Starting phenix.real_space_refine
on Wed Sep 17 22:27:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8riz_19192/09_2025/8riz_19192.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8riz_19192/09_2025/8riz_19192.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8riz_19192/09_2025/8riz_19192.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8riz_19192/09_2025/8riz_19192.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8riz_19192/09_2025/8riz_19192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8riz_19192/09_2025/8riz_19192.map"
  }
  resolution = 3.6
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      2      5.21       5
     S      76      5.16       5
     C    7431      2.51       5
     N    2021      2.21       5
     O    2323      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11862
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "B"
      Number of atoms: 3351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3351
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3358
          Classifications: {'peptide': 428}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 2448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2448
          Classifications: {'peptide': 312}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 303}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "L"
      Number of atoms: 2453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2453
          Classifications: {'peptide': 311}
          Link IDs: {'PTRANS': 8, 'TRANS': 302}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 74
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 5, 37
          Classifications: {'peptide': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 3}
      Conformer: "B"
        Number of residues, atoms: 5, 37
          Classifications: {'peptide': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 3}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'TA1': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "K"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "L"
      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}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  AILE T 920 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD1BILE T 920 " occ=0.50
    residue:
      pdb=" N  AALA T 921 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA T 921 " occ=0.50
    residue:
      pdb=" N  ALYS T 922 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS T 922 " occ=0.50
    residue:
      pdb=" N  APRO T 923 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CD BPRO T 923 " occ=0.50
    residue:
      pdb=" N  AILE T 924 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD1BILE T 924 " occ=0.50
  Time building chain proxies: 2.99, per 1000 atoms: 0.25
  Number of scatterers: 11862
  At special positions: 0
  Unit cell: (86.64, 128.877, 146.205, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      76     16.00
     P       9     15.00
     Mg      2     11.99
     O    2323      8.00
     N    2021      7.00
     C    7431      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 511.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2772

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 16 sheets defined
      44.5% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 29
    Processing helix  chain 'B' and resid 40 through 48
      removed outlier: 4.301A  pdb=" N   LEU B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ARG B  48 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 71 through 80
      removed outlier: 4.484A  pdb=" N   MET B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ASP B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER B  80 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 90
      No H-bonds generated for 'chain 'B' and resid 88 through 90'
    Processing helix  chain 'B' and resid 102 through 109
    Processing helix  chain 'B' and resid 114 through 127
    Processing helix  chain 'B' and resid 144 through 161
      removed outlier: 3.583A  pdb=" N   GLY B 148 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 195
      removed outlier: 3.598A  pdb=" N   ASN B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLN B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 216
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 3.942A  pdb=" N   LEU B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 243
      removed outlier: 3.572A  pdb=" N   ARG B 243 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 240 through 243'
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 280 through 284
    Processing helix  chain 'B' and resid 287 through 296
    Processing helix  chain 'B' and resid 324 through 339
      removed outlier: 3.904A  pdb=" N   GLN B 336 " --> pdb=" O   MET B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
    Processing helix  chain 'B' and resid 384 through 400
      removed outlier: 3.783A  pdb=" N   PHE B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 435
      removed outlier: 3.923A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   TYR B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 71 through 81
      removed outlier: 4.843A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.687A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.562A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 194
      removed outlier: 3.689A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.805A  pdb=" N   ILE A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.864A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.950A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 337
      removed outlier: 3.516A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 401
      removed outlier: 4.017A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.315A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 437
      removed outlier: 4.278A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 19 through 24
      removed outlier: 4.035A  pdb=" N   ASN K  24 " --> pdb=" O   GLU K  20 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 57 through 66
      removed outlier: 3.671A  pdb=" N   VAL K  61 " --> pdb=" O   SER K  57 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 66 through 74
      removed outlier: 3.663A  pdb=" N   LEU K  74 " --> pdb=" O   VAL K  70 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 90 through 96
    Processing helix  chain 'K' and resid 107 through 118
    Processing helix  chain 'K' and resid 119 through 122
      removed outlier: 3.650A  pdb=" N   MET K 122 " --> pdb=" O   ILE K 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 119 through 122'
    Processing helix  chain 'K' and resid 175 through 188
    Processing helix  chain 'K' and resid 237 through 241
