 0.8104 (p-80) cc_final: 0.7833 (t-170)
REVERT: D  581 THR cc_start: 0.9521 (m) cc_final: 0.9132 (p)
REVERT: D  596 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7482 (mtt-85)
REVERT: G   48 MET cc_start: 0.7713 (mtp) cc_final: 0.7387 (mtp)
REVERT: G   78 THR cc_start: 0.8456 (m) cc_final: 0.7837 (p)
REVERT: G   83 LEU cc_start: 0.7106 (tp) cc_final: 0.6651 (tp)
REVERT: G  108 TRP cc_start: 0.8336 (p-90) cc_final: 0.8119 (p90)
REVERT: G  114 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7553 (mtmm)
REVERT: B   55 ASP cc_start: 0.8164 (m-30) cc_final: 0.7107 (m-30)
REVERT: K   37 TYR cc_start: 0.5216 (m-80) cc_final: 0.4313 (m-80)
REVERT: K   47 LEU cc_start: 0.3498 (tp) cc_final: 0.3251 (tt)
REVERT: K   48 LEU cc_start: 0.8218 (mt) cc_final: 0.7862 (mt)
REVERT: E  549 HIS cc_start: 0.8025 (p-80) cc_final: 0.7708 (t-170)
REVERT: E  550 ASN cc_start: 0.9131 (t0) cc_final: 0.8599 (t0)
REVERT: E  581 THR cc_start: 0.9515 (m) cc_final: 0.9246 (p)
REVERT: H   48 MET cc_start: 0.7477 (mtp) cc_final: 0.7243 (mtp)
REVERT: H   78 THR cc_start: 0.8202 (m) cc_final: 0.7608 (p)
REVERT: H   81 MET cc_start: 0.7905 (ttp) cc_final: 0.7634 (tmm)
REVERT: H   83 LEU cc_start: 0.7587 (tp) cc_final: 0.7106 (tp)
REVERT: H  114 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7590 (ptpt)
REVERT: C  109 TYR cc_start: 0.9053 (m-80) cc_final: 0.8765 (m-80)
REVERT: C  258 GLU cc_start: 0.7918 (tp30) cc_final: 0.7394 (tp30)
REVERT: L   37 TYR cc_start: 0.5533 (m-80) cc_final: 0.4804 (m-80)
REVERT: F  550 ASN cc_start: 0.8993 (t0) cc_final: 0.8786 (t0)
REVERT: F  581 THR cc_start: 0.9509 (m) cc_final: 0.9009 (p)
REVERT: F  596 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7519 (mtt-85)
REVERT: F  597 TRP cc_start: 0.6861 (t-100) cc_final: 0.6339 (t-100)
REVERT: I   78 THR cc_start: 0.7994 (m) cc_final: 0.7360 (p)
REVERT: I   83 LEU cc_start: 0.7483 (tp) cc_final: 0.6994 (tp)
REVERT: I   94 TYR cc_start: 0.5017 (m-80) cc_final: 0.4683 (m-10)
REVERT: I  114 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7520 (ptpt)
  outliers start: 3
  outliers final: 3
  residues processed: 386
  average time/residue: 0.1427
  time to fit residues: 74.6023
Evaluate side-chains
  228 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 225
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain B residue  238 ASN
Chi-restraints excluded: chain C residue  238 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
F 549 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.150591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.096485 restraints weight = 21913.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.100050 restraints weight = 14041.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.100212 restraints weight = 11064.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.100793 restraints weight = 9229.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.101197 restraints weight = 9232.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13929  Z= 0.168
  Angle     :  0.710   8.188  18966  Z= 0.369
  Chirality :  0.046   0.223   2157
  Planarity :  0.005   0.043   2385
  Dihedral  :  8.878  73.083   2463
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.10 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  :  7.56 %
    Favored  : 90.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.19), residues: 1665
  helix:  1.95 (0.34), residues: 162
  sheet:  0.80 (0.20), residues: 630
  loop :  0.26 (0.20), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  31 
 TYR   0.017   0.002   TYR L  50 
 PHE   0.023   0.002   PHE J  72 
 TRP   0.012   0.001   TRP G  47 
 HIS   0.003   0.001   HIS C  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (13884)
  covalent geometry    : angle       0.67584 (18846)
  SS BOND              : bond        0.00447 (   15)
  SS BOND              : angle       1.12488 (   30)
  hydrogen bonds       : bond        0.04818 (  513)
  hydrogen bonds       : angle       5.69834 ( 1296)
  link_ALPHA1-3        : bond        0.00998 (    3)
  link_ALPHA1-3        : angle       3.10110 (    9)
  link_ALPHA1-6        : bond        0.00747 (    3)
  link_ALPHA1-6        : angle       1.53464 (    9)
  link_BETA1-4         : bond        0.00828 (    9)
  link_BETA1-4         : angle       4.21574 (   27)
  link_NAG-ASN         : bond        0.00665 (   15)
  link_NAG-ASN         : angle       2.71125 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 259
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8103 (m-30) cc_final: 0.7607 (m-30)
REVERT: A  229 GLU cc_start: 0.8189 (pp20) cc_final: 0.7952 (pp20)
REVERT: A  258 GLU cc_start: 0.7741 (tp30) cc_final: 0.7359 (tp30)
REVERT: J   37 TYR cc_start: 0.7824 (m-80) cc_final: 0.7384 (m-80)
REVERT: G   10 GLU cc_start: 0.5497 (mm-30) cc_final: 0.5244 (mm-30)
REVERT: G   60 TYR cc_start: 0.7781 (m-80) cc_final: 0.7521 (m-80)
REVERT: G   65 GLN cc_start: 0.8408 (tp40) cc_final: 0.8110 (tp-100)
REVERT: G   81 MET cc_start: 0.8068 (tmm) cc_final: 0.7470 (tmm)
REVERT: G  114 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8019 (mtmm)
REVERT: K   37 TYR cc_start: 0.7625 (m-80) cc_final: 0.7050 (m-80)
REVERT: H   12 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5971 (mptt)
REVERT: H   65 GLN cc_start: 0.8776 (tp40) cc_final: 0.8496 (mm-40)
REVERT: H   78 THR cc_start: 0.8568 (m) cc_final: 0.8352 (p)
REVERT: H   81 MET cc_start: 0.7597 (ttp) cc_final: 0.7375 (tmm)
REVERT: H  114 LYS cc_start: 0.8377 (ttpt) cc_final: 0.7801 (mtmm)
REVERT: C   55 ASP cc_start: 0.7844 (m-30) cc_final: 0.7493 (m-30)
REVERT: L   37 TYR cc_start: 0.7638 (m-80) cc_final: 0.6184 (m-80)
REVERT: L   72 PHE cc_start: 0.7173 (m-80) cc_final: 0.6968 (m-10)
