Starting phenix.real_space_refine
on Thu Feb 13 21:07:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e1m_8957/02_2025/6e1m_8957_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e1m_8957/02_2025/6e1m_8957.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e1m_8957/02_2025/6e1m_8957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e1m_8957/02_2025/6e1m_8957.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e1m_8957/02_2025/6e1m_8957_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e1m_8957/02_2025/6e1m_8957_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      7      9.91       5
     P       8      5.49       5
     S      40      5.16       5
     C    5932      2.51       5
     N    1326      2.21       5
     O    1600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8913
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4278
          Classifications: {'peptide': 536}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 16, 'TRANS': 519}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 81
    Chain: "B"
      Number of atoms: 4278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4278
          Classifications: {'peptide': 536}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 16, 'TRANS': 519}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 81
    Chain: "A"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 179
          Unusual residues: {' CA': 5, '3PH': 1, 'PLM': 7}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 176
          Unusual residues: {' CA': 2, '3PH': 1, 'PLM': 7}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 5.94, per 1000 atoms: 0.67
  Number of scatterers: 8913
  At special positions: 0
  Unit cell: (114.266, 91.17, 106.973, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      7     19.99
     S      40     16.00
     P       8     15.00
     O    1600      8.00
     N    1326      7.00
     C    5932      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=9, symmetry=0
  Number of additional bonds: simple=9, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 998.8 milliseconds
  

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 0 sheets defined
      74.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 44
      removed outlier: 3.629A  pdb=" N   ASP A  39 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP A  43 " --> pdb=" O   ASP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 62 through 74
      removed outlier: 3.656A  pdb=" N   LEU A  70 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 87
      removed outlier: 3.518A  pdb=" N   ALA A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'A' and resid 117 through 136
      removed outlier: 3.988A  pdb=" N   ILE A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TYR A 123 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE A 126 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 130 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   VAL A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 142
    Processing helix  chain 'A' and resid 143 through 148
      removed outlier: 3.622A  pdb=" N   TRP A 148 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 173
      removed outlier: 3.536A  pdb=" N   VAL A 160 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 199
      removed outlier: 3.927A  pdb=" N   PHE A 195 " --> pdb=" O   ARG A 191 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ILE A 199 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
      removed outlier: 3.834A  pdb=" N   LEU A 208 " --> pdb=" O   ASP A 204 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 237
      removed outlier: 4.539A  pdb=" N   ASN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 233 " --> pdb=" O   PHE A 229 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.738A  pdb=" N   THR A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 263
      removed outlier: 3.652A  pdb=" N   TYR A 256 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLN A 257 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 271
      removed outlier: 3.843A  pdb=" N   VAL A 270 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   TRP A 271 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 266 through 271'
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 278 through 280
      No H-bonds generated for 'chain 'A' and resid 278 through 280'
    Processing helix  chain 'A' and resid 281 through 295
      removed outlier: 3.745A  pdb=" N   LEU A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 335
