Starting phenix.real_space_refine
on Wed Mar  4 21:29:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yzo_14391/03_2026/7yzo_14391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yzo_14391/03_2026/7yzo_14391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yzo_14391/03_2026/7yzo_14391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yzo_14391/03_2026/7yzo_14391.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yzo_14391/03_2026/7yzo_14391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yzo_14391/03_2026/7yzo_14391.cif"
  }
  resolution = 3.4
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4287 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      66      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    8019      2.51       5
     N    2303      2.21       5
     O    2640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13068
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 2916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2916
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 7, 'TRANS': 366}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2914
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 7, 'TRANS': 366}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3010
          Classifications: {'peptide': 381}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 360}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2897
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 20, 'TRANS': 347}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 638
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "F"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 633
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 22
    residue:
      pdb=" N   GLY A 284 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY A 284 " occ=0.50
    residue:
      pdb=" N   ALA A 287 " occ=0.60
      ... (3 atoms not shown)
      pdb=" CB  ALA A 287 " occ=0.60
    residue:
      pdb=" N   THR A 290 " occ=0.70
      ... (5 atoms not shown)
      pdb=" CG2 THR A 290 " occ=0.70
    residue:
      pdb=" N   ALA A 291 " occ=0.60
      ... (3 atoms not shown)
      pdb=" CB  ALA A 291 " occ=0.60
    residue:
      pdb=" N   GLN A 292 " occ=0.70
      ... (7 atoms not shown)
      pdb=" NE2 GLN A 292 " occ=0.70
    residue:
      pdb=" N   LEU A 293 " occ=0.80
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 293 " occ=0.80
    residue:
      pdb=" N   PRO A 303 " occ=0.61
      ... (5 atoms not shown)
      pdb=" CD  PRO A 303 " occ=0.61
    residue:
      pdb=" N   PRO A 304 " occ=0.68
      ... (5 atoms not shown)
      pdb=" CD  PRO A 304 " occ=0.68
    residue:
      pdb=" N   VAL A 305 " occ=0.88
      ... (5 atoms not shown)
      pdb=" CG2 VAL A 305 " occ=0.88
    residue:
      pdb=" N   TRP A 306 " occ=0.97
      ... (12 atoms not shown)
      pdb=" CH2 TRP A 306 " occ=0.97
    residue:
      pdb=" N   LEU A 307 " occ=0.87
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 307 " occ=0.87
    residue:
      pdb=" N   ILE A 309 " occ=0.89
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 309 " occ=0.89
    ... (remaining 10 not shown)
  Time building chain proxies: 2.77, per 1000 atoms: 0.21
  Number of scatterers: 13068
  At special positions: 0
  Unit cell: (108.018, 98.487, 134.493, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      4     24.99
     S      34     16.00
     P      66     15.00
     Mg      2     11.99
     O    2640      8.00
     N    2303      7.00
     C    8019      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 470.1 milliseconds
  

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2812

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 17 sheets defined
      43.4% alpha, 17.9% beta
      31 base pairs and 54 stacking pairs defined.
    Time for finding SS restraints: 1.92
  Creating SS restraints...
