Starting phenix.real_space_refine
on Thu Feb  5 20:11:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ngm_49388/02_2026/9ngm_49388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ngm_49388/02_2026/9ngm_49388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ngm_49388/02_2026/9ngm_49388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ngm_49388/02_2026/9ngm_49388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ngm_49388/02_2026/9ngm_49388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ngm_49388/02_2026/9ngm_49388.cif"
  }
  resolution = 3.33
  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=   0.008 sd=   0.093
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6168      2.51       5
     N    1648      2.21       5
     O    1694      1.98       5
     H    9724      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19288
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 9644
          Classifications: {'peptide': 590}
          Link IDs: {'PTRANS': 19, 'TRANS': 570}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 10.25, per 1000 atoms: 0.53
  Number of scatterers: 19288
  At special positions: 0
  Unit cell: (104.06, 100.62, 141.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     O    1694      8.00
     N    1648      7.00
     C    6168      6.00
     H    9724      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 475.9 milliseconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2188

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      65.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 75
      removed outlier: 4.191A  pdb=" N   ILE A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   MET A  74 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 82
      No H-bonds generated for 'chain 'A' and resid 80 through 82'
    Processing helix  chain 'A' and resid 83 through 89
      removed outlier: 3.583A  pdb=" N   VAL A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 94
      removed outlier: 3.633A  pdb=" N   VAL A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 116
      removed outlier: 4.033A  pdb=" N   THR A 108 " --> pdb=" O   ILE A 104 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LEU A 109 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 131
      removed outlier: 3.656A  pdb=" N   PHE A 122 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE A 129 " --> pdb=" O   TYR A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 167
      removed outlier: 3.826A  pdb=" N   ILE A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 137 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A 138 " --> pdb=" O   PRO A 134 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASN A 140 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LYS A 144 " --> pdb=" O   ASN A 140 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU A 165 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU A 167 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 177
      removed outlier: 3.833A  pdb=" N   GLY A 176 " --> pdb=" O   TYR A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 189
      removed outlier: 3.867A  pdb=" N   LEU A 188 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 207
      removed outlier: 4.007A  pdb=" N   GLU A 194 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL A 201 " --> pdb=" O   CYS A 197 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   TYR A 204 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 218
      removed outlier: 3.643A  pdb=" N   LEU A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 248
      removed outlier: 4.309A  pdb=" N   ALA A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   MET A 233 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR A 236 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 275
      removed outlier: 3.552A  pdb=" N   THR A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ILE A 256 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   THR A 257 " --> pdb=" O   LYS A 253 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN A 259 " --> pdb=" O   THR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 281
      removed outlier: 3.795A  pdb=" N   PHE A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 322
      removed outlier: 3.886A  pdb=" N   GLU A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   HIS A 304 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASN A 305 " --> pdb=" O   GLU A 301 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 335
    Processing helix  chain 'A' and resid 349 through 377
      removed outlier: 4.594A  pdb=" N   GLU A 355 " --> pdb=" O   SER A 351 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 365 " --> pdb=" O   GLY A 361 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG A 366 " --> pdb=" O   ARG A 362 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A 370 " --> pdb=" O   ARG A 366 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU A 371 " --> pdb=" O   MET A 367 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY A 372 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 403
      removed outlier: 4.072A  pdb=" N   GLY A 386 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A 387 " --> pdb=" O   ARG A 383 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   HIS A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 487
      removed outlier: 3.504A  pdb=" N   GLY A 487 " --> pdb=" O   PHE A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 524
    Processing helix  chain 'A' and resid 528 through 535
    Processing helix  chain 'A' and resid 538 through 549
      removed outlier: 3.821A  pdb=" N   VAL A 549 " --> pdb=" O   TYR A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 570
      removed outlier: 3.525A  pdb=" N   ASP A 569 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A 570 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 566 through 570'
    Processing helix  chain 'A' and resid 572 through 588
    Processing helix  chain 'A' and resid 602 through 617
    Processing helix  chain 'A' and resid 626 through 632
    Processing helix  chain 'B' and resid 60 through 75
      removed outlier: 4.191A  pdb=" N   ILE B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET B  74 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 82
      No H-bonds generated for 'chain 'B' and resid 80 through 82'
    Processing helix  chain 'B' and resid 83 through 89
      removed outlier: 3.583A  pdb=" N   VAL B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 94
      removed outlier: 3.633A  pdb=" N   VAL B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 116