      removed outlier: 3.583A  pdb=" N   GLU A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   MET A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LYS A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 355
      removed outlier: 4.837A  pdb=" N   LEU A 350 " --> pdb=" O   GLN A 346 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   PHE A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLU A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 371
      removed outlier: 4.341A  pdb=" N   SER A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LYS A 365 " --> pdb=" O   PRO A 361 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLU A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 370 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 399
      removed outlier: 4.092A  pdb=" N   PHE A 388 " --> pdb=" O   ASN A 384 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLN A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 396 " --> pdb=" O   CYS A 392 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ARG A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 565
      removed outlier: 3.642A  pdb=" N   THR A 557 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE A 562 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
      Proline residue:  A 563  - end of helix
    Processing helix  chain 'A' and resid 569 through 587
      removed outlier: 3.591A  pdb=" N   PHE A 573 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER A 581 " --> pdb=" O   CYS A 577 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLN A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 600
    Processing helix  chain 'A' and resid 601 through 606
    Processing helix  chain 'A' and resid 615 through 629
      removed outlier: 3.521A  pdb=" N   GLY A 619 " --> pdb=" O   ASP A 615 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR A 622 " --> pdb=" O   ASN A 618 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE A 624 " --> pdb=" O   MET A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 643
      removed outlier: 3.819A  pdb=" N   MET A 636 " --> pdb=" O   TRP A 632 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASP A 641 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 662
      removed outlier: 3.792A  pdb=" N   PHE A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   TYR A 656 " --> pdb=" O   PHE A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 684
      removed outlier: 3.627A  pdb=" N   GLU A 678 " --> pdb=" O   ALA A 674 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   GLU A 682 " --> pdb=" O   GLU A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 692
      removed outlier: 3.816A  pdb=" N   GLY A 689 " --> pdb=" O   GLU A 685 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLN A 690 " --> pdb=" O   LYS A 686 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER A 692 " --> pdb=" O   GLN A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 704
      removed outlier: 3.577A  pdb=" N   SER A 701 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 47
      removed outlier: 4.333A  pdb=" N   VAL B  38 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASP B  39 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ASP B  43 " --> pdb=" O   ASP B  39 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE B  45 " --> pdb=" O   ALA B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 56
    Processing helix  chain 'B' and resid 62 through 74
      removed outlier: 3.892A  pdb=" N   PHE B  67 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG B  69 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B  70 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 87
      removed outlier: 3.504A  pdb=" N   ALA B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 117 through 136
      removed outlier: 4.090A  pdb=" N   ILE B 121 " --> pdb=" O   ASN B 117 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ILE B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR B 123 " --> pdb=" O   GLU B 119 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE B 126 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE B 130 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL B 133 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 142
    Processing helix  chain 'B' and resid 143 through 148
      removed outlier: 3.728A  pdb=" N   TRP B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 173
      removed outlier: 3.536A  pdb=" N   VAL B 160 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 199