REVERT: F  545 GLU cc_start: 0.8104 (pm20) cc_final: 0.7902 (pm20)
REVERT: I   10 GLU cc_start: 0.5555 (mm-30) cc_final: 0.5352 (mm-30)
REVERT: I  114 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7820 (mtmm)
  outliers start: 34
  outliers final: 18
  residues processed: 277
  average time/residue: 0.1217
  time to fit residues: 47.6280
Evaluate side-chains
  223 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain J residue   70 THR
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  593 LEU
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  238 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain E residue  593 LEU
Chi-restraints excluded: chain H residue   12 LYS
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain F residue  593 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 152 optimal weight:    8.9990
   chunk 108 optimal weight:    4.9990
   chunk 151 optimal weight:    0.0970
   chunk 99 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0050
   chunk 119 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.0198

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
K  39 GLN
H  39 GLN
H  59 ASN
C  39 HIS
I  59 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.144025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.092892 restraints weight = 22196.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.093138 restraints weight = 15822.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.093428 restraints weight = 11917.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.093539 restraints weight = 11071.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.093733 restraints weight = 10627.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13929  Z= 0.156
  Angle     :  0.639   9.596  18966  Z= 0.325
  Chirality :  0.044   0.187   2157
  Planarity :  0.004   0.040   2385
  Dihedral  :  7.886  60.677   2461
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.10 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  :  8.69 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.20), residues: 1665
  helix:  2.23 (0.38), residues: 162
  sheet:  0.70 (0.21), residues: 612
  loop :  0.09 (0.20), residues: 891

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 596 
 TYR   0.018   0.002   TYR I 117 
 PHE   0.018   0.002   PHE K  72 
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS F 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13884)
  covalent geometry    : angle       0.61489 (18846)
  SS BOND              : bond        0.00439 (   15)
  SS BOND              : angle       0.94817 (   30)
  hydrogen bonds       : bond        0.04358 (  513)
  hydrogen bonds       : angle       5.25366 ( 1296)
  link_ALPHA1-3        : bond        0.01065 (    3)
  link_ALPHA1-3        : angle       1.53888 (    9)
  link_ALPHA1-6        : bond        0.00844 (    3)
  link_ALPHA1-6        : angle       1.28266 (    9)
  link_BETA1-4         : bond        0.00882 (    9)
  link_BETA1-4         : angle       3.42404 (   27)
  link_NAG-ASN         : bond        0.00385 (   15)
  link_NAG-ASN         : angle       2.25944 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 241
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 THR cc_start: 0.9397 (m) cc_final: 0.9008 (p)
REVERT: A  267 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7325 (p)
REVERT: J   37 TYR cc_start: 0.7794 (m-80) cc_final: 0.7443 (m-80)
REVERT: G   60 TYR cc_start: 0.7920 (m-80) cc_final: 0.7706 (m-80)
REVERT: G   65 GLN cc_start: 0.8411 (tp40) cc_final: 0.7982 (mm-40)
REVERT: G   81 MET cc_start: 0.8205 (tmm) cc_final: 0.7507 (tmm)
REVERT: G  106 ARG cc_start: 0.8328 (ttm110) cc_final: 0.8126 (mtp-110)
REVERT: G  114 LYS cc_start: 0.8527 (ttpt) cc_final: 0.7957 (mtmm)
REVERT: B  103 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8311 (tt0)
REVERT: K   46 ARG cc_start: 0.7591 (mmt180) cc_final: 0.7365 (tpt170)
REVERT: K   55 ARG cc_start: 0.6790 (mtt90) cc_final: 0.6584 (mpt180)
REVERT: H   12 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5871 (mptt)
REVERT: H   38 ARG cc_start: 0.7702 (mtp-110) cc_final: 0.7082 (mtp-110)
REVERT: H   65 GLN cc_start: 0.8832 (tp40) cc_final: 0.8556 (mm-40)
REVERT: H   78 THR cc_start: 0.8709 (m) cc_final: 0.8391 (p)
REVERT: H  114 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8039 (mtmm)
REVERT: H  119 TYR cc_start: 0.8514 (p90) cc_final: 0.8023 (p90)
REVERT: L   55 ARG cc_start: 0.7145 (mtt90) cc_final: 0.6859 (mpt180)
REVERT: I  114 LYS cc_start: 0.8408 (ttpt) cc_final: 0.7796 (mtmm)
  outliers start: 51
  outliers final: 26
  residues processed: 272
  average time/residue: 0.1214
  time to fit residues: 46.9360
Evaluate side-chains
  240 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 211
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain J residue   22 SER
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  581 THR
Chi-restraints excluded: chain D residue  595 GLN
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   52 ILE
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  238 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain E residue  581 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   12 LYS
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain F residue  581 THR
Chi-restraints excluded: chain I residue   48 MET
Chi-restraints excluded: chain I residue   60 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 131 optimal weight:    5.9990
   chunk 142 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 83 optimal weight:    6.9990
   chunk 127 optimal weight:    3.9990