      removed outlier: 4.034A  pdb=" N   THR B 108 " --> pdb=" O   ILE B 104 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LEU B 109 " --> pdb=" O   GLN B 105 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 114 " --> pdb=" O   ILE B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 131
      removed outlier: 3.657A  pdb=" N   PHE B 122 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE B 129 " --> pdb=" O   TYR B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 167
      removed outlier: 3.826A  pdb=" N   ILE B 136 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 137 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 138 " --> pdb=" O   PRO B 134 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL B 139 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASN B 140 " --> pdb=" O   ILE B 136 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LYS B 144 " --> pdb=" O   ASN B 140 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU B 165 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU B 167 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 177
      removed outlier: 3.833A  pdb=" N   GLY B 176 " --> pdb=" O   TYR B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 189
      removed outlier: 3.867A  pdb=" N   LEU B 188 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 207
      removed outlier: 4.007A  pdb=" N   GLU B 194 " --> pdb=" O   THR B 190 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL B 201 " --> pdb=" O   CYS B 197 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   TYR B 204 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 218
      removed outlier: 3.643A  pdb=" N   LEU B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 248
      removed outlier: 4.309A  pdb=" N   ALA B 231 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   MET B 233 " --> pdb=" O   GLY B 229 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 275
      removed outlier: 3.552A  pdb=" N   THR B 255 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ILE B 256 " --> pdb=" O   GLY B 252 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   THR B 257 " --> pdb=" O   LYS B 253 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN B 259 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 281
      removed outlier: 3.796A  pdb=" N   PHE B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 322
      removed outlier: 3.885A  pdb=" N   GLU B 288 " --> pdb=" O   GLY B 284 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   HIS B 304 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASN B 305 " --> pdb=" O   GLU B 301 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 335
    Processing helix  chain 'B' and resid 349 through 377
      removed outlier: 4.595A  pdb=" N   GLU B 355 " --> pdb=" O   SER B 351 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU B 365 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG B 366 " --> pdb=" O   ARG B 362 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 370 " --> pdb=" O   ARG B 366 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU B 371 " --> pdb=" O   MET B 367 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY B 372 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 403
      removed outlier: 4.072A  pdb=" N   GLY B 386 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE B 387 " --> pdb=" O   ARG B 383 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   HIS B 403 " --> pdb=" O   LYS B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 487
      removed outlier: 3.504A  pdb=" N   GLY B 487 " --> pdb=" O   PHE B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 524
    Processing helix  chain 'B' and resid 528 through 535
    Processing helix  chain 'B' and resid 538 through 549
      removed outlier: 3.821A  pdb=" N   VAL B 549 " --> pdb=" O   TYR B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 570
      removed outlier: 3.525A  pdb=" N   ASP B 569 " --> pdb=" O   ASP B 566 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL B 570 " --> pdb=" O   TRP B 567 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 566 through 570'
    Processing helix  chain 'B' and resid 572 through 588
    Processing helix  chain 'B' and resid 602 through 617
    Processing helix  chain 'B' and resid 626 through 632
    Processing sheet with id=AA1, first strand: chain 'A' and resid 430 through 435
      removed outlier: 6.822A  pdb=" N   ALA A 430 " --> pdb=" O   PHE A 493 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLY A 495 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU A 432 " --> pdb=" O   GLY A 495 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ARG A 496 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASP A 443 " --> pdb=" O   ARG A 496 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   THR A 498 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LYS A 441 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE A 440 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 463 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 505 through 508
      removed outlier: 6.854A  pdb=" N   PHE A 506 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 469 " --> pdb=" O   LEU A 620 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ASN A 468 " --> pdb=" O   TYR A 635 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   LEU A 637 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU A 470 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 430 through 435
      removed outlier: 6.822A  pdb=" N   ALA B 430 " --> pdb=" O   PHE B 493 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLY B 495 " --> pdb=" O   ALA B 430 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLU B 432 " --> pdb=" O   GLY B 495 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ARG B 496 " --> pdb=" O   ASP B 443 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASP B 443 " --> pdb=" O   ARG B 496 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   THR B 498 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LYS B 441 " --> pdb=" O   THR B 498 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 440 " --> pdb=" O   VAL B 463 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL B 463 " --> pdb=" O   ILE B 440 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 505 through 508
      removed outlier: 6.854A  pdb=" N   PHE B 506 " --> pdb=" O   ILE B 593 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL B 469 " --> pdb=" O   LEU B 620 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   ASN B 468 " --> pdb=" O   TYR B 635 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   LEU B 637 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU B 470 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)

    492 hydrogen bonds defined for protein.