      removed outlier: 3.987A  pdb=" N   PHE B 195 " --> pdb=" O   ARG B 191 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE B 199 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
      removed outlier: 3.870A  pdb=" N   LEU B 208 " --> pdb=" O   ASP B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 237
      removed outlier: 4.624A  pdb=" N   ASN B 218 " --> pdb=" O   GLY B 214 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE B 233 " --> pdb=" O   PHE B 229 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
      removed outlier: 3.730A  pdb=" N   THR B 246 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 263
      removed outlier: 3.596A  pdb=" N   TYR B 256 " --> pdb=" O   GLY B 252 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLN B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 271
      removed outlier: 3.862A  pdb=" N   VAL B 270 " --> pdb=" O   ASN B 266 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TRP B 271 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 266 through 271'
    Processing helix  chain 'B' and resid 278 through 280
      No H-bonds generated for 'chain 'B' and resid 278 through 280'
    Processing helix  chain 'B' and resid 281 through 295
      removed outlier: 4.092A  pdb=" N   PHE B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL B 289 " --> pdb=" O   PHE B 285 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 335
      removed outlier: 3.540A  pdb=" N   GLU B 310 " --> pdb=" O   ASP B 306 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   MET B 322 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LYS B 329 " --> pdb=" O   ARG B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 354
    Processing helix  chain 'B' and resid 360 through 371
      removed outlier: 4.260A  pdb=" N   SER B 364 " --> pdb=" O   LEU B 360 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   LYS B 365 " --> pdb=" O   PRO B 361 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   GLU B 366 " --> pdb=" O   LYS B 362 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY B 369 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 399
      removed outlier: 3.642A  pdb=" N   ASP B 390 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   GLN B 393 " --> pdb=" O   ALA B 389 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA B 396 " --> pdb=" O   CYS B 392 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ARG B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 565
      removed outlier: 3.508A  pdb=" N   ILE B 555 " --> pdb=" O   TYR B 551 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR B 557 " --> pdb=" O   ALA B 553 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ILE B 562 " --> pdb=" O   PHE B 558 " (cutoff:3.500A)
      Proline residue:  B 563  - end of helix
    Processing helix  chain 'B' and resid 569 through 587
      removed outlier: 3.588A  pdb=" N   PHE B 573 " --> pdb=" O   LEU B 569 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER B 581 " --> pdb=" O   CYS B 577 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLN B 585 " --> pdb=" O   SER B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 597 through 600
    Processing helix  chain 'B' and resid 601 through 606
    Processing helix  chain 'B' and resid 615 through 629
      removed outlier: 3.509A  pdb=" N   THR B 622 " --> pdb=" O   ASN B 618 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE B 624 " --> pdb=" O   MET B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 643
      removed outlier: 3.812A  pdb=" N   MET B 636 " --> pdb=" O   TRP B 632 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASP B 641 " --> pdb=" O   GLU B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 645 through 647
      No H-bonds generated for 'chain 'B' and resid 645 through 647'
    Processing helix  chain 'B' and resid 648 through 660
      removed outlier: 3.775A  pdb=" N   PHE B 652 " --> pdb=" O   SER B 648 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TYR B 656 " --> pdb=" O   PHE B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 684
      removed outlier: 3.526A  pdb=" N   GLU B 678 " --> pdb=" O   ALA B 674 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   GLU B 682 " --> pdb=" O   GLU B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 691
    Processing helix  chain 'B' and resid 697 through 702
      removed outlier: 3.676A  pdb=" N   SER B 701 " --> pdb=" O   ASN B 697 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 3.13 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1421