   chunk 158 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  39 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.139270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.085827 restraints weight = 22226.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.087383 restraints weight = 16709.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.088254 restraints weight = 12416.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.088528 restraints weight = 10866.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.088720 restraints weight = 10999.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13929  Z= 0.235
  Angle     :  0.692   8.964  18966  Z= 0.347
  Chirality :  0.047   0.199   2157
  Planarity :  0.005   0.079   2385
  Dihedral  :  7.155  50.453   2461
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.10 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  :  8.76 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.20), residues: 1665
  helix:  1.94 (0.38), residues: 162
  sheet:  0.13 (0.20), residues: 657
  loop : -0.01 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG G  38 
 TYR   0.021   0.002   TYR I 119 
 PHE   0.025   0.002   PHE A 132 
 TRP   0.010   0.001   TRP I  36 
 HIS   0.005   0.002   HIS C 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 (13884)
  covalent geometry    : angle       0.67030 (18846)
  SS BOND              : bond        0.00409 (   15)
  SS BOND              : angle       0.69294 (   30)
  hydrogen bonds       : bond        0.04593 (  513)
  hydrogen bonds       : angle       5.10184 ( 1296)
  link_ALPHA1-3        : bond        0.00928 (    3)
  link_ALPHA1-3        : angle       2.75032 (    9)
  link_ALPHA1-6        : bond        0.00755 (    3)
  link_ALPHA1-6        : angle       1.12623 (    9)
  link_BETA1-4         : bond        0.00610 (    9)
  link_BETA1-4         : angle       3.48173 (   27)
  link_NAG-ASN         : bond        0.00154 (   15)
  link_NAG-ASN         : angle       2.02822 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 213
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 SER cc_start: 0.7927 (OUTLIER) cc_final: 0.7178 (p)
REVERT: G   60 TYR cc_start: 0.8048 (m-80) cc_final: 0.7768 (m-80)
REVERT: G   65 GLN cc_start: 0.8434 (tp40) cc_final: 0.8012 (mm-40)
REVERT: G   81 MET cc_start: 0.8443 (tmm) cc_final: 0.7558 (tmm)
REVERT: G  114 LYS cc_start: 0.8612 (ttpt) cc_final: 0.7919 (mtmm)
REVERT: B   65 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8874 (p)
REVERT: K    2 ILE cc_start: 0.6759 (mt) cc_final: 0.6540 (mt)
REVERT: K   37 TYR cc_start: 0.7542 (m-80) cc_final: 0.7104 (m-80)
REVERT: H   12 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5862 (mptt)
REVERT: H   81 MET cc_start: 0.8008 (tmm) cc_final: 0.7558 (tmm)
REVERT: H   86 LEU cc_start: 0.6988 (mt) cc_final: 0.6610 (mp)
REVERT: H  119 TYR cc_start: 0.8660 (p90) cc_final: 0.8294 (p90)
REVERT: L   37 TYR cc_start: 0.7617 (m-80) cc_final: 0.6137 (m-80)
REVERT: L   63 PHE cc_start: 0.7836 (m-80) cc_final: 0.7030 (m-80)
REVERT: I   86 LEU cc_start: 0.6808 (mt) cc_final: 0.6409 (mp)
REVERT: I  120 MET cc_start: 0.8661 (mpp) cc_final: 0.8315 (mpp)
  outliers start: 56
  outliers final: 35
  residues processed: 245
  average time/residue: 0.1257
  time to fit residues: 43.5386
Evaluate side-chains
  239 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 201
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain J residue   22 SER
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   70 THR
Chi-restraints excluded: chain J residue  101 GLN
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  581 THR
Chi-restraints excluded: chain D residue  595 GLN
Chi-restraints excluded: chain G residue   12 LYS
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain G residue  121 ASP
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  238 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain K residue   29 VAL
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain E residue  520 THR
Chi-restraints excluded: chain E residue  581 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   12 LYS
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue  109 PHE
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain F residue  581 THR
Chi-restraints excluded: chain I residue   52 ILE
Chi-restraints excluded: chain I residue   60 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 149 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 47 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 157 optimal weight:    1.9990
   chunk 147 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
J  39 GLN
G  39 GLN
C  39 HIS
F 595 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.137622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.087921 restraints weight = 22656.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.087205 restraints weight = 16374.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.087038 restraints weight = 12990.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.087171 restraints weight = 12135.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.087308 restraints weight = 11754.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040  13929  Z= 0.279
  Angle     :  0.704   6.716  18966  Z= 0.352
  Chirality :  0.047   0.168   2157
  Planarity :  0.005   0.054   2385
  Dihedral  :  7.057  55.774   2461
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.70 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 10.03 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.20), residues: 1665
  helix:  2.04 (0.39), residues: 159
  sheet: -0.13 (0.20), residues: 660
  loop : -0.14 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  31 
 TYR   0.020   0.002   TYR B 214 
 PHE   0.023   0.002   PHE E 592 
 TRP   0.009   0.001   TRP A 104 