    Processing helix  chain 'C' and resid 42 through 56
      removed outlier: 3.831A  pdb=" N   LEU C  47 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE C  50 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 104
    Processing helix  chain 'C' and resid 128 through 141
    Processing helix  chain 'C' and resid 143 through 151
      removed outlier: 4.345A  pdb=" N   ARG C 149 " --> pdb=" O   GLY C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 164
    Processing helix  chain 'C' and resid 165 through 178
    Processing helix  chain 'C' and resid 180 through 201
    Processing helix  chain 'C' and resid 876 through 887
    Processing helix  chain 'C' and resid 889 through 891
      No H-bonds generated for 'chain 'C' and resid 889 through 891'
    Processing helix  chain 'C' and resid 892 through 900
    Processing helix  chain 'C' and resid 900 through 919
      removed outlier: 3.591A  pdb=" N   LEU C 910 " --> pdb=" O   ASN C 906 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ARG C 917 " --> pdb=" O   GLN C 913 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 947 through 951
      removed outlier: 3.544A  pdb=" N   THR C 950 " --> pdb=" O   ASP C 947 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU C 951 " --> pdb=" O   THR C 948 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 947 through 951'
    Processing helix  chain 'C' and resid 952 through 970
    Processing helix  chain 'C' and resid 985 through 989
      removed outlier: 3.801A  pdb=" N   THR C 988 " --> pdb=" O   GLY C 985 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 990 through 1006
      removed outlier: 3.615A  pdb=" N   ASP C 995 " --> pdb=" O   SER C 991 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1017 through 1024
    Processing helix  chain 'C' and resid 1042 through 1046
    Processing helix  chain 'D' and resid 42 through 56
      removed outlier: 3.865A  pdb=" N   LEU D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 104
    Processing helix  chain 'D' and resid 128 through 141
    Processing helix  chain 'D' and resid 143 through 151
      removed outlier: 4.263A  pdb=" N   ARG D 149 " --> pdb=" O   GLY D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 178
      removed outlier: 3.741A  pdb=" N   LEU D 172 " --> pdb=" O   GLU D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 199
      removed outlier: 3.634A  pdb=" N   GLN D 184 " --> pdb=" O   GLU D 180 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU D 199 " --> pdb=" O   SER D 195 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 875 through 887
    Processing helix  chain 'D' and resid 889 through 891
      No H-bonds generated for 'chain 'D' and resid 889 through 891'
    Processing helix  chain 'D' and resid 892 through 900
      removed outlier: 3.665A  pdb=" N   ARG D 896 " --> pdb=" O   GLY D 892 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 900 through 919
      removed outlier: 4.507A  pdb=" N   ARG D 917 " --> pdb=" O   GLN D 913 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU D 918 " --> pdb=" O   GLN D 914 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 949 through 951
      No H-bonds generated for 'chain 'D' and resid 949 through 951'
    Processing helix  chain 'D' and resid 952 through 971
      removed outlier: 4.052A  pdb=" N   VAL D 971 " --> pdb=" O   LEU D 967 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 990 through 1006
      removed outlier: 4.528A  pdb=" N   THR D 996 " --> pdb=" O   GLU D 992 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1018 through 1024
      removed outlier: 4.107A  pdb=" N   GLU D1022 " --> pdb=" O   GLU D1018 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG D1023 " --> pdb=" O   ALA D1019 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1043 through 1046
    Processing helix  chain 'A' and resid 20 through 39
    Processing helix  chain 'A' and resid 56 through 70
    Processing helix  chain 'A' and resid 86 through 93
      removed outlier: 4.365A  pdb=" N   SER A  93 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 99
      removed outlier: 3.836A  pdb=" N   PHE A  99 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
      removed outlier: 3.650A  pdb=" N   ILE A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 173
      removed outlier: 3.598A  pdb=" N   GLN A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 212
    Processing helix  chain 'A' and resid 245 through 249
    Processing helix  chain 'A' and resid 285 through 294
    Processing helix  chain 'A' and resid 295 through 297
      No H-bonds generated for 'chain 'A' and resid 295 through 297'
    Processing helix  chain 'A' and resid 319 through 328
      removed outlier: 3.527A  pdb=" N   LYS A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 372
      removed outlier: 3.582A  pdb=" N   LEU A 372 " --> pdb=" O   ARG A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 394
      removed outlier: 3.888A  pdb=" N   GLN A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   ARG A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 39
      removed outlier: 3.750A  pdb=" N   TRP B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 74
      removed outlier: 3.573A  pdb=" N   ARG B  60 " --> pdb=" O   PRO B  56 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN B  71 " --> pdb=" O   VAL B  67 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLN B  72 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR B  73 " --> pdb=" O   ASN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 99
      removed outlier: 4.084A  pdb=" N   PHE B  99 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 137
    Processing helix  chain 'B' and resid 154 through 173
    Processing helix  chain 'B' and resid 208 through 212
      removed outlier: 3.744A  pdb=" N   PHE B 212 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 249
      removed outlier: 3.600A  pdb=" N   GLU B 248 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   CYS B 249 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 245 through 249'
    Processing helix  chain 'B' and resid 285 through 293
      removed outlier: 3.518A  pdb=" N   ALA B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 297
    Processing helix  chain 'B' and resid 316 through 329