        1.31 -     1.43: 2512
        1.43 -     1.56: 5069
        1.56 -     1.68: 34
        1.68 -     1.81: 62
  Bond restraints: 9098
  Sorted by residual:
  bond pdb=" OG1 TPO B  26 "
       pdb=" P   TPO B  26 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" OG1 TPO A  29 "
       pdb=" P   TPO A  29 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.02e+01
  bond pdb=" OG1 TPO B  29 "
       pdb=" P   TPO B  29 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" OG1 TPO A  26 "
       pdb=" P   TPO A  26 "
    ideal  model  delta    sigma   weight residual
    1.717  1.614  0.103 2.00e-02 2.50e+03 2.67e+01
  bond pdb=" O1P TPO A  29 "
       pdb=" P   TPO A  29 "
    ideal  model  delta    sigma   weight residual
    1.525  1.610 -0.085 2.00e-02 2.50e+03 1.79e+01
  ... (remaining 9093 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.25: 11915
        4.25 -     8.51: 317
        8.51 -    12.76: 41
       12.76 -    17.02: 4
       17.02 -    21.27: 1
  Bond angle restraints: 12278
  Sorted by residual:
  angle pdb=" N   LEU A 610 "
        pdb=" CA  LEU A 610 "
        pdb=" C   LEU A 610 "
      ideal   model   delta    sigma   weight residual
     110.80   95.78   15.02 2.13e+00 2.20e-01 4.97e+01
  angle pdb=" C   LEU A 609 "
        pdb=" N   LEU A 610 "
        pdb=" CA  LEU A 610 "
      ideal   model   delta    sigma   weight residual
     121.54  134.53  -12.99 1.91e+00 2.74e-01 4.62e+01
  angle pdb=" CA  LEU A 610 "
        pdb=" CB  LEU A 610 "
        pdb=" CG  LEU A 610 "
      ideal   model   delta    sigma   weight residual
     116.30  137.57  -21.27 3.50e+00 8.16e-02 3.69e+01
  angle pdb=" C   THR B 263 "
        pdb=" N   THR B 264 "
        pdb=" CA  THR B 264 "
      ideal   model   delta    sigma   weight residual
     121.54  132.70  -11.16 1.91e+00 2.74e-01 3.41e+01
  angle pdb=" C   THR A 263 "
        pdb=" N   THR A 264 "
        pdb=" CA  THR A 264 "
      ideal   model   delta    sigma   weight residual
     121.54  131.82  -10.28 1.91e+00 2.74e-01 2.89e+01
  ... (remaining 12273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.95: 4623
       13.95 -    27.89: 514
       27.89 -    41.84: 130
       41.84 -    55.78: 67
       55.78 -    69.73: 38
  Dihedral angle restraints: 5372
    sinusoidal: 2210
      harmonic: 3162
  Sorted by residual:
  dihedral pdb=" CA  PHE B 611 "
           pdb=" C   PHE B 611 "
           pdb=" N   ASN B 612 "
           pdb=" CA  ASN B 612 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -128.46  -51.54     0      5.00e+00 4.00e-02 1.06e+02
  dihedral pdb=" CA  PHE A 611 "
           pdb=" C   PHE A 611 "
           pdb=" N   ASN A 612 "
           pdb=" CA  ASN A 612 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.19  -47.81     0      5.00e+00 4.00e-02 9.14e+01
  dihedral pdb=" CA  ILE B 660 "
           pdb=" C   ILE B 660 "
           pdb=" N   LEU B 661 "
           pdb=" CA  LEU B 661 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.62   40.38     0      5.00e+00 4.00e-02 6.52e+01
  ... (remaining 5369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1049
       0.083 -    0.166: 273
       0.166 -    0.249: 35
       0.249 -    0.333: 8
       0.333 -    0.416: 5
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CB  ILE B 186 "
            pdb=" CA  ILE B 186 "
            pdb=" CG1 ILE B 186 "
            pdb=" CG2 ILE B 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.42 2.00e-01 2.50e+01 4.32e+00
  chirality pdb=" CB  ILE A 186 "
            pdb=" CA  ILE A 186 "
            pdb=" CG1 ILE A 186 "
            pdb=" CG2 ILE A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.41 2.00e-01 2.50e+01 4.25e+00
  chirality pdb=" CB  ILE A 649 "
            pdb=" CA  ILE A 649 "
            pdb=" CG1 ILE A 649 "
            pdb=" CG2 ILE A 649 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.76e+00
  ... (remaining 1367 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 305 "   -0.020 2.00e-02 2.50e+03   2.36e-02 1.12e+01
        pdb=" CG  TYR A 305 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 305 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 305 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 305 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 305 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 305 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 305 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 305 "   -0.022 2.00e-02 2.50e+03   2.33e-02 1.09e+01