      removed outlier: 3.553A  pdb=" N   LYS K 240 " --> pdb=" O   LYS K 237 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 245 through 271
    Processing helix  chain 'K' and resid 280 through 286
    Processing helix  chain 'K' and resid 305 through 307
      No H-bonds generated for 'chain 'K' and resid 305 through 307'
    Processing helix  chain 'K' and resid 308 through 323
      removed outlier: 4.102A  pdb=" N   ALA K 322 " --> pdb=" O   PHE K 318 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   LYS K 323 " --> pdb=" O   GLY K 319 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 19 through 26
      removed outlier: 3.612A  pdb=" N   VAL L  23 " --> pdb=" O   ASN L  19 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 57 through 76
      removed outlier: 4.890A  pdb=" N   LYS L  67 " --> pdb=" O   ASN L  63 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LYS L  68 " --> pdb=" O   ASP L  64 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   ILE L  69 " --> pdb=" O   CYS L  65 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 90 through 96
    Processing helix  chain 'L' and resid 106 through 123
    Processing helix  chain 'L' and resid 175 through 191
      removed outlier: 3.537A  pdb=" N   VAL L 179 " --> pdb=" O   SER L 175 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 196 through 203
    Processing helix  chain 'L' and resid 256 through 271
    Processing helix  chain 'L' and resid 280 through 290
      removed outlier: 3.619A  pdb=" N   ARG L 284 " --> pdb=" O   SER L 280 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASP L 288 " --> pdb=" O   ARG L 284 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   SER L 289 " --> pdb=" O   ILE L 285 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 308 through 323
    Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94
      removed outlier: 8.416A  pdb=" N   VAL B  93 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LEU B  67 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   VAL B  68 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLU B   3 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   GLN B 136 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL B   5 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   THR B 138 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   ILE B   7 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 9.335A  pdb=" N   SER B 140 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 8.965A  pdb=" N   ALA B   9 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56
    Processing sheet with id=AA3, first strand: chain 'B' and resid 272 through 273
      removed outlier: 6.758A  pdb=" N   SER B 374 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   PHE B 319 " --> pdb=" O   SER B 374 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   THR B 376 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ALA B 317 " --> pdb=" O   THR B 376 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ILE B 378 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL B 315 " --> pdb=" O   ILE B 378 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   ASN B 380 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94
      removed outlier: 8.153A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   GLU A   3 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   LEU A 136 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   PHE A 138 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE A   7 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273
    Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273
      removed outlier: 3.549A  pdb=" N   ASN A 380 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 50 through 51
      removed outlier: 3.830A  pdb=" N   ARG K  50 " --> pdb=" O   VAL K  11 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASN K  78 " --> pdb=" O   ARG K 295 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   THR K 297 " --> pdb=" O   ASN K  78 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   THR K  80 " --> pdb=" O   THR K 297 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   VAL K 299 " --> pdb=" O   THR K  80 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   PHE K  82 " --> pdb=" O   VAL K 299 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   CYS K 301 " --> pdb=" O   PHE K  82 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TYR K  84 " --> pdb=" O   CYS K 301 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY K  79 " --> pdb=" O   TYR K 228 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   VAL K 230 " --> pdb=" O   GLY K  79 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE K  81 " --> pdb=" O   VAL K 230 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLU K 127 " --> pdb=" O   GLU K 215 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 50 through 51
      removed outlier: 3.830A  pdb=" N   ARG K  50 " --> pdb=" O   VAL K  11 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASN K  78 " --> pdb=" O   ARG K 295 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   THR K 297 " --> pdb=" O   ASN K  78 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   THR K  80 " --> pdb=" O   THR K 297 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   VAL K 299 " --> pdb=" O   THR K  80 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   PHE K  82 " --> pdb=" O   VAL K 299 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   CYS K 301 " --> pdb=" O   PHE K  82 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TYR K  84 " --> pdb=" O   CYS K 301 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY K  79 " --> pdb=" O   TYR K 228 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   VAL K 230 " --> pdb=" O   GLY K  79 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE K  81 " --> pdb=" O   VAL K 230 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLU K 127 " --> pdb=" O   GLU K 215 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG K 171 " --> pdb=" O   VAL K 132 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 32 through 34
      removed outlier: 3.660A  pdb=" N   THR K  38 " --> pdb=" O   GLN K  34 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL K  39 " --> pdb=" O   TYR K  46 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 155 through 157
    Processing sheet with id=AB3, first strand: chain 'K' and resid 192 through 193
    Processing sheet with id=AB4, first strand: chain 'L' and resid 50 through 52