    1476 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: 4.12

  Time building geometry restraints manager: 2.38 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 9616
        1.03 -     1.22: 108
        1.22 -     1.42: 4116
        1.42 -     1.61: 5562
        1.61 -     1.81: 92
  Bond restraints: 19494
  Sorted by residual:
  bond pdb=" N   ARG B 344 "
       pdb=" H   ARG B 344 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   ARG A 344 "
       pdb=" H   ARG A 344 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   ILE A 225 "
       pdb=" H   ILE A 225 "
    ideal  model  delta    sigma   weight residual
    0.860  1.009 -0.149 2.00e-02 2.50e+03 5.56e+01
  bond pdb=" N   ILE B 225 "
       pdb=" H   ILE B 225 "
    ideal  model  delta    sigma   weight residual
    0.860  1.009 -0.149 2.00e-02 2.50e+03 5.56e+01
  bond pdb=" N   LEU A 221 "
       pdb=" H   LEU A 221 "
    ideal  model  delta    sigma   weight residual
    0.860  1.009 -0.149 2.00e-02 2.50e+03 5.56e+01
  ... (remaining 19489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.10: 35208
       21.10 -    42.20: 0
       42.20 -    63.30: 0
       63.30 -    84.40: 0
       84.40 -   105.50: 2
  Bond angle restraints: 35210
  Sorted by residual:
  angle pdb=" C   PRO A 343 "
        pdb=" N   ARG A 344 "
        pdb=" H   ARG A 344 "
      ideal   model   delta    sigma   weight residual
     122.64   17.14  105.50 3.00e+00 1.11e-01 1.24e+03
  angle pdb=" C   PRO B 343 "
        pdb=" N   ARG B 344 "
        pdb=" H   ARG B 344 "
      ideal   model   delta    sigma   weight residual
     122.64   17.14  105.50 3.00e+00 1.11e-01 1.24e+03
  angle pdb=" CB  ARG B 484 "
        pdb=" CG  ARG B 484 "
        pdb=" CD  ARG B 484 "
      ideal   model   delta    sigma   weight residual
     111.30  119.43   -8.13 2.30e+00 1.89e-01 1.25e+01
  angle pdb=" CB  ARG A 484 "
        pdb=" CG  ARG A 484 "
        pdb=" CD  ARG A 484 "
      ideal   model   delta    sigma   weight residual
     111.30  119.43   -8.13 2.30e+00 1.89e-01 1.25e+01
  angle pdb=" CA  GLU A 432 "
        pdb=" CB  GLU A 432 "
        pdb=" CG  GLU A 432 "
      ideal   model   delta    sigma   weight residual
     114.10  120.29   -6.19 2.00e+00 2.50e-01 9.58e+00
  ... (remaining 35205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.24: 8178
       14.24 -    28.48: 626
       28.48 -    42.72: 157
       42.72 -    56.96: 119
       56.96 -    71.21: 10
  Dihedral angle restraints: 9090
    sinusoidal: 4966
      harmonic: 4124
  Sorted by residual:
  dihedral pdb=" CA  TYR A 282 "
           pdb=" C   TYR A 282 "
           pdb=" N   ASN A 283 "
           pdb=" CA  ASN A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.16   15.84     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  TYR B 282 "
           pdb=" C   TYR B 282 "
           pdb=" N   ASN B 283 "
           pdb=" CA  ASN B 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.18   15.82     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  ILE A 182 "
           pdb=" CB  ILE A 182 "
           pdb=" CG1 ILE A 182 "
           pdb=" CD1 ILE A 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  109.63  -49.63     3      1.50e+01 4.44e-03 8.80e+00
  ... (remaining 9087 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 866
       0.029 -    0.058: 403
       0.058 -    0.087: 105
       0.087 -    0.116: 60
       0.116 -    0.144: 26
  Chirality restraints: 1460
  Sorted by residual:
  chirality pdb=" CA  TYR A 635 "
            pdb=" N   TYR A 635 "
            pdb=" C   TYR A 635 "
            pdb=" CB  TYR A 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  ILE A 650 "
            pdb=" N   ILE A 650 "
            pdb=" C   ILE A 650 "
            pdb=" CB  ILE A 650 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CA  ILE B 650 "
            pdb=" N   ILE B 650 "
            pdb=" C   ILE B 650 "
            pdb=" CB  ILE B 650 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1457 not shown)

  Planarity restraints: 2802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 224 "   -0.061 2.00e-02 2.50e+03   1.09e-01 1.18e+02
        pdb=" N   ILE B 225 "    0.188 2.00e-02 2.50e+03
        pdb=" CA  ILE B 225 "   -0.051 2.00e-02 2.50e+03
        pdb=" H   ILE B 225 "   -0.076 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 224 "    0.061 2.00e-02 2.50e+03   1.09e-01 1.18e+02
        pdb=" N   ILE A 225 "   -0.188 2.00e-02 2.50e+03
        pdb=" CA  ILE A 225 "    0.051 2.00e-02 2.50e+03