      removed outlier: 4.583A  pdb=" N   ARG B 322 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 323 " --> pdb=" O   ASP B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 373
      removed outlier: 3.841A  pdb=" N   LEU B 372 " --> pdb=" O   ARG B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 395
      removed outlier: 4.529A  pdb=" N   ARG B 382 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 21
      removed outlier: 6.561A  pdb=" N   GLY C  16 " --> pdb=" O   ASN C  10 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLU C  84 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LEU C   6 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   GLU C  82 " --> pdb=" O   LEU C   6 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU C  80 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   ASN C  10 " --> pdb=" O   GLU C  78 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLU C  78 " --> pdb=" O   ASN C  10 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU C 116 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 153
      removed outlier: 6.522A  pdb=" N   LEU C 980 " --> pdb=" O   GLY C1012 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ILE C1014 " --> pdb=" O   LEU C 980 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LEU C 982 " --> pdb=" O   ILE C1014 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 922 through 926
    Processing sheet with id=AA4, first strand: chain 'C' and resid 1031 through 1032
    Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 21
      removed outlier: 6.610A  pdb=" N   GLY D  16 " --> pdb=" O   ASN D  10 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ILE D   3 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLU D  86 " --> pdb=" O   ILE D   3 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D  78 " (cutoff:3.500A)
      removed outlier: 11.406A  pdb=" N   GLU D  78 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU D 116 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 152 through 153
      removed outlier: 6.132A  pdb=" N   PHE D  33 " --> pdb=" O   VAL D1013 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ALA D  34 " --> pdb=" O   ILE D1028 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   VAL D1030 " --> pdb=" O   ALA D  34 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR D  36 " --> pdb=" O   VAL D1030 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   LYS D1032 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 924 through 926
    Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105
      removed outlier: 6.429A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   VAL A 105 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   VAL A  79 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ILE A  43 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   LEU A  80 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL A  45 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ARG A   2 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ILE A  44 " --> pdb=" O   ARG A   2 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LEU A   4 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   ALA A  46 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   THR A   6 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL A 255 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   ASN A 270 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LEU A 257 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   VAL A 268 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   THR A 259 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 14 through 15
    Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 116
    Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 182
      removed outlier: 6.827A  pdb=" N   ALA A 181 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   VAL A 235 " --> pdb=" O   ILE A 229 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 229 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 279 through 284
      removed outlier: 6.754A  pdb=" N   VAL A 305 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   VAL A 335 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LEU A 307 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.580A  pdb=" N   LEU B  77 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   VAL B 105 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   VAL B  79 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE B  43 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   LEU B  80 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL B  45 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ARG B   2 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ILE B  44 " --> pdb=" O   ARG B   2 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU B   4 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ALA B  46 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   THR B   6 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   VAL B 255 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ASN B 270 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU B 257 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   VAL B 268 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   THR B 259 " --> pdb=" O   GLU B 266 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 14 through 15
    Processing sheet with id=AB6, first strand: chain 'B' and resid 114 through 116
    Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 183
      removed outlier: 6.518A  pdb=" N   ALA B 181 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ILE B 218 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 279 through 284
      removed outlier: 3.587A  pdb=" N   GLY B 284 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
      removed outlier: 9.377A  pdb=" N   VAL B 305 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 8.737A  pdb=" N   LEU B 337 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LEU B 307 " --> pdb=" O   LEU B 337 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   ARG B 339 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ILE B 309 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)

    519 hydrogen bonds defined for protein.