        pdb=" CG  TYR B 305 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 305 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 305 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 305 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 305 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 305 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 305 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 106 "    0.034 2.00e-02 2.50e+03   2.27e-02 1.03e+01
        pdb=" CG  TYR A 106 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 106 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 106 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 106 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 106 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 106 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 106 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 81
        2.56 -     3.15: 7067
        3.15 -     3.73: 13320
        3.73 -     4.32: 19471
        4.32 -     4.90: 31248
  Nonbonded interactions: 71187
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 114 "
            pdb=" OD2 ASP B 615 "
     model   vdw
     1.976 3.040
  nonbonded pdb=" OH  TYR A 114 "
            pdb=" OD2 ASP A 615 "
     model   vdw
     2.001 3.040
  nonbonded pdb=" OH  TYR A 305 "
            pdb=" OE2 GLU A 673 "
     model   vdw
     2.043 3.040
  nonbonded pdb=" OH  TYR B 305 "
            pdb=" OE2 GLU B 673 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" O   TYR A 579 "
            pdb=" OH  TYR A 651 "
     model   vdw
     2.151 3.040
  ... (remaining 71182 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 22 through 707 or resid 801 through 802 or resid 806 throu \ 
gh 809))
  selection = (chain 'B' and (resid 22 through 707 or resid 801 through 802 or resid 806 throu \ 
gh 809))
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.360
  Find NCS groups from input model:        0.350
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
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      :  0.018   0.139   9098  Z= 1.127
  Angle     :  1.611  21.272  12278  Z= 0.790
  Chirality :  0.079   0.416   1370
  Planarity :  0.009   0.073   1500
  Dihedral  : 14.976  69.726   3328
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.41 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.23 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.68 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.95 (0.17), residues: 1046
  helix: -4.07 (0.10), residues: 718
  sheet:  None (None), residues: 0
  loop : -3.05 (0.29), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.006   TRP B 632 
 HIS   0.008   0.005   HIS A  27 
 PHE   0.042   0.006   PHE B 652 
 TYR   0.058   0.007   TYR A 305 
 ARG   0.006   0.001   ARG A 700 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 HIS cc_start: 0.7170 (t70) cc_final: 0.6879 (t70)
REVERT: A   43 ASP cc_start: 0.8658 (m-30) cc_final: 0.8315 (m-30)
REVERT: A  115 LEU cc_start: 0.8069 (mt) cc_final: 0.7823 (mt)
REVERT: A  119 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6951 (mm-30)
REVERT: A  204 ASP cc_start: 0.7425 (m-30) cc_final: 0.6986 (m-30)
REVERT: A  210 SER cc_start: 0.8445 (m) cc_final: 0.8069 (p)
REVERT: A  319 MET cc_start: 0.7973 (tpt) cc_final: 0.7490 (tpt)
REVERT: A  324 ARG cc_start: 0.5677 (tpt-90) cc_final: 0.5353 (mtp180)
REVERT: A  388 PHE cc_start: 0.8079 (t80) cc_final: 0.7832 (t80)
REVERT: A  607 ASP cc_start: 0.8407 (t70) cc_final: 0.7978 (t70)
REVERT: A  634 VAL cc_start: 0.8995 (t) cc_final: 0.8663 (m)
REVERT: A  637 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6835 (tm-30)
REVERT: A  673 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7390 (mm-30)
REVERT: A  677 THR cc_start: 0.7191 (m) cc_final: 0.6903 (p)
REVERT: A  682 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6409 (tp30)
REVERT: B  107 TYR cc_start: 0.5114 (p90) cc_final: 0.4476 (m-10)
REVERT: B  204 ASP cc_start: 0.7273 (m-30) cc_final: 0.6972 (m-30)
REVERT: B  210 SER cc_start: 0.8468 (m) cc_final: 0.8127 (p)
REVERT: B  255 LEU cc_start: 0.8735 (tp) cc_final: 0.8497 (tp)
REVERT: B  319 MET cc_start: 0.7939 (tpt) cc_final: 0.7605 (tpt)
REVERT: B  324 ARG cc_start: 0.5538 (tpt-90) cc_final: 0.5301 (mtp180)
REVERT: B  338 LYS cc_start: 0.8773 (mttt) cc_final: 0.7596 (tptt)
REVERT: B  384 ASN cc_start: 0.6237 (t0) cc_final: 0.5844 (t0)
REVERT: B  607 ASP cc_start: 0.8500 (t0) cc_final: 0.8284 (t0)
REVERT: B  626 LEU cc_start: 0.8728 (mt) cc_final: 0.8523 (mp)
REVERT: B  634 VAL cc_start: 0.8841 (t) cc_final: 0.8489 (m)