      removed outlier: 7.472A  pdb=" N   VAL L  11 " --> pdb=" O   ARG L  50 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   PHE L  52 " --> pdb=" O   VAL L  11 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   CYS L  13 " --> pdb=" O   PHE L  52 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   LYS L  10 " --> pdb=" O   ILE L 298 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE L 300 " --> pdb=" O   LYS L  10 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   MET L  12 " --> pdb=" O   ILE L 300 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   CYS L 302 " --> pdb=" O   MET L  12 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   ARG L  14 " --> pdb=" O   CYS L 302 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   THR L  80 " --> pdb=" O   THR L 297 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   VAL L 299 " --> pdb=" O   THR L  80 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   PHE L  82 " --> pdb=" O   VAL L 299 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   CYS L 301 " --> pdb=" O   PHE L  82 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   TYR L  84 " --> pdb=" O   CYS L 301 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL L 230 " --> pdb=" O   ILE L  81 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLU L 136 " --> pdb=" O   ARG L 143 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ARG L 143 " --> pdb=" O   GLU L 136 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 50 through 52
      removed outlier: 7.472A  pdb=" N   VAL L  11 " --> pdb=" O   ARG L  50 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   PHE L  52 " --> pdb=" O   VAL L  11 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   CYS L  13 " --> pdb=" O   PHE L  52 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   LYS L  10 " --> pdb=" O   ILE L 298 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE L 300 " --> pdb=" O   LYS L  10 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   MET L  12 " --> pdb=" O   ILE L 300 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   CYS L 302 " --> pdb=" O   MET L  12 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   ARG L  14 " --> pdb=" O   CYS L 302 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   THR L  80 " --> pdb=" O   THR L 297 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   VAL L 299 " --> pdb=" O   THR L  80 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   PHE L  82 " --> pdb=" O   VAL L 299 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   CYS L 301 " --> pdb=" O   PHE L  82 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   TYR L  84 " --> pdb=" O   CYS L 301 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL L 230 " --> pdb=" O   ILE L  81 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 32 through 33
    Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156

    572 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2059
        1.32 -     1.44: 3155
        1.44 -     1.56: 6751
        1.56 -     1.69: 20
        1.69 -     1.81: 117
  Bond restraints: 12102
  Sorted by residual:
  bond pdb=" N   ASP K 231 "
       pdb=" CA  ASP K 231 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.27e-02 6.20e+03 8.46e+00
  bond pdb=" CG  HIS K 191 "
       pdb=" CD2 HIS K 191 "
    ideal  model  delta    sigma   weight residual
    1.354  1.331  0.023 1.10e-02 8.26e+03 4.42e+00
  bond pdb=" C5  ADP L1002 "
       pdb=" C6  ADP L1002 "
    ideal  model  delta    sigma   weight residual
    1.490  1.450  0.040 2.00e-02 2.50e+03 4.10e+00
  bond pdb=" C4  ADP L1002 "
       pdb=" C5  ADP L1002 "
    ideal  model  delta    sigma   weight residual
    1.490  1.451  0.039 2.00e-02 2.50e+03 3.83e+00
  bond pdb=" N   ARG K 190 "
       pdb=" CA  ARG K 190 "
    ideal  model  delta    sigma   weight residual
    1.454  1.480 -0.026 1.34e-02 5.57e+03 3.80e+00
  ... (remaining 12097 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 16219
        2.32 -     4.63: 147
        4.63 -     6.95: 27
        6.95 -     9.27: 6
        9.27 -    11.58: 5
  Bond angle restraints: 16404
  Sorted by residual:
  angle pdb=" CA  ASP K 231 "
        pdb=" CB  ASP K 231 "
        pdb=" CG  ASP K 231 "
      ideal   model   delta    sigma   weight residual
     112.60  117.65   -5.05 1.00e+00 1.00e+00 2.55e+01
  angle pdb=" C10 TA1 B 502 "
        pdb=" C18 TA1 B 502 "
        pdb=" C20 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     104.78  116.36  -11.58 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" CA  ARG K 190 "
        pdb=" C   ARG K 190 "
        pdb=" O   ARG K 190 "
      ideal   model   delta    sigma   weight residual
     122.01  118.46    3.55 1.05e+00 9.07e-01 1.15e+01
  angle pdb=" C14 TA1 B 502 "
        pdb=" C11 TA1 B 502 "
        pdb=" O04 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     119.42  109.49    9.93 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" C1' ADP L1002 "
        pdb=" C2' ADP L1002 "
        pdb=" C3' ADP L1002 "
      ideal   model   delta    sigma   weight residual
     111.00  101.14    9.86 3.00e+00 1.11e-01 1.08e+01
  ... (remaining 16399 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.87: 7188
       33.87 -    67.74: 126
       67.74 -   101.61: 8
      101.61 -   135.49: 17
      135.49 -   169.36: 5
  Dihedral angle restraints: 7344
    sinusoidal: 3032
      harmonic: 4312
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -121.37 -169.36     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -52.60  157.19     1      2.00e+01 2.50e-03 4.61e+01
  dihedral pdb=" O5' GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  135.43  138.69     1      2.00e+01 2.50e-03 4.20e+01
  ... (remaining 7341 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1287
       0.040 -    0.080: 383
       0.080 -    0.119: 130
       0.119 -    0.159: 13
       0.159 -    0.199: 3
  Chirality restraints: 1816
  Sorted by residual:
  chirality pdb=" C3' GTP A 501 "
            pdb=" C2' GTP A 501 "
            pdb=" C4' GTP A 501 "
            pdb=" O3' GTP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.67    0.20 2.00e-01 2.50e+01 9.88e-01
  chirality pdb=" C3' ADP L1002 "
            pdb=" C2' ADP L1002 "
            pdb=" C4' ADP L1002 "
            pdb=" O3' ADP L1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.71    0.20 2.00e-01 2.50e+01 9.51e-01
  chirality pdb=" C21 TA1 B 502 "
            pdb=" C20 TA1 B 502 "
            pdb=" C24 TA1 B 502 "
            pdb=" O09 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.49    0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 1813 not shown)

  Planarity restraints: 2114
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ADP L1002 "   -0.050 2.00e-02 2.50e+03   2.07e-02 1.18e+01
        pdb=" C2  ADP L1002 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4  ADP L1002 "    0.020 2.00e-02 2.50e+03
        pdb=" C5  ADP L1002 "    0.013 2.00e-02 2.50e+03
        pdb=" C6  ADP L1002 "   -0.006 2.00e-02 2.50e+03
        pdb=" C8  ADP L1002 "    0.007 2.00e-02 2.50e+03
        pdb=" N1  ADP L1002 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3  ADP L1002 "    0.016 2.00e-02 2.50e+03