 HIS   0.005   0.002   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 (13884)
  covalent geometry    : angle       0.68622 (18846)
  SS BOND              : bond        0.00454 (   15)
  SS BOND              : angle       0.68613 (   30)
  hydrogen bonds       : bond        0.04649 (  513)
  hydrogen bonds       : angle       5.01591 ( 1296)
  link_ALPHA1-3        : bond        0.00961 (    3)
  link_ALPHA1-3        : angle       2.42752 (    9)
  link_ALPHA1-6        : bond        0.00928 (    3)
  link_ALPHA1-6        : angle       1.03158 (    9)
  link_BETA1-4         : bond        0.00739 (    9)
  link_BETA1-4         : angle       3.25401 (   27)
  link_NAG-ASN         : bond        0.00179 (   15)
  link_NAG-ASN         : angle       1.92282 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 205
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7252 (p)
REVERT: D  510 LYS cc_start: 0.8529 (mttt) cc_final: 0.7546 (mmtt)
REVERT: G    3 GLN cc_start: 0.7527 (pm20) cc_final: 0.7300 (pm20)
REVERT: G   38 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7072 (mtm-85)
REVERT: G   64 PHE cc_start: 0.7806 (m-80) cc_final: 0.7471 (m-80)
REVERT: G   65 GLN cc_start: 0.8465 (tp40) cc_final: 0.8045 (mm-40)
REVERT: G   81 MET cc_start: 0.8402 (tmm) cc_final: 0.7531 (tmm)
REVERT: G  111 GLU cc_start: 0.8281 (pp20) cc_final: 0.7989 (pp20)
REVERT: B   65 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8875 (p)
REVERT: K   37 TYR cc_start: 0.7588 (m-80) cc_final: 0.6616 (m-80)
REVERT: H   81 MET cc_start: 0.8007 (tmm) cc_final: 0.7708 (tmm)
REVERT: H   86 LEU cc_start: 0.7110 (mt) cc_final: 0.6784 (mp)
REVERT: L   37 TYR cc_start: 0.7733 (m-80) cc_final: 0.7191 (m-10)
REVERT: L   63 PHE cc_start: 0.7623 (m-80) cc_final: 0.7010 (m-80)
REVERT: F  510 LYS cc_start: 0.8571 (mttt) cc_final: 0.7733 (mmtt)
REVERT: I   86 LEU cc_start: 0.6868 (mt) cc_final: 0.6637 (mp)
REVERT: I  119 TYR cc_start: 0.8602 (p90) cc_final: 0.8236 (p90)
  outliers start: 60
  outliers final: 44
  residues processed: 242
  average time/residue: 0.1232
  time to fit residues: 41.8427
Evaluate side-chains
  242 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 196
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain J residue   22 SER
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   48 LEU
Chi-restraints excluded: chain J residue   70 THR
Chi-restraints excluded: chain J residue   73 THR
Chi-restraints excluded: chain J residue  101 GLN
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  581 THR
Chi-restraints excluded: chain D residue  595 GLN
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  238 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain K residue   29 VAL
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain E residue  520 THR
Chi-restraints excluded: chain E residue  581 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue  109 PHE
Chi-restraints excluded: chain H residue  111 GLU
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  274 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain F residue  545 GLU
Chi-restraints excluded: chain F residue  581 THR
Chi-restraints excluded: chain F residue  595 GLN
Chi-restraints excluded: chain I residue   60 TYR
Chi-restraints excluded: chain I residue  109 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 146 optimal weight:    0.9990
   chunk 127 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 124 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D 595 GLN
I  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.140533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.088916 restraints weight = 22283.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.090012 restraints weight = 15935.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.090004 restraints weight = 11413.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.090029 restraints weight = 11612.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.090564 restraints weight = 10737.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13929  Z= 0.123
  Angle     :  0.601   8.103  18966  Z= 0.298
  Chirality :  0.044   0.160   2157
  Planarity :  0.004   0.060   2385
  Dihedral  :  6.477  50.985   2461
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.16 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 12.43 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.21), residues: 1665
  helix:  2.47 (0.39), residues: 162
  sheet: -0.02 (0.20), residues: 660
  loop : -0.09 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 596 
 TYR   0.018   0.001   TYR H 117 
 PHE   0.022   0.001   PHE E 592 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13884)
  covalent geometry    : angle       0.58484 (18846)
  SS BOND              : bond        0.00369 (   15)
  SS BOND              : angle       0.70385 (   30)
  hydrogen bonds       : bond        0.03785 (  513)
  hydrogen bonds       : angle       4.70306 ( 1296)
  link_ALPHA1-3        : bond        0.01186 (    3)
  link_ALPHA1-3        : angle       1.70575 (    9)
  link_ALPHA1-6        : bond        0.00849 (    3)
  link_ALPHA1-6        : angle       1.24276 (    9)
  link_BETA1-4         : bond        0.00698 (    9)
  link_BETA1-4         : angle       2.65180 (   27)
  link_NAG-ASN         : bond        0.00285 (   15)
  link_NAG-ASN         : angle       1.83773 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 215
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  267 SER cc_start: 0.7955 (OUTLIER) cc_final: 0.7244 (p)
REVERT: J    2 ILE cc_start: 0.6708 (mt) cc_final: 0.6498 (mt)
REVERT: J   63 PHE cc_start: 0.7449 (m-80) cc_final: 0.6835 (m-80)
REVERT: G    3 GLN cc_start: 0.7751 (pm20) cc_final: 0.7519 (pm20)