    1470 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      80 hydrogen bonds
      160 hydrogen bond angles
      0 basepair planarities
      31 basepair parallelities
      54 stacking parallelities
  Total time for adding SS restraints: 2.45

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3897
        1.34 -     1.45: 2323
        1.45 -     1.57: 7028
        1.57 -     1.69: 128
        1.69 -     1.81: 52
  Bond restraints: 13428
  Sorted by residual:
  bond pdb=" C4  ADP D1101 "
       pdb=" C5  ADP D1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" C4  ADP C1101 "
       pdb=" C5  ADP C1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" C5  ADP D1101 "
       pdb=" C6  ADP D1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" C5  ADP C1101 "
       pdb=" C6  ADP C1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.408  0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" N   ILE A 223 "
       pdb=" CA  ILE A 223 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.17e-02 7.31e+03 1.01e+01
  ... (remaining 13423 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 18281
        2.69 -     5.37: 172
        5.37 -     8.06: 18
        8.06 -    10.75: 6
       10.75 -    13.44: 4
  Bond angle restraints: 18481
  Sorted by residual:
  angle pdb=" C   ASN D  12 "
        pdb=" CA  ASN D  12 "
        pdb=" CB  ASN D  12 "
      ideal   model   delta    sigma   weight residual
     116.54  109.97    6.57 1.15e+00 7.56e-01 3.26e+01
  angle pdb=" CA  GLY A 221 "
        pdb=" C   GLY A 221 "
        pdb=" O   GLY A 221 "
      ideal   model   delta    sigma   weight residual
     121.61  115.82    5.79 1.05e+00 9.07e-01 3.04e+01
  angle pdb=" CA  GLY B 221 "
        pdb=" C   GLY B 221 "
        pdb=" O   GLY B 221 "
      ideal   model   delta    sigma   weight residual
     121.78  117.04    4.74 9.10e-01 1.21e+00 2.71e+01
  angle pdb=" PA  ADP C1101 "
        pdb=" O3A ADP C1101 "
        pdb=" PB  ADP C1101 "
      ideal   model   delta    sigma   weight residual
     120.50  133.94  -13.44 3.00e+00 1.11e-01 2.01e+01
  angle pdb=" PA  ADP D1101 "
        pdb=" O3A ADP D1101 "
        pdb=" PB  ADP D1101 "
      ideal   model   delta    sigma   weight residual
     120.50  133.52  -13.02 3.00e+00 1.11e-01 1.88e+01
  ... (remaining 18476 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.22: 7212
       25.22 -    50.44: 568
       50.44 -    75.66: 115
       75.66 -   100.88: 10
      100.88 -   126.09: 3
  Dihedral angle restraints: 7908
    sinusoidal: 3573
      harmonic: 4335
  Sorted by residual:
  dihedral pdb=" C5' ADP D1101 "
           pdb=" O5' ADP D1101 "
           pdb=" PA  ADP D1101 "
           pdb=" O2A ADP D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   66.10 -126.09     1      2.00e+01 2.50e-03 3.81e+01
  dihedral pdb=" O2A ADP D1101 "
           pdb=" O3A ADP D1101 "
           pdb=" PA  ADP D1101 "
           pdb=" PB  ADP D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   65.40 -125.40     1      2.00e+01 2.50e-03 3.79e+01
  dihedral pdb=" O1B ADP D1101 "
           pdb=" O3A ADP D1101 "
           pdb=" PB  ADP D1101 "
           pdb=" PA  ADP D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   57.79 -117.80     1      2.00e+01 2.50e-03 3.52e+01
  ... (remaining 7905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1827
       0.058 -    0.115: 272
       0.115 -    0.173: 23
       0.173 -    0.231: 3
       0.231 -    0.288: 4
  Chirality restraints: 2129
  Sorted by residual:
  chirality pdb=" CA  TYR A 237 "
            pdb=" N   TYR A 237 "
            pdb=" C   TYR A 237 "
            pdb=" CB  TYR A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" C3' ADP C1101 "
            pdb=" C2' ADP C1101 "
            pdb=" C4' ADP C1101 "
            pdb=" O3' ADP C1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.76    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C3' ADP D1101 "
            pdb=" C2' ADP D1101 "
            pdb=" C4' ADP D1101 "
            pdb=" O3' ADP D1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.75    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 2126 not shown)

  Planarity restraints: 2167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  58 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.68e+00
        pdb=" N   PRO D  59 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D  59 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D  59 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  47 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.91e+00
        pdb=" C   GLY A  47 "    0.024 2.00e-02 2.50e+03
        pdb=" O   GLY A  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP A  48 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  41 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.76e+00
        pdb=" C   ALA D  41 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ALA D  41 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY D  42 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2164 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 12
        2.18 -     2.86: 4382
        2.86 -     3.54: 18347
        3.54 -     4.22: 30527
        4.22 -     4.90: 52538
  Nonbonded interactions: 105806
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  48 "
            pdb="MN    MN A 501 "
     model   vdw
     1.498 2.320