        pdb=" N6  ADP L1002 "   -0.015 2.00e-02 2.50e+03
        pdb=" N7  ADP L1002 "   -0.003 2.00e-02 2.50e+03
        pdb=" N9  ADP L1002 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  31 "    0.036 5.00e-02 4.00e+02   5.53e-02 4.89e+00
        pdb=" N   PRO B  32 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 324 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO A 325 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 325 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 325 "    0.025 5.00e-02 4.00e+02
  ... (remaining 2111 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 125
        2.59 -     3.17: 9737
        3.17 -     3.74: 17885
        3.74 -     4.32: 24442
        4.32 -     4.90: 41516
  Nonbonded interactions: 93705
  Sorted by model distance:
  nonbonded pdb=" O3G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.010 2.170
  nonbonded pdb=" O   TYR L 277 "
            pdb=" OG1 THR L 283 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OG1 THR L  92 "
            pdb="MG    MG L1001 "
     model   vdw
     2.211 2.170
  nonbonded pdb=" O   GLY L  90 "
            pdb=" OG1 THR L  94 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER L 175 "
            pdb=" OD1 ASP L 177 "
     model   vdw
     2.230 3.040
  ... (remaining 93700 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 'K' and (resid 8 through 236 or resid 255 through 1001))
  selection = (chain 'L' and (resid 8 through 64 or (resid 65 through 66 and (name N or name C \ 
A or name C or name O or name CB )) or resid 67 through 191 or (resid 192 throug \ 
h 193 and (name N or name CA or name C or name O or name CB )) or resid 194 or r \ 
esid 199 through 323 or resid 1002))
}

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=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.960
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
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      :  0.008   0.814  12103  Z= 0.753
  Angle     :  0.605  11.583  16404  Z= 0.298
  Chirality :  0.043   0.199   1816
  Planarity :  0.004   0.055   2114
  Dihedral  : 15.376 169.357   4572
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  8.42 %
    Favored  : 91.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.22), residues: 1469
  helix:  1.55 (0.22), residues: 580
  sheet:  0.95 (0.32), residues: 280
  loop : -1.34 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.008   0.001   TYR A 312 
 PHE   0.008   0.001   PHE A 255 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.007   0.001   HIS K 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (12102)
  covalent geometry    : angle       0.60472 (16404)
  hydrogen bonds       : bond        0.17490 (  517)
  hydrogen bonds       : angle       6.23101 ( 1656)
  Misc. bond           : bond        0.81415 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 309
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 MET cc_start: 0.8919 (mmt) cc_final: 0.8623 (mmt)
REVERT: B   90 ASP cc_start: 0.8793 (t0) cc_final: 0.8154 (t0)
REVERT: B   93 VAL cc_start: 0.9409 (t) cc_final: 0.9175 (m)
REVERT: B  124 LYS cc_start: 0.8116 (tptt) cc_final: 0.7656 (ttpt)
REVERT: B  197 ASN cc_start: 0.8081 (m-40) cc_final: 0.7876 (m110)
REVERT: B  202 TYR cc_start: 0.8806 (m-80) cc_final: 0.8572 (m-80)
REVERT: B  282 GLN cc_start: 0.8783 (mp10) cc_final: 0.7607 (mp10)
REVERT: B  326 LYS cc_start: 0.8888 (tttm) cc_final: 0.8685 (tmtt)
REVERT: A  205 ASP cc_start: 0.8827 (p0) cc_final: 0.8513 (p0)
REVERT: A  377 MET cc_start: 0.8057 (ttp) cc_final: 0.7841 (tmm)
REVERT: A  390 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8157 (ptp90)
REVERT: A  425 MET cc_start: 0.9154 (mmm) cc_final: 0.8486 (tpp)
REVERT: L  197 MET cc_start: 0.3078 (tpt) cc_final: 0.2403 (ttt)
  outliers start: 2
  outliers final: 0
  residues processed: 310
  average time/residue: 0.1212
  time to fit residues: 51.8223
Evaluate side-chains
  158 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    4.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 HIS
A 256 GLN
K  93 HIS
K 160 ASN
** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 320 GLN
L  19 ASN
L 196 ASN
L 211 ASN
L 320 GLN
L 327 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.109133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.074480 restraints weight = 28337.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.076833 restraints weight = 13196.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.078341 restraints weight = 8028.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.079301 restraints weight = 5797.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.079978 restraints weight = 4665.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    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 = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.104  12103  Z= 0.236
  Angle     :  0.674  10.916  16404  Z= 0.338
  Chirality :  0.046   0.304   1816
  Planarity :  0.004   0.050   2114
  Dihedral  : 12.110 171.250   1765
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.66 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.22), residues: 1469
  helix:  1.38 (0.22), residues: 600
  sheet:  1.04 (0.32), residues: 276
  loop : -1.33 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L 321 
 TYR   0.013   0.002   TYR L  62 
 PHE   0.022   0.002   PHE L 116 
 TRP   0.010   0.001   TRP A  21 
 HIS   0.006   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (12102)
  covalent geometry    : angle       0.67393 (16404)
  hydrogen bonds       : bond        0.05286 (  517)
  hydrogen bonds       : angle       4.60610 ( 1656)
  Misc. bond           : bond        0.00842 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.7956 (tptt) cc_final: 0.7425 (ttpt)
REVERT: B  282 GLN cc_start: 0.8549 (mp10) cc_final: 0.8342 (mp10)
REVERT: A  196 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6798 (pm20)
REVERT: A  205 ASP cc_start: 0.8526 (p0) cc_final: 0.8316 (p0)
REVERT: A  377 MET cc_start: 0.7885 (ttp) cc_final: 0.7557 (tmm)
REVERT: A  425 MET cc_start: 0.8991 (mmm) cc_final: 0.8357 (tpp)
REVERT: K   48 PHE cc_start: 0.8860 (m-80) cc_final: 0.8445 (m-10)
REVERT: K  219 THR cc_start: 0.8141 (m) cc_final: 0.7219 (p)
REVERT: K  312 THR cc_start: 0.9264 (m) cc_final: 0.9005 (p)
REVERT: K  316 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8864 (mp)
REVERT: L   12 MET cc_start: 0.4602 (tpp) cc_final: 0.4259 (mmt)
REVERT: L   52 PHE cc_start: 0.2076 (m-80) cc_final: 0.1647 (m-80)
REVERT: L  197 MET cc_start: 0.4835 (tpt) cc_final: 0.3567 (ttt)
  outliers start: 37
  outliers final: 22
  residues processed: 188
  average time/residue: 0.1055
  time to fit residues: 28.4164
Evaluate side-chains
  166 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  300 ILE