REVERT: G   12 LYS cc_start: 0.7506 (tptt) cc_final: 0.7252 (tppt)
REVERT: G   64 PHE cc_start: 0.7785 (m-80) cc_final: 0.7551 (m-80)
REVERT: G   65 GLN cc_start: 0.8365 (tp40) cc_final: 0.7994 (mm-40)
REVERT: G   81 MET cc_start: 0.8360 (tmm) cc_final: 0.8077 (tmm)
REVERT: G  111 GLU cc_start: 0.8441 (pp20) cc_final: 0.8104 (pp20)
REVERT: G  114 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8025 (ptmt)
REVERT: G  119 TYR cc_start: 0.8453 (p90) cc_final: 0.8241 (p90)
REVERT: G  120 MET cc_start: 0.8468 (mpp) cc_final: 0.7887 (mpp)
REVERT: B   65 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8768 (p)
REVERT: K   37 TYR cc_start: 0.7562 (m-80) cc_final: 0.6905 (m-80)
REVERT: E  587 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7484 (ttp-170)
REVERT: H   81 MET cc_start: 0.7893 (tmm) cc_final: 0.7607 (tmm)
REVERT: H   86 LEU cc_start: 0.7006 (mt) cc_final: 0.6724 (mp)
REVERT: L   63 PHE cc_start: 0.7620 (m-80) cc_final: 0.7168 (m-80)
REVERT: I   82 GLU cc_start: 0.7356 (pp20) cc_final: 0.7155 (pp20)
REVERT: I   86 LEU cc_start: 0.6854 (mt) cc_final: 0.6650 (mp)
REVERT: I  119 TYR cc_start: 0.8589 (p90) cc_final: 0.8230 (p90)
  outliers start: 36
  outliers final: 28
  residues processed: 236
  average time/residue: 0.1194
  time to fit residues: 40.2454
Evaluate side-chains
  233 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain J residue   22 SER
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   73 THR
Chi-restraints excluded: chain J residue  101 GLN
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  595 GLN
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain E residue  520 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue  109 PHE
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain I residue   60 TYR
Chi-restraints excluded: chain I residue  109 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 131 optimal weight:   20.0000
   chunk 126 optimal weight:    0.9990
   chunk 140 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0370
   chunk 136 optimal weight:   20.0000
   chunk 135 optimal weight:    2.9990
   chunk 146 optimal weight:    2.9990
   overall best weight:    0.8662

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.141971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.090706 restraints weight = 22292.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.092094 restraints weight = 16282.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.092445 restraints weight = 12191.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.092562 restraints weight = 11405.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.092876 restraints weight = 11037.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.4928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13929  Z= 0.133
  Angle     :  0.598   8.333  18966  Z= 0.295
  Chirality :  0.044   0.155   2157
  Planarity :  0.004   0.040   2385
  Dihedral  :  5.998  48.173   2457
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.82 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.79 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.21), residues: 1665
  helix:  2.59 (0.39), residues: 162
  sheet:  0.10 (0.21), residues: 630
  loop : -0.11 (0.21), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 596 
 TYR   0.026   0.001   TYR J  50 
 PHE   0.022   0.001   PHE E 592 
 TRP   0.009   0.001   TRP I  47 
 HIS   0.002   0.001   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (13884)
  covalent geometry    : angle       0.58215 (18846)
  SS BOND              : bond        0.00376 (   15)
  SS BOND              : angle       0.68460 (   30)
  hydrogen bonds       : bond        0.03746 (  513)
  hydrogen bonds       : angle       4.60848 ( 1296)
  link_ALPHA1-3        : bond        0.01123 (    3)
  link_ALPHA1-3        : angle       1.83711 (    9)
  link_ALPHA1-6        : bond        0.00867 (    3)
  link_ALPHA1-6        : angle       1.23396 (    9)
  link_BETA1-4         : bond        0.00646 (    9)
  link_BETA1-4         : angle       2.70270 (   27)
  link_NAG-ASN         : bond        0.00185 (   15)
  link_NAG-ASN         : angle       1.69992 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 208
  time to evaluate  : 0.515 
Fit side-chains
REVERT: A  267 SER cc_start: 0.7953 (OUTLIER) cc_final: 0.7238 (p)
REVERT: J    2 ILE cc_start: 0.6718 (mt) cc_final: 0.6517 (mt)
REVERT: J   63 PHE cc_start: 0.7422 (m-80) cc_final: 0.6859 (m-80)
REVERT: J  101 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6702 (mm110)
REVERT: G    3 GLN cc_start: 0.7845 (pm20) cc_final: 0.7629 (pm20)
REVERT: G   31 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7853 (mtt-85)
REVERT: G   38 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7189 (mtm-85)
REVERT: G   64 PHE cc_start: 0.7680 (m-80) cc_final: 0.7387 (m-80)
REVERT: G   65 GLN cc_start: 0.8383 (tp40) cc_final: 0.8001 (mm-40)
REVERT: G   81 MET cc_start: 0.8291 (tmm) cc_final: 0.8032 (tmm)
REVERT: G  106 ARG cc_start: 0.8052 (mtp-110) cc_final: 0.7840 (ttm110)
REVERT: G  111 GLU cc_start: 0.8518 (pp20) cc_final: 0.8164 (pp20)
REVERT: G  114 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8029 (ptmt)
REVERT: G  120 MET cc_start: 0.8455 (mpp) cc_final: 0.7865 (mpp)
REVERT: B   65 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8703 (p)
REVERT: K   37 TYR cc_start: 0.7594 (m-80) cc_final: 0.6869 (m-80)
REVERT: E  587 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7493 (ttp-170)
REVERT: H   81 MET cc_start: 0.7796 (tmm) cc_final: 0.7591 (tmm)
REVERT: H   86 LEU cc_start: 0.7039 (mt) cc_final: 0.6780 (mp)
REVERT: H  114 LYS cc_start: 0.8501 (ttpt) cc_final: 0.7954 (ptpt)
REVERT: L   63 PHE cc_start: 0.7574 (m-80) cc_final: 0.7125 (m-80)