        pdb=" H   ILE A 225 "    0.076 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 221 "   -0.057 2.00e-02 2.50e+03   1.01e-01 1.02e+02
        pdb=" N   THR B 222 "    0.174 2.00e-02 2.50e+03
        pdb=" CA  THR B 222 "   -0.050 2.00e-02 2.50e+03
        pdb=" H   THR B 222 "   -0.068 2.00e-02 2.50e+03
  ... (remaining 2799 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 38
        1.95 -     2.61: 21381
        2.61 -     3.28: 56675
        3.28 -     3.94: 66283
        3.94 -     4.60: 105478
  Nonbonded interactions: 249855
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 343 "
            pdb=" H   ARG B 344 "
     model   vdw
     1.288 1.960
  nonbonded pdb=" O   PRO A 343 "
            pdb=" H   ARG A 344 "
     model   vdw
     1.288 1.960
  nonbonded pdb=" O   LEU B 629 "
            pdb=" HD1 HIS B 633 "
     model   vdw
     1.678 2.450
  nonbonded pdb=" O   LEU A 629 "
            pdb=" HD1 HIS A 633 "
     model   vdw
     1.678 2.450
  nonbonded pdb=" O   ILE B 136 "
            pdb="HD22 ASN B 140 "
     model   vdw
     1.689 2.450
  ... (remaining 249850 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.830
  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:             0.080
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     24.900
  Find NCS groups from input model:        0.120
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9770  Z= 0.184
  Angle     :  0.688   8.134  13182  Z= 0.357
  Chirality :  0.042   0.144   1460
  Planarity :  0.004   0.030   1664
  Dihedral  : 10.554  71.206   3662
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.26), residues: 1172
  helix:  0.96 (0.20), residues: 760
  sheet: -0.94 (0.64), residues: 68
  loop : -2.78 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 614 
 TYR   0.012   0.002   TYR B 358 
 PHE   0.024   0.002   PHE A 506 
 TRP   0.004   0.001   TRP B 630 
 HIS   0.003   0.001   HIS B 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 9770)
  covalent geometry    : angle       0.68843 (13182)
  hydrogen bonds       : bond        0.15265 (  492)
  hydrogen bonds       : angle       4.75420 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8753 (mmt) cc_final: 0.8419 (mmt)
REVERT: A  379 ARG cc_start: 0.7295 (ptp-170) cc_final: 0.6709 (mmt180)
REVERT: A  568 MET cc_start: 0.7522 (mmt) cc_final: 0.7313 (mmt)
REVERT: A  579 MET cc_start: 0.7925 (tpt) cc_final: 0.7403 (tpt)
REVERT: B   92 MET cc_start: 0.8753 (mmt) cc_final: 0.8417 (mmt)
REVERT: B  246 ARG cc_start: 0.7830 (tpt170) cc_final: 0.7626 (tpp80)
REVERT: B  379 ARG cc_start: 0.7272 (ptp-170) cc_final: 0.6702 (mmt180)
REVERT: B  568 MET cc_start: 0.7531 (mmt) cc_final: 0.7320 (mmt)
REVERT: B  579 MET cc_start: 0.7922 (tpt) cc_final: 0.7404 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2128
  time to fit residues: 30.0845
Evaluate side-chains
  85 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0470
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
A 548 ASN
B 177 ASN
B 548 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.211447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.164020 restraints weight = 31309.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.92
r_work: 0.3442 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   9770  Z= 0.130
  Angle     :  0.537  16.033  13182  Z= 0.290
  Chirality :  0.037   0.145   1460
  Planarity :  0.003   0.028   1664
  Dihedral  :  3.950  17.721   1320
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  5.17 %
    Favored  : 94.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.26), residues: 1172
  helix:  1.13 (0.20), residues: 760
  sheet: -0.86 (0.65), residues: 68
  loop : -2.79 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 344 
 TYR   0.012   0.001   TYR B 358 
 PHE   0.009   0.001   PHE A 621 
 TRP   0.003   0.000   TRP B 630 
 HIS   0.003   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9770)
  covalent geometry    : angle       0.53724 (13182)
  hydrogen bonds       : bond        0.06243 (  492)
  hydrogen bonds       : angle       3.87050 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8655 (mmt) cc_final: 0.8283 (mmt)
REVERT: A  187 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7794 (tm-30)
REVERT: A  379 ARG cc_start: 0.7284 (ptp-170) cc_final: 0.6853 (mmt180)
REVERT: A  395 MET cc_start: 0.8285 (mtm) cc_final: 0.8061 (mtp)
REVERT: A  579 MET cc_start: 0.7935 (tpt) cc_final: 0.7305 (tpt)
REVERT: A  650 ILE cc_start: 0.4522 (OUTLIER) cc_final: 0.4170 (pt)
REVERT: B   92 MET cc_start: 0.8660 (mmt) cc_final: 0.8291 (mmt)