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  316 LEU
Chi-restraints excluded: chain L residue  162 VAL
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  263 ASN
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 103 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 125 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.108586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.073934 restraints weight = 28587.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.076250 restraints weight = 13347.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.077795 restraints weight = 8209.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.078760 restraints weight = 5900.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.079315 restraints weight = 4798.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    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 = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.102  12103  Z= 0.220
  Angle     :  0.617   6.345  16404  Z= 0.313
  Chirality :  0.046   0.342   1816
  Planarity :  0.004   0.070   2114
  Dihedral  : 10.128 166.504   1765
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.90 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.22), residues: 1469
  helix:  1.34 (0.21), residues: 600
  sheet:  0.94 (0.32), residues: 277
  loop : -1.39 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 156 
 TYR   0.012   0.001   TYR A 161 
 PHE   0.013   0.001   PHE L 116 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.006   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (12102)
  covalent geometry    : angle       0.61724 (16404)
  hydrogen bonds       : bond        0.04995 (  517)
  hydrogen bonds       : angle       4.39920 ( 1656)
  Misc. bond           : bond        0.00361 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 141
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  282 GLN cc_start: 0.8446 (mp10) cc_final: 0.8227 (mp10)
REVERT: A  196 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7352 (mt-10)
REVERT: A  425 MET cc_start: 0.9035 (mmm) cc_final: 0.8479 (tpt)
REVERT: K   34 GLN cc_start: 0.7295 (mm110) cc_final: 0.7000 (mm-40)
REVERT: K   48 PHE cc_start: 0.8877 (m-80) cc_final: 0.8307 (m-10)
REVERT: K  316 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8818 (mp)
REVERT: L   52 PHE cc_start: 0.2069 (m-80) cc_final: 0.1535 (m-80)
REVERT: L  197 MET cc_start: 0.5023 (tpt) cc_final: 0.3874 (ttt)
  outliers start: 47
  outliers final: 35
  residues processed: 174
  average time/residue: 0.0900
  time to fit residues: 23.4910
Evaluate side-chains
  164 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain K residue   73 VAL
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue  122 MET
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  184 ASP
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  272 SER
Chi-restraints excluded: chain K residue  300 ILE
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  316 LEU
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  263 ASN
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 145 optimal weight:   30.0000
   chunk 59 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 93 optimal weight:    0.6980
   chunk 120 optimal weight:   20.0000
   chunk 133 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   8 HIS
A 256 GLN
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.110391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.075586 restraints weight = 28237.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.077997 restraints weight = 13136.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.079555 restraints weight = 8018.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.080616 restraints weight = 5739.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.081252 restraints weight = 4583.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12103  Z= 0.114
  Angle     :  0.558  10.089  16404  Z= 0.278
  Chirality :  0.044   0.273   1816
  Planarity :  0.004   0.051   2114
  Dihedral  :  9.605 160.644   1765
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.91 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.22), residues: 1469
  helix:  1.71 (0.22), residues: 593
  sheet:  1.01 (0.32), residues: 284
  loop : -1.22 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 308 
 TYR   0.008   0.001   TYR A 161 
 PHE   0.012   0.001   PHE L 208 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12102)
  covalent geometry    : angle       0.55780 (16404)
  hydrogen bonds       : bond        0.03792 (  517)
  hydrogen bonds       : angle       4.01640 ( 1656)
  Misc. bond           : bond        0.00195 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 151
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8750 (tptt)
REVERT: B  431 GLU cc_start: 0.8121 (tt0) cc_final: 0.7908 (mt-10)
REVERT: A  154 MET cc_start: 0.8703 (tpp) cc_final: 0.8495 (tpp)
REVERT: A  377 MET cc_start: 0.7969 (tmm) cc_final: 0.7721 (tmm)
REVERT: A  425 MET cc_start: 0.9094 (mmm) cc_final: 0.8446 (tpp)
REVERT: K   48 PHE cc_start: 0.8759 (m-80) cc_final: 0.8417 (m-10)
REVERT: L   32 LYS cc_start: 0.7104 (tptp) cc_final: 0.6601 (mmmt)
REVERT: L  197 MET cc_start: 0.4963 (tpt) cc_final: 0.3817 (ttt)
  outliers start: 35
  outliers final: 25
  residues processed: 173
  average time/residue: 0.0951
  time to fit residues: 24.8088
Evaluate side-chains
  160 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  184 ASP
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  272 SER
Chi-restraints excluded: chain K residue  273 THR
Chi-restraints excluded: chain K residue  300 ILE
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 77 optimal weight:    0.4980
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 95 optimal weight:    8.9990
   chunk 87 optimal weight:    0.0050
   chunk 117 optimal weight:   30.0000
   chunk 131 optimal weight:    8.9990
   overall best weight:    3.5000

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 256 GLN
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.108241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.073602 restraints weight = 29156.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.075947 restraints weight = 13629.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.077475 restraints weight = 8330.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.078501 restraints weight = 5997.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.078994 restraints weight = 4807.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    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 = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  12103  Z= 0.182
  Angle     :  0.583   6.888  16404  Z= 0.292
  Chirality :  0.045   0.254   1816
  Planarity :  0.004   0.051   2114
  Dihedral  :  9.441 155.216   1765