  nonbonded pdb=" OD2 ASP A  48 "
            pdb="MN    MN A 502 "
     model   vdw
     1.600 2.320
  nonbonded pdb=" OD1 ASN B  83 "
            pdb="MN    MN B 502 "
     model   vdw
     1.806 2.320
  nonbonded pdb=" O3B ADP C1101 "
            pdb="MG    MG C1102 "
     model   vdw
     1.816 2.170
  nonbonded pdb=" OD2 ASP B  48 "
            pdb="MN    MN B 502 "
     model   vdw
     1.931 2.320
  ... (remaining 105801 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 137 or resid 153 through 343 or resid 356 throug \ 
h 502))
  selection = (chain 'B' and (resid 1 through 189 or resid 204 through 502))
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 200 or resid 875 through 1102))
  selection = (chain 'D' and (resid 1 through 200 or resid 875 through 1102))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.160
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
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      :  0.004   0.109  13428  Z= 0.244
  Angle     :  0.703  13.436  18481  Z= 0.399
  Chirality :  0.042   0.288   2129
  Planarity :  0.003   0.048   2167
  Dihedral  : 17.730 126.095   5096
  Min Nonbonded Distance : 1.498

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.31 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.79 (0.23), residues: 1479
  helix:  1.66 (0.23), residues: 547
  sheet:  0.38 (0.34), residues: 231
  loop : -0.29 (0.25), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 976 
 TYR   0.014   0.001   TYR C 882 
 PHE   0.014   0.001   PHE C 895 
 TRP   0.010   0.001   TRP A   9 
 HIS   0.009   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (13428)
  covalent geometry    : angle       0.70273 (18481)
  hydrogen bonds       : bond        0.15164 (  599)
  hydrogen bonds       : angle       5.84475 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.449 
Fit side-chains
REVERT: C  179 THR cc_start: 0.7860 (p) cc_final: 0.7607 (p)
REVERT: A  185 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1025
  time to fit residues: 21.4968
Evaluate side-chains
  100 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0010
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.0790

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

Flipped N/Q/H residues before XYZ refinement:
C1005 ASN
A 110 HIS
A 224 HIS
A 318 HIS
A 392 HIS
B  84 GLN
B 222 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.098566 restraints weight = 19591.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.19
r_work: 0.3061 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13428  Z= 0.188
  Angle     :  0.604   8.071  18481  Z= 0.315
  Chirality :  0.042   0.182   2129
  Planarity :  0.004   0.052   2167
  Dihedral  : 18.884 135.888   2299
  Min Nonbonded Distance : 1.834

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.30 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.60 (0.23), residues: 1479
  helix:  1.57 (0.23), residues: 548
  sheet: -0.08 (0.32), residues: 260
  loop : -0.31 (0.26), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 149 
 TYR   0.013   0.002   TYR B 237 
 PHE   0.017   0.001   PHE C  85 
 TRP   0.008   0.001   TRP B   9 
 HIS   0.012   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (13428)
  covalent geometry    : angle       0.60414 (18481)
  hydrogen bonds       : bond        0.04362 (  599)
  hydrogen bonds       : angle       4.78092 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.500 
Fit side-chains
REVERT: D   66 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8058 (tm-30)
REVERT: A  185 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8818 (pp)
REVERT: B  373 GLU cc_start: 0.7828 (tp30) cc_final: 0.7541 (tp30)
  outliers start: 14
  outliers final: 7
  residues processed: 122
  average time/residue: 0.1066
  time to fit residues: 19.2680
Evaluate side-chains
  107 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain C residue  983 ASP
Chi-restraints excluded: chain D residue   68 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  392 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0020
   chunk 129 optimal weight:    0.4980
   chunk 106 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 72 optimal weight:    0.2980
   chunk 145 optimal weight:    2.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
A 318 HIS
A 392 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.098760 restraints weight = 19916.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.27
r_work: 0.3045 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13428  Z= 0.141
  Angle     :  0.557   7.045  18481  Z= 0.292
  Chirality :  0.040   0.158   2129
  Planarity :  0.004   0.051   2167
  Dihedral  : 18.877 139.816   2299
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.20 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.63 (0.23), residues: 1479
  helix:  1.63 (0.23), residues: 548
  sheet: -0.07 (0.33), residues: 261
  loop : -0.33 (0.26), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 149 
 TYR   0.013   0.001   TYR B 237 
 PHE   0.013   0.001   PHE C  85 
 TRP   0.006   0.001   TRP B 296 
 HIS   0.014   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (13428)
  covalent geometry    : angle       0.55663 (18481)
  hydrogen bonds       : bond        0.03815 (  599)
  hydrogen bonds       : angle       4.50494 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   51 ASP cc_start: 0.8626 (t0) cc_final: 0.8360 (t0)