REVERT: B  187 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: B  379 ARG cc_start: 0.7279 (ptp-170) cc_final: 0.6864 (mmt180)
REVERT: B  395 MET cc_start: 0.8272 (mtm) cc_final: 0.8052 (mtp)
REVERT: B  579 MET cc_start: 0.7937 (tpt) cc_final: 0.7303 (tpt)
REVERT: B  650 ILE cc_start: 0.4522 (OUTLIER) cc_final: 0.4172 (pt)
  outliers start: 6
  outliers final: 2
  residues processed: 93
  average time/residue: 0.2454
  time to fit residues: 30.3744
Evaluate side-chains
  88 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 548 ASN
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 ASN
** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.210623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.160145 restraints weight = 31192.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 3.05
r_work: 0.3465 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9770  Z= 0.127
  Angle     :  0.532  16.201  13182  Z= 0.285
  Chirality :  0.037   0.132   1460
  Planarity :  0.003   0.030   1664
  Dihedral  :  3.894  16.738   1320
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.51 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.26), residues: 1172
  helix:  1.05 (0.20), residues: 770
  sheet: -0.72 (0.66), residues: 68
  loop : -2.72 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 484 
 TYR   0.013   0.001   TYR B 358 
 PHE   0.010   0.001   PHE B 461 
 TRP   0.003   0.001   TRP B 561 
 HIS   0.002   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9770)
  covalent geometry    : angle       0.53173 (13182)
  hydrogen bonds       : bond        0.06211 (  492)
  hydrogen bonds       : angle       3.77245 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8646 (mmt) cc_final: 0.8316 (mmt)
REVERT: A  187 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: A  379 ARG cc_start: 0.7241 (ptp-170) cc_final: 0.6921 (mmt180)
REVERT: A  395 MET cc_start: 0.8297 (mtm) cc_final: 0.8053 (mtp)
REVERT: A  579 MET cc_start: 0.7955 (tpt) cc_final: 0.7208 (tpt)
REVERT: A  650 ILE cc_start: 0.4431 (OUTLIER) cc_final: 0.4122 (pt)
REVERT: B   92 MET cc_start: 0.8646 (mmt) cc_final: 0.8320 (mmt)
REVERT: B  187 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: B  379 ARG cc_start: 0.7235 (ptp-170) cc_final: 0.6922 (mmt180)
REVERT: B  395 MET cc_start: 0.8295 (mtm) cc_final: 0.8054 (mtp)
REVERT: B  579 MET cc_start: 0.7954 (tpt) cc_final: 0.7203 (tpt)
REVERT: B  650 ILE cc_start: 0.4448 (OUTLIER) cc_final: 0.4139 (pt)
  outliers start: 6
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1952
  time to fit residues: 23.7541
Evaluate side-chains
  86 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0570
   chunk 95 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 107 optimal weight:    7.9990
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
A 304 HIS
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.210991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.156075 restraints weight = 31157.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.85
r_work: 0.3528 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   9770  Z= 0.115
  Angle     :  0.512  16.517  13182  Z= 0.274
  Chirality :  0.037   0.128   1460
  Planarity :  0.003   0.032   1664
  Dihedral  :  3.770  15.678   1320
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  7.18 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.26), residues: 1172
  helix:  1.14 (0.20), residues: 768
  sheet: -0.68 (0.57), residues: 88
  loop : -2.83 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 614 
 TYR   0.011   0.001   TYR B 358 
 PHE   0.013   0.001   PHE B 337 
 TRP   0.003   0.000   TRP A 630 
 HIS   0.002   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9770)
  covalent geometry    : angle       0.51220 (13182)
  hydrogen bonds       : bond        0.05743 (  492)
  hydrogen bonds       : angle       3.62465 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8675 (mmt) cc_final: 0.8411 (mmt)
REVERT: A  187 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: A  379 ARG cc_start: 0.7317 (ptp-170) cc_final: 0.6957 (mmt180)
REVERT: A  395 MET cc_start: 0.8335 (mtm) cc_final: 0.8087 (mtp)
REVERT: A  579 MET cc_start: 0.7940 (tpt) cc_final: 0.7284 (tpt)
REVERT: A  650 ILE cc_start: 0.4367 (OUTLIER) cc_final: 0.3998 (pt)
REVERT: B   92 MET cc_start: 0.8679 (mmt) cc_final: 0.8415 (mmt)
REVERT: B  187 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: B  379 ARG cc_start: 0.7321 (ptp-170) cc_final: 0.6958 (mmt180)
REVERT: B  395 MET cc_start: 0.8326 (mtm) cc_final: 0.8080 (mtp)
REVERT: B  579 MET cc_start: 0.7951 (tpt) cc_final: 0.7283 (tpt)