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.83 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.22), residues: 1469
  helix:  1.63 (0.22), residues: 590
  sheet:  1.03 (0.33), residues: 277
  loop : -1.24 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 308 
 TYR   0.013   0.001   TYR A 224 
 PHE   0.014   0.001   PHE L 318 
 TRP   0.009   0.001   TRP A  21 
 HIS   0.005   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (12102)
  covalent geometry    : angle       0.58327 (16404)
  hydrogen bonds       : bond        0.04458 (  517)
  hydrogen bonds       : angle       4.08323 ( 1656)
  Misc. bond           : bond        0.00249 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 ASP cc_start: 0.8682 (t0) cc_final: 0.8035 (t0)
REVERT: A  196 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7358 (mt-10)
REVERT: A  377 MET cc_start: 0.8079 (tmm) cc_final: 0.7841 (tmm)
REVERT: A  425 MET cc_start: 0.9032 (mmm) cc_final: 0.8500 (tpt)
REVERT: K   48 PHE cc_start: 0.8778 (m-80) cc_final: 0.8292 (m-10)
REVERT: K  311 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8345 (pt0)
REVERT: L   32 LYS cc_start: 0.7007 (tptp) cc_final: 0.6500 (mmmt)
REVERT: L   39 VAL cc_start: 0.4249 (OUTLIER) cc_final: 0.3803 (m)
REVERT: L  197 MET cc_start: 0.5042 (tpt) cc_final: 0.3904 (ttt)
  outliers start: 48
  outliers final: 35
  residues processed: 171
  average time/residue: 0.0935
  time to fit residues: 23.9951
Evaluate side-chains
  168 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  376 CYS
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain K residue  122 MET
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  300 ILE
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  311 GLU
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  263 ASN
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 121 optimal weight:   30.0000
   chunk 29 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 135 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 136 optimal weight:   20.0000
   chunk 120 optimal weight:    7.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  31 GLN
A 256 GLN
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.106198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.071794 restraints weight = 29093.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.074096 restraints weight = 13775.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.075575 restraints weight = 8435.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.076557 restraints weight = 6097.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.077182 restraints weight = 4927.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.116  12103  Z= 0.255
  Angle     :  0.651  13.294  16404  Z= 0.328
  Chirality :  0.046   0.252   1816
  Planarity :  0.004   0.050   2114
  Dihedral  :  9.328 149.144   1765
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 15.29 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.22), residues: 1469
  helix:  1.25 (0.21), residues: 604
  sheet:  1.01 (0.33), residues: 270
  loop : -1.32 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 243 
 TYR   0.013   0.001   TYR L 138 
 PHE   0.013   0.002   PHE B 296 
 TRP   0.010   0.001   TRP A  21 
 HIS   0.006   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 (12102)
  covalent geometry    : angle       0.65117 (16404)
  hydrogen bonds       : bond        0.05265 (  517)
  hydrogen bonds       : angle       4.35005 ( 1656)
  Misc. bond           : bond        0.00303 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 137
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8844 (tptt)
REVERT: B  124 LYS cc_start: 0.7996 (tptt) cc_final: 0.7521 (ttpt)
REVERT: B  137 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8559 (tt)
REVERT: A  196 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7487 (mt-10)
REVERT: A  377 MET cc_start: 0.8166 (tmm) cc_final: 0.7856 (tmm)
REVERT: A  425 MET cc_start: 0.8930 (mmm) cc_final: 0.8397 (tpp)
REVERT: K   48 PHE cc_start: 0.8869 (m-80) cc_final: 0.8369 (m-10)
REVERT: K  311 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8291 (pt0)
REVERT: L   12 MET cc_start: 0.5923 (mmp) cc_final: 0.4392 (mmm)
REVERT: L   32 LYS cc_start: 0.7126 (tptp) cc_final: 0.6584 (mmmt)
REVERT: L   39 VAL cc_start: 0.4441 (OUTLIER) cc_final: 0.3985 (m)
REVERT: L  197 MET cc_start: 0.5001 (tpt) cc_final: 0.3775 (ttt)
  outliers start: 59
  outliers final: 44
  residues processed: 177
  average time/residue: 0.0942
  time to fit residues: 24.6326
Evaluate side-chains
  179 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 130
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  376 CYS
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain K residue   73 VAL
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue  122 MET
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  300 ILE
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  311 GLU
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue  214 GLN
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  263 ASN
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 77 optimal weight:    0.0980
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9990
   chunk 136 optimal weight:   30.0000
   chunk 78 optimal weight:   10.0000
   chunk 123 optimal weight:    0.3980
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 253 ASN
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.109739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.075122 restraints weight = 28761.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.077518 restraints weight = 13310.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.079047 restraints weight = 8082.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.080082 restraints weight = 5804.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.080686 restraints weight = 4646.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12103  Z= 0.108
  Angle     :  0.564  10.952  16404  Z= 0.279
  Chirality :  0.044   0.216   1816
  Planarity :  0.004   0.054   2114
  Dihedral  :  8.751 146.411   1765
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.30 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.23), residues: 1469
  helix:  1.71 (0.22), residues: 596
  sheet:  1.07 (0.33), residues: 270
  loop : -1.23 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 308 
 TYR   0.008   0.001   TYR B 432 
 PHE   0.013   0.001   PHE B 418 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (12102)
  covalent geometry    : angle       0.56407 (16404)
  hydrogen bonds       : bond        0.03519 (  517)
  hydrogen bonds       : angle       3.87842 ( 1656)
  Misc. bond           : bond        0.00150 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 147
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8776 (tppt)