REVERT: A  185 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8841 (pp)
  outliers start: 16
  outliers final: 10
  residues processed: 118
  average time/residue: 0.1047
  time to fit residues: 18.4738
Evaluate side-chains
  111 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain C residue  983 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain B residue  205 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 148 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0670
   chunk 127 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.3724

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
A 318 HIS
A 392 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.124198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.094522 restraints weight = 20010.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.25
r_work: 0.3004 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13428  Z= 0.218
  Angle     :  0.613   7.288  18481  Z= 0.319
  Chirality :  0.042   0.165   2129
  Planarity :  0.004   0.050   2167
  Dihedral  : 19.103 132.101   2299
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.77 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.44 (0.23), residues: 1479
  helix:  1.52 (0.22), residues: 541
  sheet: -0.17 (0.33), residues: 254
  loop : -0.47 (0.25), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 976 
 TYR   0.014   0.002   TYR A  63 
 PHE   0.017   0.002   PHE C 147 
 TRP   0.008   0.001   TRP C  96 
 HIS   0.010   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (13428)
  covalent geometry    : angle       0.61290 (18481)
  hydrogen bonds       : bond        0.04191 (  599)
  hydrogen bonds       : angle       4.56389 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.426 
Fit side-chains
REVERT: D  905 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8363 (m-30)
REVERT: A  185 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9039 (pp)
REVERT: B  394 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6431 (mp)
  outliers start: 26
  outliers final: 17
  residues processed: 119
  average time/residue: 0.1013
  time to fit residues: 18.1593
Evaluate side-chains
  109 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  983 ASP
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue  905 ASP
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  394 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 126 optimal weight:    0.7980
   chunk 148 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 140 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.125146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.095192 restraints weight = 19947.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.27
r_work: 0.3014 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13428  Z= 0.178
  Angle     :  0.585   7.829  18481  Z= 0.303
  Chirality :  0.041   0.151   2129
  Planarity :  0.004   0.051   2167
  Dihedral  : 19.057 122.529   2299
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.27 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.46 (0.23), residues: 1479
  helix:  1.57 (0.23), residues: 541
  sheet: -0.23 (0.33), residues: 259
  loop : -0.45 (0.25), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 149 
 TYR   0.011   0.002   TYR B 237 
 PHE   0.014   0.001   PHE C  85 
 TRP   0.007   0.001   TRP C  96 
 HIS   0.014   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (13428)
  covalent geometry    : angle       0.58487 (18481)
  hydrogen bonds       : bond        0.03890 (  599)
  hydrogen bonds       : angle       4.46063 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.389 
Fit side-chains
REVERT: D  197 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7126 (tpt-90)
REVERT: A  185 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8984 (pp)
REVERT: B  394 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6378 (mp)
  outliers start: 26
  outliers final: 17
  residues processed: 124
  average time/residue: 0.1056
  time to fit residues: 19.5767
Evaluate side-chains
  111 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   68 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  394 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 131 optimal weight:    0.0050
   chunk 35 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 118 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5174

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
A 392 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.127430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.097300 restraints weight = 19875.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.31
r_work: 0.3055 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13428  Z= 0.123
  Angle     :  0.547   6.977  18481  Z= 0.284
  Chirality :  0.039   0.148   2129
  Planarity :  0.003   0.052   2167
  Dihedral  : 18.828 117.292   2299
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.68 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.65 (0.23), residues: 1479
  helix:  1.80 (0.23), residues: 541
  sheet: -0.16 (0.33), residues: 259
  loop : -0.39 (0.25), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 976 
 TYR   0.012   0.001   TYR B 237 
 PHE   0.014   0.001   PHE C  33 
 TRP   0.006   0.001   TRP C  96 
 HIS   0.012   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (13428)