REVERT: B  650 ILE cc_start: 0.4367 (OUTLIER) cc_final: 0.3999 (pt)
  outliers start: 6
  outliers final: 2
  residues processed: 84
  average time/residue: 0.2152
  time to fit residues: 25.6749
Evaluate side-chains
  82 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:    0.0470
   chunk 8 optimal weight:    0.6980
   chunk 116 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9980
   chunk 108 optimal weight:    6.9990
   chunk 103 optimal weight:    0.0070
   overall best weight:    0.5096

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.212438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.158762 restraints weight = 30952.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 1.93
r_work: 0.3548 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   9770  Z= 0.099
  Angle     :  0.497  16.594  13182  Z= 0.263
  Chirality :  0.036   0.127   1460
  Planarity :  0.003   0.031   1664
  Dihedral  :  3.644  14.908   1320
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  7.95 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.26), residues: 1172
  helix:  1.37 (0.20), residues: 762
  sheet: -0.66 (0.58), residues: 88
  loop : -2.78 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 614 
 TYR   0.010   0.001   TYR B 358 
 PHE   0.010   0.001   PHE A 461 
 TRP   0.003   0.000   TRP B 630 
 HIS   0.002   0.000   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 9770)
  covalent geometry    : angle       0.49652 (13182)
  hydrogen bonds       : bond        0.05130 (  492)
  hydrogen bonds       : angle       3.49904 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8696 (mmt) cc_final: 0.8467 (mmt)
REVERT: A  187 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: A  379 ARG cc_start: 0.7295 (ptp-170) cc_final: 0.6961 (mmt-90)
REVERT: A  579 MET cc_start: 0.7942 (tpt) cc_final: 0.7223 (tpt)
REVERT: A  612 HIS cc_start: 0.7755 (t-90) cc_final: 0.7470 (t-170)
REVERT: A  650 ILE cc_start: 0.4284 (OUTLIER) cc_final: 0.3863 (pt)
REVERT: B   92 MET cc_start: 0.8689 (mmt) cc_final: 0.8461 (mmt)
REVERT: B  187 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: B  379 ARG cc_start: 0.7308 (ptp-170) cc_final: 0.6963 (mmt-90)
REVERT: B  579 MET cc_start: 0.7960 (tpt) cc_final: 0.7220 (tpt)
REVERT: B  612 HIS cc_start: 0.7752 (t-90) cc_final: 0.7465 (t-170)
REVERT: B  650 ILE cc_start: 0.4285 (OUTLIER) cc_final: 0.3865 (pt)
  outliers start: 8
  outliers final: 2
  residues processed: 86
  average time/residue: 0.2075
  time to fit residues: 25.1626
Evaluate side-chains
  84 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 113 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 115 optimal weight:   20.0000
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 468 ASN
B 304 HIS
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 468 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.209683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.153319 restraints weight = 31005.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 1.71
r_work: 0.3519 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9770  Z= 0.123
  Angle     :  0.516  16.712  13182  Z= 0.275
  Chirality :  0.037   0.127   1460
  Planarity :  0.003   0.032   1664
  Dihedral  :  3.717  15.138   1320
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.81 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.26), residues: 1172
  helix:  1.13 (0.20), residues: 770
  sheet: -0.62 (0.59), residues: 88
  loop : -2.73 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  96 
 TYR   0.013   0.001   TYR B 358 
 PHE   0.015   0.001   PHE B 337 
 TRP   0.002   0.001   TRP A 630 
 HIS   0.002   0.001   HIS B 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9770)
  covalent geometry    : angle       0.51553 (13182)
  hydrogen bonds       : bond        0.06045 (  492)
  hydrogen bonds       : angle       3.59115 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8684 (mmt) cc_final: 0.8464 (mmt)
REVERT: A  187 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: A  379 ARG cc_start: 0.7278 (ptp-170) cc_final: 0.6917 (mmt-90)
REVERT: A  579 MET cc_start: 0.7945 (tpt) cc_final: 0.7202 (tpt)
REVERT: A  650 ILE cc_start: 0.4326 (OUTLIER) cc_final: 0.3874 (pt)
REVERT: B   92 MET cc_start: 0.8682 (mmt) cc_final: 0.8463 (mmt)
REVERT: B  187 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7686 (tm-30)
REVERT: B  379 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.6918 (mmt-90)
REVERT: B  579 MET cc_start: 0.7955 (tpt) cc_final: 0.7196 (tpt)
REVERT: B  650 ILE cc_start: 0.4312 (OUTLIER) cc_final: 0.3867 (pt)