REVERT: B   90 ASP cc_start: 0.8735 (t0) cc_final: 0.8091 (t0)
REVERT: B  110 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8418 (mt-10)
REVERT: A  377 MET cc_start: 0.7987 (tmm) cc_final: 0.7754 (tmm)
REVERT: A  425 MET cc_start: 0.8948 (mmm) cc_final: 0.8424 (tpp)
REVERT: K   95 MET cc_start: 0.9162 (mmm) cc_final: 0.8766 (mmm)
REVERT: K  311 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8156 (pt0)
REVERT: L   12 MET cc_start: 0.6094 (mmp) cc_final: 0.4470 (mmm)
REVERT: L   32 LYS cc_start: 0.7245 (tptp) cc_final: 0.6759 (mmmt)
REVERT: L   39 VAL cc_start: 0.4462 (OUTLIER) cc_final: 0.3986 (m)
REVERT: L  129 HIS cc_start: 0.6309 (m-70) cc_final: 0.5832 (m90)
REVERT: L  197 MET cc_start: 0.5180 (tpt) cc_final: 0.4122 (ttt)
REVERT: L  320 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.6244 (mm-40)
  outliers start: 40
  outliers final: 28
  residues processed: 177
  average time/residue: 0.1006
  time to fit residues: 25.8260
Evaluate side-chains
  165 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain K residue  122 MET
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  311 GLU
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue  214 GLN
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  320 GLN
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 107 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 120 optimal weight:   10.0000
   chunk 106 optimal weight:    6.9990
   chunk 110 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 111 optimal weight:    3.9990
   chunk 93 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.106916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.072608 restraints weight = 29088.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.074830 restraints weight = 14075.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.076314 restraints weight = 8785.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.077271 restraints weight = 6353.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.077893 restraints weight = 5113.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100  12103  Z= 0.222
  Angle     :  0.629  13.346  16404  Z= 0.315
  Chirality :  0.045   0.237   1816
  Planarity :  0.004   0.054   2114
  Dihedral  :  8.785 146.291   1765
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 16.60 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.22), residues: 1469
  helix:  1.43 (0.22), residues: 606
  sheet:  0.80 (0.32), residues: 284
  loop : -1.22 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 321 
 TYR   0.011   0.001   TYR L 138 
 PHE   0.012   0.001   PHE B 377 
 TRP   0.007   0.001   TRP A  21 
 HIS   0.006   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 (12102)
  covalent geometry    : angle       0.62909 (16404)
  hydrogen bonds       : bond        0.04741 (  517)
  hydrogen bonds       : angle       4.15754 ( 1656)
  Misc. bond           : bond        0.00270 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 134
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8810 (tptt)
REVERT: B   90 ASP cc_start: 0.8709 (t0) cc_final: 0.8075 (t0)
REVERT: B  124 LYS cc_start: 0.7978 (tptt) cc_final: 0.7530 (ttpt)
REVERT: B  137 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8480 (tt)
REVERT: A  196 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7486 (mt-10)
REVERT: A  377 MET cc_start: 0.8105 (tmm) cc_final: 0.7832 (tmm)
REVERT: A  425 MET cc_start: 0.9046 (mmm) cc_final: 0.8397 (tpp)
REVERT: K   95 MET cc_start: 0.9155 (mmm) cc_final: 0.8734 (mmm)
REVERT: K  311 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8216 (pt0)
REVERT: L   32 LYS cc_start: 0.7266 (tptp) cc_final: 0.6787 (mmmt)
REVERT: L   39 VAL cc_start: 0.4525 (OUTLIER) cc_final: 0.4068 (m)
REVERT: L  129 HIS cc_start: 0.6268 (m-70) cc_final: 0.5851 (m90)
REVERT: L  197 MET cc_start: 0.5072 (tpt) cc_final: 0.3953 (ttt)
  outliers start: 52
  outliers final: 37
  residues processed: 174
  average time/residue: 0.0906
  time to fit residues: 23.4302
Evaluate side-chains
  171 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 129
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  376 CYS
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain K residue  122 MET
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  300 ILE
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  311 GLU
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue  214 GLN
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  263 ASN
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 100 optimal weight:    0.2980
   chunk 95 optimal weight:    6.9990
   chunk 116 optimal weight:    0.0870
   chunk 141 optimal weight:    7.9990
   chunk 122 optimal weight:   30.0000
   chunk 67 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.2764

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

Flipped N/Q/H residues before XYZ refinement:
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.108565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.074003 restraints weight = 28461.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.076354 restraints weight = 13463.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.077881 restraints weight = 8266.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.078825 restraints weight = 5940.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.079428 restraints weight = 4795.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    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 = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12103  Z= 0.139
  Angle     :  0.598  15.009  16404  Z= 0.298
  Chirality :  0.044   0.216   1816
  Planarity :  0.004   0.055   2114
  Dihedral  :  8.607 146.175   1765
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.30 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.22), residues: 1469
  helix:  1.58 (0.22), residues: 603
  sheet:  1.01 (0.33), residues: 273
  loop : -1.23 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 308 
 TYR   0.013   0.001   TYR K 134 
 PHE   0.011   0.001   PHE K 208 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.004   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (12102)
  covalent geometry    : angle       0.59761 (16404)
  hydrogen bonds       : bond        0.04080 (  517)
  hydrogen bonds       : angle       3.97671 ( 1656)
  Misc. bond           : bond        0.00194 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 131
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8743 (tptt)
REVERT: B   90 ASP cc_start: 0.8697 (t0) cc_final: 0.8052 (t0)
REVERT: B  110 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8406 (mt-10)
REVERT: B  124 LYS cc_start: 0.7918 (tptt) cc_final: 0.7439 (ttpt)
REVERT: B  137 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8458 (tt)