REVERT: I   65 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8589 (tp40)
REVERT: I   82 GLU cc_start: 0.7473 (pp20) cc_final: 0.7212 (pp20)
REVERT: I   86 LEU cc_start: 0.6929 (mt) cc_final: 0.6719 (mp)
REVERT: I  119 TYR cc_start: 0.8642 (p90) cc_final: 0.8303 (p90)
  outliers start: 43
  outliers final: 32
  residues processed: 238
  average time/residue: 0.1148
  time to fit residues: 39.4387
Evaluate side-chains
  237 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 201
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain J residue   22 SER
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   73 THR
Chi-restraints excluded: chain J residue  101 GLN
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  581 THR
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   52 ILE
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain G residue   60 TYR
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain E residue  520 THR
Chi-restraints excluded: chain E residue  581 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  274 ILE
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain I residue   60 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    9.9990
   chunk 131 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 156 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
H  59 ASN
C  39 HIS
C  44 GLN
L  27 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.086133 restraints weight = 22425.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.088451 restraints weight = 14670.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.089926 restraints weight = 11460.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.090754 restraints weight = 9894.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.091281 restraints weight = 9089.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13929  Z= 0.229
  Angle     :  0.666   8.129  18966  Z= 0.330
  Chirality :  0.046   0.155   2157
  Planarity :  0.004   0.041   2385
  Dihedral  :  6.097  51.860   2457
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.12 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 11.79 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.21), residues: 1665
  helix:  1.60 (0.40), residues: 177
  sheet:  0.12 (0.22), residues: 600
  loop : -0.18 (0.21), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 596 
 TYR   0.021   0.002   TYR J  50 
 PHE   0.022   0.002   PHE E 592 
 TRP   0.011   0.001   TRP I  47 
 HIS   0.005   0.002   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 (13884)
  covalent geometry    : angle       0.65147 (18846)
  SS BOND              : bond        0.00408 (   15)
  SS BOND              : angle       0.61308 (   30)
  hydrogen bonds       : bond        0.04421 (  513)
  hydrogen bonds       : angle       4.76600 ( 1296)
  link_ALPHA1-3        : bond        0.00997 (    3)
  link_ALPHA1-3        : angle       2.25928 (    9)
  link_ALPHA1-6        : bond        0.00926 (    3)
  link_ALPHA1-6        : angle       1.07410 (    9)
  link_BETA1-4         : bond        0.00566 (    9)
  link_BETA1-4         : angle       2.85841 (   27)
  link_NAG-ASN         : bond        0.00126 (   15)
  link_NAG-ASN         : angle       1.59668 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 203
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  267 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7279 (p)
REVERT: J   37 TYR cc_start: 0.7766 (m-10) cc_final: 0.6947 (m-10)
REVERT: J   63 PHE cc_start: 0.7440 (m-80) cc_final: 0.6862 (m-80)
REVERT: G    3 GLN cc_start: 0.7851 (pm20) cc_final: 0.7623 (pm20)
REVERT: G   38 ARG cc_start: 0.7573 (mtp-110) cc_final: 0.7110 (mtm-85)
REVERT: G   64 PHE cc_start: 0.7728 (m-80) cc_final: 0.7525 (m-80)
REVERT: G   65 GLN cc_start: 0.8360 (tp40) cc_final: 0.8117 (mm-40)
REVERT: G   81 MET cc_start: 0.8392 (tmm) cc_final: 0.8125 (tmm)
REVERT: G  111 GLU cc_start: 0.8465 (pp20) cc_final: 0.8125 (pp20)
REVERT: G  114 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8081 (ptmt)
REVERT: G  120 MET cc_start: 0.8436 (mpp) cc_final: 0.7950 (mpp)
REVERT: E  587 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7372 (ttp-170)
REVERT: H   81 MET cc_start: 0.7984 (tmm) cc_final: 0.7687 (tmm)
REVERT: H   86 LEU cc_start: 0.7070 (mt) cc_final: 0.6841 (mp)
REVERT: L   37 TYR cc_start: 0.7811 (m-80) cc_final: 0.7518 (m-10)
REVERT: L   63 PHE cc_start: 0.7515 (m-80) cc_final: 0.7115 (m-80)
REVERT: L   84 PHE cc_start: 0.6930 (m-80) cc_final: 0.6675 (m-80)
REVERT: I  119 TYR cc_start: 0.8713 (p90) cc_final: 0.8376 (p90)
  outliers start: 53
  outliers final: 37
  residues processed: 235
  average time/residue: 0.1146
  time to fit residues: 38.8789
Evaluate side-chains
  235 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 196
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   73 THR
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  581 THR
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   60 TYR
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain K residue   29 VAL
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain E residue  520 THR
Chi-restraints excluded: chain E residue  581 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue  109 PHE
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  274 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain F residue  581 THR
Chi-restraints excluded: chain I residue   60 TYR
Chi-restraints excluded: chain I residue  109 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 84 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 27 optimal weight:   20.0000