  outliers start: 6
  outliers final: 2
  residues processed: 84
  average time/residue: 0.2196
  time to fit residues: 26.1757
Evaluate side-chains
  82 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 548 ASN
B 548 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.208054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.153127 restraints weight = 31178.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 1.84
r_work: 0.3482 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9770  Z= 0.144
  Angle     :  0.530  16.757  13182  Z= 0.285
  Chirality :  0.038   0.128   1460
  Planarity :  0.004   0.038   1664
  Dihedral  :  3.805  14.920   1320
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.00 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.26), residues: 1172
  helix:  1.03 (0.20), residues: 766
  sheet: -0.53 (0.58), residues: 88
  loop : -2.83 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.014   0.001   TYR B 358 
 PHE   0.016   0.001   PHE B 337 
 TRP   0.003   0.001   TRP B 490 
 HIS   0.002   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9770)
  covalent geometry    : angle       0.53040 (13182)
  hydrogen bonds       : bond        0.06571 (  492)
  hydrogen bonds       : angle       3.68303 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: A  379 ARG cc_start: 0.7306 (ptp-170) cc_final: 0.6927 (mmt-90)
REVERT: A  579 MET cc_start: 0.7948 (tpt) cc_final: 0.7184 (tpt)
REVERT: A  650 ILE cc_start: 0.4446 (OUTLIER) cc_final: 0.3980 (pt)
REVERT: B  187 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7708 (tm-30)
REVERT: B  379 ARG cc_start: 0.7320 (ptp-170) cc_final: 0.6926 (mmt-90)
REVERT: B  579 MET cc_start: 0.7966 (tpt) cc_final: 0.7182 (tpt)
REVERT: B  650 ILE cc_start: 0.4436 (OUTLIER) cc_final: 0.3966 (pt)
  outliers start: 6
  outliers final: 2
  residues processed: 84
  average time/residue: 0.2064
  time to fit residues: 24.4871
Evaluate side-chains
  80 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0980
   chunk 16 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 88 optimal weight:    0.6980
   chunk 116 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.205189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.129667 restraints weight = 31337.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.42
r_work: 0.3331 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9770  Z= 0.123
  Angle     :  0.513  16.752  13182  Z= 0.274
  Chirality :  0.037   0.126   1460
  Planarity :  0.004   0.038   1664
  Dihedral  :  3.746  14.951   1320
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  8.81 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.26), residues: 1172
  helix:  1.06 (0.20), residues: 766
  sheet: -0.52 (0.57), residues: 88
  loop : -2.82 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 335 
 TYR   0.013   0.001   TYR B 358 
 PHE   0.012   0.001   PHE B 337 
 TRP   0.002   0.001   TRP B 490 
 HIS   0.002   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9770)
  covalent geometry    : angle       0.51271 (13182)
  hydrogen bonds       : bond        0.06145 (  492)
  hydrogen bonds       : angle       3.61523 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7586 (tm-30)
REVERT: A  379 ARG cc_start: 0.7286 (ptp-170) cc_final: 0.6720 (mmt-90)
REVERT: A  579 MET cc_start: 0.7957 (tpt) cc_final: 0.7233 (tpt)
REVERT: A  650 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.4009 (pt)
REVERT: B  187 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: B  379 ARG cc_start: 0.7312 (ptp-170) cc_final: 0.6725 (mmt-90)
REVERT: B  579 MET cc_start: 0.7959 (tpt) cc_final: 0.7243 (tpt)
REVERT: B  650 ILE cc_start: 0.4501 (OUTLIER) cc_final: 0.4021 (pt)
  outliers start: 8
  outliers final: 6
  residues processed: 78
  average time/residue: 0.2133
  time to fit residues: 23.2658
Evaluate side-chains
  82 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  630 TRP
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  630 TRP
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 86 optimal weight:    0.3980
   chunk 69 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 111 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.206257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.127416 restraints weight = 31171.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.16
r_work: 0.3391 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   9770  Z= 0.112
  Angle     :  0.502  16.706  13182  Z= 0.268
  Chirality :  0.037   0.126   1460
  Planarity :  0.003   0.037   1664
  Dihedral  :  3.660  14.843   1320