REVERT: A  196 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7341 (mt-10)
REVERT: A  377 MET cc_start: 0.8010 (tmm) cc_final: 0.7789 (tmm)
REVERT: A  425 MET cc_start: 0.9006 (mmm) cc_final: 0.8514 (tpp)
REVERT: K   95 MET cc_start: 0.9167 (mmm) cc_final: 0.8762 (mmm)
REVERT: K  311 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8158 (pt0)
REVERT: L   12 MET cc_start: 0.6240 (mmp) cc_final: 0.4626 (mmm)
REVERT: L   32 LYS cc_start: 0.7204 (tptp) cc_final: 0.6756 (mmmt)
REVERT: L   39 VAL cc_start: 0.4695 (OUTLIER) cc_final: 0.4216 (m)
REVERT: L  129 HIS cc_start: 0.6323 (m-70) cc_final: 0.5925 (m90)
REVERT: L  197 MET cc_start: 0.5207 (tpt) cc_final: 0.4154 (ttt)
  outliers start: 45
  outliers final: 34
  residues processed: 164
  average time/residue: 0.1007
  time to fit residues: 24.2800
Evaluate side-chains
  170 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 131
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain K residue  122 MET
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  300 ILE
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  311 GLU
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue  214 GLN
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  263 ASN
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 122 optimal weight:   40.0000
   chunk 120 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0970
   chunk 141 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 GLN
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.109257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.074771 restraints weight = 28587.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.077124 restraints weight = 13387.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.078698 restraints weight = 8184.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.079721 restraints weight = 5851.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.080275 restraints weight = 4688.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    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 = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12103  Z= 0.122
  Angle     :  0.571   8.177  16404  Z= 0.285
  Chirality :  0.043   0.208   1816
  Planarity :  0.004   0.055   2114
  Dihedral  :  8.401 145.669   1765
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.61 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.23), residues: 1469
  helix:  1.70 (0.22), residues: 598
  sheet:  0.91 (0.33), residues: 280
  loop : -1.12 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 161 
 TYR   0.011   0.001   TYR K 134 
 PHE   0.011   0.001   PHE A 255 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12102)
  covalent geometry    : angle       0.57084 (16404)
  hydrogen bonds       : bond        0.03732 (  517)
  hydrogen bonds       : angle       3.89772 ( 1656)
  Misc. bond           : bond        0.00164 (    1)

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

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

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2938 Ramachandran restraints generated.
    1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 137
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8727 (tptt)
REVERT: B   90 ASP cc_start: 0.8722 (t0) cc_final: 0.8074 (t0)
REVERT: B  124 LYS cc_start: 0.7958 (tptt) cc_final: 0.7478 (ttpt)
REVERT: B  137 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8470 (tt)
REVERT: B  419 THR cc_start: 0.9280 (m) cc_final: 0.9032 (p)
REVERT: A  196 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7334 (mt-10)
REVERT: A  425 MET cc_start: 0.8985 (mmm) cc_final: 0.8420 (tpp)
REVERT: A  430 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8285 (mmtm)
REVERT: K   95 MET cc_start: 0.9173 (mmm) cc_final: 0.8778 (mmm)
REVERT: K  117 ASN cc_start: 0.8796 (m-40) cc_final: 0.8460 (t0)
REVERT: K  311 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8137 (pt0)
REVERT: L   12 MET cc_start: 0.6131 (mmp) cc_final: 0.4782 (mmm)
REVERT: L   32 LYS cc_start: 0.7262 (tptp) cc_final: 0.6816 (mmmt)
REVERT: L   39 VAL cc_start: 0.4453 (OUTLIER) cc_final: 0.3944 (m)
REVERT: L  129 HIS cc_start: 0.6327 (m-70) cc_final: 0.5943 (m90)
REVERT: L  197 MET cc_start: 0.5188 (tpt) cc_final: 0.4150 (ttt)
REVERT: L  317 LEU cc_start: 0.5894 (tp) cc_final: 0.5466 (pp)
  outliers start: 40
  outliers final: 33
  residues processed: 167
  average time/residue: 0.1021
  time to fit residues: 25.2247
Evaluate side-chains
  168 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain K residue  122 MET
Chi-restraints excluded: chain K residue  132 VAL
Chi-restraints excluded: chain K residue  210 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  302 CYS
Chi-restraints excluded: chain K residue  311 GLU
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue  214 GLN
Chi-restraints excluded: chain L residue  223 LEU
Chi-restraints excluded: chain L residue  263 ASN
Chi-restraints excluded: chain L residue  278 ARG
Chi-restraints excluded: chain L residue  306 SER
Chi-restraints excluded: chain L residue  332 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 135 optimal weight:    7.9990
   chunk 136 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0570
   chunk 114 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 139 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 97 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.110910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.076504 restraints weight = 28717.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.078930 restraints weight = 13280.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.080484 restraints weight = 8028.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.081540 restraints weight = 5742.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.082162 restraints weight = 4558.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12103  Z= 0.104
  Angle     :  0.571   8.476  16404  Z= 0.285
  Chirality :  0.043   0.217   1816
  Planarity :  0.004   0.056   2114
  Dihedral  :  8.193 145.936   1765
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.07 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.23), residues: 1469
  helix:  1.79 (0.22), residues: 595
  sheet:  1.13 (0.33), residues: 272
  loop : -1.09 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 110 
 TYR   0.010   0.001   TYR K 138 
 PHE   0.011   0.001   PHE A 255 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.002   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (12102)
  covalent geometry    : angle       0.57134 (16404)
  hydrogen bonds       : bond        0.03293 (  517)
  hydrogen bonds       : angle       3.82316 ( 1656)
  Misc. bond           : bond        0.00104 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2312.30 seconds
wall clock time: 40 minutes 42.72 seconds (2442.72 seconds total)