  covalent geometry    : angle       0.54670 (18481)
  hydrogen bonds       : bond        0.03404 (  599)
  hydrogen bonds       : angle       4.25597 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.440 
Fit side-chains
REVERT: C  998 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8033 (mt)
REVERT: D  197 ARG cc_start: 0.7486 (tpp80) cc_final: 0.7042 (tpt-90)
REVERT: A   51 ASP cc_start: 0.8565 (t0) cc_final: 0.8343 (t0)
REVERT: A  185 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9020 (pp)
  outliers start: 24
  outliers final: 17
  residues processed: 129
  average time/residue: 0.0998
  time to fit residues: 19.2142
Evaluate side-chains
  121 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain C residue  998 LEU
Chi-restraints excluded: chain C residue 1043 SER
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   68 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  275 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 120 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 141 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 131 optimal weight:    0.0070
   chunk 134 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 HIS
A 392 HIS
B 211 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.126732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.096763 restraints weight = 19789.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.28
r_work: 0.3043 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13428  Z= 0.145
  Angle     :  0.575  15.415  18481  Z= 0.295
  Chirality :  0.040   0.160   2129
  Planarity :  0.003   0.051   2167
  Dihedral  : 18.821 117.555   2299
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.31 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.60 (0.23), residues: 1479
  helix:  1.71 (0.23), residues: 542
  sheet: -0.15 (0.33), residues: 259
  loop : -0.41 (0.25), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 976 
 TYR   0.011   0.001   TYR B 237 
 PHE   0.013   0.001   PHE C  33 
 TRP   0.006   0.001   TRP C  96 
 HIS   0.016   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13428)
  covalent geometry    : angle       0.57500 (18481)
  hydrogen bonds       : bond        0.03506 (  599)
  hydrogen bonds       : angle       4.27250 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.414 
Fit side-chains
REVERT: C  998 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8082 (mt)
REVERT: D  197 ARG cc_start: 0.7487 (tpp80) cc_final: 0.7043 (tpt-90)
REVERT: A   51 ASP cc_start: 0.8578 (t0) cc_final: 0.8342 (t0)
REVERT: A  185 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9027 (pp)
REVERT: A  347 ARG cc_start: 0.8149 (ptt-90) cc_final: 0.7822 (ptt90)
  outliers start: 26
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1062
  time to fit residues: 19.4619
Evaluate side-chains
  119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain C residue  998 LEU
Chi-restraints excluded: chain C residue 1043 SER
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   68 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  275 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 120 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 145 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.125362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.095283 restraints weight = 19756.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.28
r_work: 0.3015 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13428  Z= 0.184
  Angle     :  0.599  12.700  18481  Z= 0.308
  Chirality :  0.041   0.155   2129
  Planarity :  0.004   0.050   2167
  Dihedral  : 18.931 118.264   2299
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.84 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.49 (0.23), residues: 1479
  helix:  1.64 (0.23), residues: 543
  sheet: -0.23 (0.33), residues: 259
  loop : -0.47 (0.25), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 976 
 TYR   0.012   0.001   TYR C 182 
 PHE   0.015   0.001   PHE C  85 
 TRP   0.006   0.001   TRP C  96 
 HIS   0.011   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (13428)
  covalent geometry    : angle       0.59909 (18481)
  hydrogen bonds       : bond        0.03819 (  599)
  hydrogen bonds       : angle       4.34220 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: C  180 GLU cc_start: 0.8378 (mp0) cc_final: 0.8040 (mp0)
REVERT: C  998 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8023 (mt)
REVERT: D  197 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7178 (tpp80)
REVERT: A  185 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9110 (pp)
REVERT: A  347 ARG cc_start: 0.8185 (ptt-90) cc_final: 0.7852 (ptt90)
  outliers start: 31
  outliers final: 22
  residues processed: 124
  average time/residue: 0.1062
  time to fit residues: 19.4848
Evaluate side-chains
  119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain C residue  998 LEU
Chi-restraints excluded: chain C residue 1043 SER
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1010 THR
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  275 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 136 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   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 110 HIS
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.126423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.096662 restraints weight = 19868.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.15