   chunk 161 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 129 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 128 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
K  27 GLN
C  39 HIS
C  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.090651 restraints weight = 22539.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.089611 restraints weight = 20506.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.090693 restraints weight = 16976.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.090726 restraints weight = 14734.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.090846 restraints weight = 14003.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.5275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13929  Z= 0.224
  Angle     :  0.671  10.417  18966  Z= 0.333
  Chirality :  0.046   0.147   2157
  Planarity :  0.004   0.038   2385
  Dihedral  :  6.144  53.683   2457
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.54 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 12.36 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.21), residues: 1665
  helix:  1.53 (0.40), residues: 177
  sheet:  0.09 (0.22), residues: 603
  loop : -0.24 (0.21), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F 596 
 TYR   0.021   0.002   TYR J  50 
 PHE   0.021   0.002   PHE E 592 
 TRP   0.012   0.001   TRP I  47 
 HIS   0.004   0.002   HIS F 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (13884)
  covalent geometry    : angle       0.65959 (18846)
  SS BOND              : bond        0.00422 (   15)
  SS BOND              : angle       0.62970 (   30)
  hydrogen bonds       : bond        0.04306 (  513)
  hydrogen bonds       : angle       4.78531 ( 1296)
  link_ALPHA1-3        : bond        0.00968 (    3)
  link_ALPHA1-3        : angle       1.96800 (    9)
  link_ALPHA1-6        : bond        0.00926 (    3)
  link_ALPHA1-6        : angle       1.13437 (    9)
  link_BETA1-4         : bond        0.00524 (    9)
  link_BETA1-4         : angle       2.57437 (   27)
  link_NAG-ASN         : bond        0.00120 (   15)
  link_NAG-ASN         : angle       1.52994 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 206
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  267 SER cc_start: 0.8161 (OUTLIER) cc_final: 0.7298 (p)
REVERT: J   63 PHE cc_start: 0.7398 (m-80) cc_final: 0.6932 (m-80)
REVERT: G    3 GLN cc_start: 0.7906 (pm20) cc_final: 0.7675 (pm20)
REVERT: G   36 TRP cc_start: 0.8006 (m100) cc_final: 0.7640 (m100)
REVERT: G   38 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7175 (mtm-85)
REVERT: G   95 PHE cc_start: 0.6108 (m-80) cc_final: 0.5742 (m-80)
REVERT: G  111 GLU cc_start: 0.8472 (pp20) cc_final: 0.8147 (pp20)
REVERT: G  120 MET cc_start: 0.8431 (mpp) cc_final: 0.8007 (mpp)
REVERT: B   65 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8733 (p)
REVERT: K   37 TYR cc_start: 0.7820 (m-10) cc_final: 0.7598 (m-10)
REVERT: E  587 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7467 (ttp-170)
REVERT: L   37 TYR cc_start: 0.7875 (m-80) cc_final: 0.7602 (m-10)
REVERT: L   63 PHE cc_start: 0.7475 (m-80) cc_final: 0.7165 (m-80)
REVERT: L   84 PHE cc_start: 0.7000 (m-80) cc_final: 0.6737 (m-80)
REVERT: I   38 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7790 (mtm110)
REVERT: I   46 GLU cc_start: 0.7353 (pm20) cc_final: 0.7128 (pm20)
REVERT: I   48 MET cc_start: 0.7482 (ptm) cc_final: 0.7213 (ptm)
REVERT: I  119 TYR cc_start: 0.8754 (p90) cc_final: 0.8412 (p90)
  outliers start: 45
  outliers final: 36
  residues processed: 231
  average time/residue: 0.1149
  time to fit residues: 38.5814
Evaluate side-chains
  238 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 199
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   73 THR
Chi-restraints excluded: chain D residue  542 ILE
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  581 THR
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   60 TYR
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain K residue   29 VAL
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue   73 THR
Chi-restraints excluded: chain E residue  520 THR
Chi-restraints excluded: chain E residue  581 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue  109 PHE
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  274 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain F residue  581 THR
Chi-restraints excluded: chain I residue   60 TYR
Chi-restraints excluded: chain I residue  109 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 151 optimal weight:    6.9990
   chunk 101 optimal weight:    9.9990
   chunk 95 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0170
   chunk 110 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0822

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

Flipped N/Q/H residues before XYZ refinement:
L  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.140421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.091965 restraints weight = 22424.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.090714 restraints weight = 16345.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.090654 restraints weight = 13880.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.090767 restraints weight = 12993.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.090946 restraints weight = 12420.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.5394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13929  Z= 0.152
  Angle     :  0.633   9.677  18966  Z= 0.313
  Chirality :  0.044   0.153   2157
  Planarity :  0.004   0.041   2385
  Dihedral  :  5.897  50.509   2457
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.94 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 12.71 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.21), residues: 1665