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.39 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.26), residues: 1172
  helix:  1.12 (0.20), residues: 768
  sheet: -0.48 (0.57), residues: 88
  loop : -2.77 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.012   0.001   TYR B 358 
 PHE   0.012   0.001   PHE A 337 
 TRP   0.004   0.001   TRP B 630 
 HIS   0.003   0.001   HIS A 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9770)
  covalent geometry    : angle       0.50192 (13182)
  hydrogen bonds       : bond        0.05721 (  492)
  hydrogen bonds       : angle       3.55954 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7563 (tm-30)
REVERT: A  379 ARG cc_start: 0.7207 (ptp-170) cc_final: 0.6675 (mmt180)
REVERT: A  579 MET cc_start: 0.7937 (tpt) cc_final: 0.7187 (tpt)
REVERT: A  650 ILE cc_start: 0.4450 (OUTLIER) cc_final: 0.3964 (pt)
REVERT: B  187 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7574 (tm-30)
REVERT: B  379 ARG cc_start: 0.7238 (ptp-170) cc_final: 0.6680 (mmt180)
REVERT: B  579 MET cc_start: 0.7939 (tpt) cc_final: 0.7192 (tpt)
REVERT: B  650 ILE cc_start: 0.4465 (OUTLIER) cc_final: 0.3971 (pt)
  outliers start: 8
  outliers final: 6
  residues processed: 78
  average time/residue: 0.1831
  time to fit residues: 20.2914
Evaluate side-chains
  82 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  630 TRP
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  630 TRP
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 49 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.205784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.126752 restraints weight = 31384.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.13
r_work: 0.3384 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   9770  Z= 0.118
  Angle     :  0.508  16.706  13182  Z= 0.271
  Chirality :  0.037   0.127   1460
  Planarity :  0.004   0.039   1664
  Dihedral  :  3.668  14.828   1320
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.29 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.26), residues: 1172
  helix:  1.08 (0.20), residues: 768
  sheet: -0.40 (0.58), residues: 88
  loop : -2.77 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 484 
 TYR   0.013   0.001   TYR B 358 
 PHE   0.012   0.001   PHE A 337 
 TRP   0.003   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9770)
  covalent geometry    : angle       0.50766 (13182)
  hydrogen bonds       : bond        0.05894 (  492)
  hydrogen bonds       : angle       3.57492 ( 1476)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: A  379 ARG cc_start: 0.7203 (ptp-170) cc_final: 0.6643 (mmt-90)
REVERT: A  579 MET cc_start: 0.7874 (tpt) cc_final: 0.7126 (tpt)
REVERT: A  650 ILE cc_start: 0.4381 (OUTLIER) cc_final: 0.3888 (pt)
REVERT: B  187 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7556 (tm-30)
REVERT: B  379 ARG cc_start: 0.7224 (ptp-170) cc_final: 0.6644 (mmt-90)
REVERT: B  579 MET cc_start: 0.7886 (tpt) cc_final: 0.7127 (tpt)
REVERT: B  650 ILE cc_start: 0.4386 (OUTLIER) cc_final: 0.3887 (pt)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.2026
  time to fit residues: 21.8868
Evaluate side-chains
  80 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  630 TRP
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  630 TRP
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 81 optimal weight:    0.0050
   chunk 99 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.206708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127848 restraints weight = 31395.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.16
r_work: 0.3392 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9770  Z= 0.105
  Angle     :  0.501  16.728  13182  Z= 0.266
  Chirality :  0.036   0.127   1460
  Planarity :  0.003   0.036   1664
  Dihedral  :  3.611  14.698   1320
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.48 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.26), residues: 1172
  helix:  1.13 (0.20), residues: 768
  sheet: -0.36 (0.58), residues: 88
  loop : -2.74 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.011   0.001   TYR B 358 
 PHE   0.010   0.001   PHE A 337 
 TRP   0.004   0.001   TRP A 630 
 HIS   0.002   0.000   HIS B 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9770)
  covalent geometry    : angle       0.50062 (13182)
  hydrogen bonds       : bond        0.05517 (  492)
  hydrogen bonds       : angle       3.52348 ( 1476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4629.70 seconds
wall clock time: 79 minutes 8.79 seconds (4748.79 seconds total)