r_work: 0.3062 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13428  Z= 0.145
  Angle     :  0.578  11.635  18481  Z= 0.297
  Chirality :  0.040   0.150   2129
  Planarity :  0.003   0.051   2167
  Dihedral  : 18.865 115.895   2299
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.38 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.56 (0.23), residues: 1479
  helix:  1.70 (0.23), residues: 543
  sheet: -0.19 (0.32), residues: 263
  loop : -0.45 (0.25), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 976 
 TYR   0.012   0.001   TYR B 237 
 PHE   0.013   0.001   PHE C  33 
 TRP   0.006   0.001   TRP C  96 
 HIS   0.020   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (13428)
  covalent geometry    : angle       0.57775 (18481)
  hydrogen bonds       : bond        0.03604 (  599)
  hydrogen bonds       : angle       4.28387 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.421 
Fit side-chains
REVERT: C  180 GLU cc_start: 0.8517 (mp0) cc_final: 0.8186 (mp0)
REVERT: C  927 LYS cc_start: 0.8352 (tppt) cc_final: 0.8084 (tttm)
REVERT: C  998 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8062 (mt)
REVERT: D  197 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7027 (tpt-90)
REVERT: A  185 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9098 (pp)
REVERT: A  347 ARG cc_start: 0.8388 (ptt-90) cc_final: 0.8068 (ptt90)
  outliers start: 23
  outliers final: 21
  residues processed: 117
  average time/residue: 0.1052
  time to fit residues: 18.1698
Evaluate side-chains
  119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain C residue  998 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   68 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 104 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.126521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096694 restraints weight = 19783.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.15
r_work: 0.3070 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13428  Z= 0.148
  Angle     :  0.577  10.862  18481  Z= 0.297
  Chirality :  0.040   0.149   2129
  Planarity :  0.003   0.051   2167
  Dihedral  : 18.829 114.740   2299
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.07 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.56 (0.23), residues: 1479
  helix:  1.72 (0.23), residues: 543
  sheet: -0.18 (0.33), residues: 263
  loop : -0.46 (0.25), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 976 
 TYR   0.012   0.001   TYR B 237 
 PHE   0.013   0.001   PHE C  33 
 TRP   0.007   0.001   TRP C  96 
 HIS   0.017   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (13428)
  covalent geometry    : angle       0.57683 (18481)
  hydrogen bonds       : bond        0.03577 (  599)
  hydrogen bonds       : angle       4.27039 ( 1630)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.369 
Fit side-chains
REVERT: C  180 GLU cc_start: 0.8507 (mp0) cc_final: 0.8181 (mp0)
REVERT: C  896 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7959 (ttm110)
REVERT: C  998 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8066 (mt)
REVERT: D  197 ARG cc_start: 0.7465 (tpp80) cc_final: 0.7040 (tpt-90)
REVERT: A  185 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9113 (pp)
REVERT: A  347 ARG cc_start: 0.8373 (ptt-90) cc_final: 0.8057 (ptt90)
  outliers start: 28
  outliers final: 24
  residues processed: 124
  average time/residue: 0.1062
  time to fit residues: 19.4346
Evaluate side-chains
  122 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  910 LEU
Chi-restraints excluded: chain C residue  998 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   68 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue 1010 THR
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 61 optimal weight:    0.2980
   chunk 153 optimal weight:    3.9990
   chunk 136 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0370
   chunk 7 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 148 optimal weight:    3.9990
   chunk 143 optimal weight:    5.9990
   chunk 116 optimal weight:    0.7980
   chunk 135 optimal weight:    3.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
A 164 HIS
A 392 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.128605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.098945 restraints weight = 19558.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.18
r_work: 0.3100 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13428  Z= 0.118
  Angle     :  0.549   9.575  18481  Z= 0.284
  Chirality :  0.039   0.148   2129
  Planarity :  0.003   0.052   2167
  Dihedral  : 18.574 108.925   2299
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.23 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.69 (0.23), residues: 1479
  helix:  1.77 (0.23), residues: 555
  sheet: -0.10 (0.33), residues: 265
  loop : -0.38 (0.26), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 976 
 TYR   0.013   0.001   TYR B 237 
 PHE   0.013   0.001   PHE C  33 
 TRP   0.007   0.001   TRP B 296 
 HIS   0.015   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (13428)
  covalent geometry    : angle       0.54902 (18481)
  hydrogen bonds       : bond        0.03224 (  599)
  hydrogen bonds       : angle       4.14338 ( 1630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2712.81 seconds
wall clock time: 47 minutes 13.31 seconds (2833.31 seconds total)