  helix:  1.76 (0.40), residues: 177
  sheet:  0.13 (0.22), residues: 603
  loop : -0.17 (0.21), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K  78 
 TYR   0.023   0.001   TYR J  50 
 PHE   0.020   0.001   PHE E 592 
 TRP   0.010   0.001   TRP I  47 
 HIS   0.003   0.001   HIS F 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (13884)
  covalent geometry    : angle       0.62182 (18846)
  SS BOND              : bond        0.00381 (   15)
  SS BOND              : angle       0.61121 (   30)
  hydrogen bonds       : bond        0.03906 (  513)
  hydrogen bonds       : angle       4.65826 ( 1296)
  link_ALPHA1-3        : bond        0.01090 (    3)
  link_ALPHA1-3        : angle       1.63584 (    9)
  link_ALPHA1-6        : bond        0.00888 (    3)
  link_ALPHA1-6        : angle       1.27523 (    9)
  link_BETA1-4         : bond        0.00531 (    9)
  link_BETA1-4         : angle       2.39094 (   27)
  link_NAG-ASN         : bond        0.00106 (   15)
  link_NAG-ASN         : angle       1.48626 (   45)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 203
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  174 THR cc_start: 0.9285 (m) cc_final: 0.8994 (p)
REVERT: A  267 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7201 (p)
REVERT: J   37 TYR cc_start: 0.7647 (m-10) cc_final: 0.6940 (m-10)
REVERT: J   63 PHE cc_start: 0.7406 (m-80) cc_final: 0.6876 (m-80)
REVERT: G   38 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.7217 (mtm-85)
REVERT: G  106 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7442 (mmm-85)
REVERT: G  111 GLU cc_start: 0.8490 (pp20) cc_final: 0.8102 (pp20)
REVERT: G  120 MET cc_start: 0.8398 (mpp) cc_final: 0.7923 (mpp)
REVERT: B   65 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8703 (p)
REVERT: E  587 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7449 (ttp-170)
REVERT: H   48 MET cc_start: 0.7744 (ptm) cc_final: 0.7517 (ptp)
REVERT: H   83 LEU cc_start: 0.6614 (tp) cc_final: 0.6407 (tt)
REVERT: L   37 TYR cc_start: 0.7705 (m-80) cc_final: 0.6955 (m-10)
REVERT: L   84 PHE cc_start: 0.6823 (m-80) cc_final: 0.6568 (m-80)
REVERT: I   38 ARG cc_start: 0.8228 (mtm180) cc_final: 0.7749 (mtm110)
REVERT: I   48 MET cc_start: 0.7513 (ptm) cc_final: 0.7271 (ptm)
REVERT: I  119 TYR cc_start: 0.8773 (p90) cc_final: 0.8414 (p90)
  outliers start: 40
  outliers final: 36
  residues processed: 224
  average time/residue: 0.1119
  time to fit residues: 36.5591
Evaluate side-chains
  233 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 194
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   73 THR
Chi-restraints excluded: chain D residue  548 MET
Chi-restraints excluded: chain D residue  581 THR
Chi-restraints excluded: chain G residue   48 MET
Chi-restraints excluded: chain G residue   60 TYR
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain K residue   29 VAL
Chi-restraints excluded: chain K residue   34 LEU
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue   73 THR
Chi-restraints excluded: chain E residue  520 THR
Chi-restraints excluded: chain E residue  587 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue  109 PHE
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  274 ILE
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain F residue  581 THR
Chi-restraints excluded: chain I residue   60 TYR
Chi-restraints excluded: chain I residue  109 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 132 optimal weight:    5.9990
   chunk 156 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  39 HIS
C  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.138375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.088748 restraints weight = 22689.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.088915 restraints weight = 17106.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.089102 restraints weight = 14613.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.089400 restraints weight = 13065.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.089441 restraints weight = 12590.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.5497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  13929  Z= 0.229
  Angle     :  0.693   9.415  18966  Z= 0.342
  Chirality :  0.046   0.147   2157
  Planarity :  0.004   0.043   2385
  Dihedral  :  5.976  51.961   2457
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.08 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 12.78 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.21), residues: 1665
  helix:  1.56 (0.40), residues: 177
  sheet:  0.11 (0.22), residues: 597
  loop : -0.25 (0.21), residues: 891

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K  78 
 TYR   0.020   0.002   TYR J  50 
 PHE   0.020   0.002   PHE E 592 
 TRP   0.011   0.001   TRP I  47 
 HIS   0.005   0.002   HIS F 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 (13884)
  covalent geometry    : angle       0.68233 (18846)
  SS BOND              : bond        0.00401 (   15)
  SS BOND              : angle       0.60865 (   30)
  hydrogen bonds       : bond        0.04401 (  513)
  hydrogen bonds       : angle       4.78725 ( 1296)
  link_ALPHA1-3        : bond        0.00991 (    3)
  link_ALPHA1-3        : angle       2.08427 (    9)
  link_ALPHA1-6        : bond        0.00938 (    3)
  link_ALPHA1-6        : angle       1.11381 (    9)
  link_BETA1-4         : bond        0.00504 (    9)
  link_BETA1-4         : angle       2.60666 (   27)
  link_NAG-ASN         : bond        0.00169 (   15)
  link_NAG-ASN         : angle       1.47671 (   45)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2072.42 seconds
wall clock time: 36 minutes 37.89 seconds (2197.89 seconds total)