REVERT: B  673 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7369 (mm-30)
REVERT: B  677 THR cc_start: 0.7336 (m) cc_final: 0.7055 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 290
  average time/residue: 0.2220
  time to fit residues: 87.6101
Evaluate side-chains
  211 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 210
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  612 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0000
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 242 GLN
A 585 GLN
A 618 ASN
** B  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
B 242 GLN
B 257 GLN
B 585 GLN
B 618 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.231325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.178957 restraints weight = 9271.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 2.32
r_work: 0.3892 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3747 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9098  Z= 0.239
  Angle     :  0.786  11.760  12278  Z= 0.403
  Chirality :  0.044   0.198   1370
  Planarity :  0.006   0.064   1500
  Dihedral  : 15.022  59.628   1452
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.93 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.22), residues: 1046
  helix: -2.18 (0.16), residues: 720
  sheet:  None (None), residues: 0
  loop : -2.58 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  92 
 HIS   0.007   0.002   HIS B  27 
 PHE   0.024   0.002   PHE B  67 
 TYR   0.025   0.003   TYR A 141 
 ARG   0.008   0.001   ARG B 200 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 243
  time to evaluate  : 0.979 
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   27 HIS cc_start: 0.6850 (t70) cc_final: 0.6629 (t70)
REVERT: A  115 LEU cc_start: 0.8259 (mt) cc_final: 0.7873 (mt)
REVERT: A  119 GLU cc_start: 0.7842 (mm-30) cc_final: 0.6881 (tm-30)
REVERT: A  166 ASP cc_start: 0.8139 (t0) cc_final: 0.7506 (t0)
REVERT: A  200 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7941 (ttp-170)
REVERT: A  210 SER cc_start: 0.8576 (m) cc_final: 0.8082 (p)
REVERT: A  319 MET cc_start: 0.8349 (tpt) cc_final: 0.7848 (tpt)
REVERT: A  550 ARG cc_start: 0.6891 (ttm-80) cc_final: 0.6529 (ttm-80)
REVERT: A  607 ASP cc_start: 0.8234 (t70) cc_final: 0.7868 (m-30)
REVERT: A  626 LEU cc_start: 0.9109 (mt) cc_final: 0.8886 (mp)
REVERT: A  634 VAL cc_start: 0.8973 (t) cc_final: 0.8633 (m)
REVERT: A  656 TYR cc_start: 0.8666 (t80) cc_final: 0.8105 (t80)
REVERT: A  660 ILE cc_start: 0.6195 (mm) cc_final: 0.5865 (tp)
REVERT: A  676 PHE cc_start: 0.7704 (m-10) cc_final: 0.7279 (m-10)
REVERT: A  677 THR cc_start: 0.7138 (m) cc_final: 0.6676 (p)
REVERT: A  678 GLU cc_start: 0.6658 (mp0) cc_final: 0.6034 (mp0)
REVERT: A  682 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6320 (tp30)
REVERT: B  115 LEU cc_start: 0.8070 (mt) cc_final: 0.7724 (mt)
REVERT: B  166 ASP cc_start: 0.8161 (t0) cc_final: 0.7606 (t0)
REVERT: B  200 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7885 (ttp-170)
REVERT: B  210 SER cc_start: 0.8598 (m) cc_final: 0.8196 (p)
REVERT: B  319 MET cc_start: 0.8230 (tpt) cc_final: 0.7810 (tpt)
REVERT: B  324 ARG cc_start: 0.5669 (tpt-90) cc_final: 0.5446 (mmm160)
REVERT: B  338 LYS cc_start: 0.8837 (mttt) cc_final: 0.7627 (tptt)
REVERT: B  607 ASP cc_start: 0.8276 (t0) cc_final: 0.7954 (t0)
REVERT: B  677 THR cc_start: 0.7313 (m) cc_final: 0.6961 (p)
  outliers start: 17
  outliers final: 9
  residues processed: 256
  average time/residue: 0.2189
  time to fit residues: 76.4488
Evaluate side-chains
  220 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 211
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain B residue  101 CYS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  233 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 85 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 134 HIS
** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 GLN
B 134 HIS
B 585 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.234538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.182637 restraints weight = 9490.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 2.24
r_work: 0.3932 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3789 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9098  Z= 0.233
  Angle     :  0.715  10.392  12278  Z= 0.361
  Chirality :  0.042   0.153   1370
  Planarity :  0.005   0.068   1500
  Dihedral  : 13.621  60.744   1452
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.38 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.24), residues: 1046
  helix: -1.31 (0.17), residues: 728
  sheet:  None (None), residues: 0
  loop : -2.27 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  92 
 HIS   0.007   0.001   HIS B  27 
 PHE   0.018   0.002   PHE B 624 
 TYR   0.021   0.002   TYR B 256 
 ARG   0.005   0.000   ARG B 200 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 226
  time to evaluate  : 0.941 
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   33 LYS cc_start: 0.8469 (pptt) cc_final: 0.8154 (ptpp)
REVERT: A   96 ASN cc_start: 0.8022 (p0) cc_final: 0.7635 (p0)
REVERT: A  115 LEU cc_start: 0.8191 (mt) cc_final: 0.7803 (mt)
REVERT: A  119 GLU cc_start: 0.7904 (mm-30) cc_final: 0.6963 (tm-30)
REVERT: A  153 ASN cc_start: 0.8111 (m110) cc_final: 0.7883 (m110)
REVERT: A  166 ASP cc_start: 0.8235 (t0) cc_final: 0.7602 (t0)
REVERT: A  200 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7904 (ttp-170)
REVERT: A  210 SER cc_start: 0.8559 (m) cc_final: 0.8117 (p)
REVERT: A  279 ARG cc_start: 0.9094 (mmt-90) cc_final: 0.6841 (mmt180)
REVERT: A  319 MET cc_start: 0.8334 (tpt) cc_final: 0.7969 (tpt)
REVERT: A  388 PHE cc_start: 0.7891 (t80) cc_final: 0.7463 (t80)
REVERT: A  634 VAL cc_start: 0.8930 (t) cc_final: 0.8673 (m)
REVERT: A  660 ILE cc_start: 0.6160 (mm) cc_final: 0.5757 (tp)
REVERT: A  676 PHE cc_start: 0.7702 (m-10) cc_final: 0.7311 (m-10)
REVERT: A  677 THR cc_start: 0.7061 (m) cc_final: 0.6514 (p)
REVERT: A  678 GLU cc_start: 0.6753 (mp0) cc_final: 0.6093 (mp0)
REVERT: A  682 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6401 (tp30)
REVERT: B  115 LEU cc_start: 0.7991 (mt) cc_final: 0.7679 (mt)
REVERT: B  137 PHE cc_start: 0.8852 (t80) cc_final: 0.8326 (t80)
REVERT: B  166 ASP cc_start: 0.8266 (t0) cc_final: 0.7722 (t0)
REVERT: B  210 SER cc_start: 0.8670 (m) cc_final: 0.8273 (p)
REVERT: B  263 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7198 (t)
REVERT: B  319 MET cc_start: 0.8305 (tpt) cc_final: 0.7878 (tpt)
REVERT: B  338 LYS cc_start: 0.8798 (mttt) cc_final: 0.7641 (tptt)
REVERT: B  607 ASP cc_start: 0.8104 (t0) cc_final: 0.7540 (m-30)
REVERT: B  663 LEU cc_start: 0.8699 (mt) cc_final: 0.8392 (mt)
REVERT: B  677 THR cc_start: 0.7358 (m) cc_final: 0.7002 (p)
REVERT: B  682 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6307 (tp30)
  outliers start: 19
  outliers final: 14
  residues processed: 238
  average time/residue: 0.2089
  time to fit residues: 68.6895
Evaluate side-chains
  225 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 210
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  101 CYS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  658 ILE
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 86 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 91 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    0.2980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 346 GLN
** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 585 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.235053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.181627 restraints weight = 9396.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4107 rms_B_bonded: 2.31
r_work: 0.3944 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3805 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9098  Z= 0.212
  Angle     :  0.689   9.121  12278  Z= 0.343
  Chirality :  0.042   0.202   1370
  Planarity :  0.004   0.067   1500
  Dihedral  : 12.710  63.244   1452
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 12.83 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.25), residues: 1046
  helix: -0.75 (0.18), residues: 732
  sheet:  None (None), residues: 0
  loop : -2.06 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  92 
 HIS   0.007   0.002   HIS B  27 
 PHE   0.028   0.001   PHE A  65 
 TYR   0.022   0.002   TYR B 216 
 ARG   0.002   0.000   ARG A 104 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 216
  time to evaluate  : 0.995 
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   33 LYS cc_start: 0.8558 (pptt) cc_final: 0.8284 (ptpp)
REVERT: A   96 ASN cc_start: 0.8043 (p0) cc_final: 0.7680 (p0)
REVERT: A  115 LEU cc_start: 0.8127 (mt) cc_final: 0.7674 (mt)
REVERT: A  119 GLU cc_start: 0.7913 (mm-30) cc_final: 0.6990 (tm-30)
REVERT: A  137 PHE cc_start: 0.8889 (t80) cc_final: 0.8561 (t80)
REVERT: A  166 ASP cc_start: 0.8176 (t0) cc_final: 0.7681 (t0)
REVERT: A  200 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7949 (ttp-170)
REVERT: A  210 SER cc_start: 0.8099 (m) cc_final: 0.7663 (p)
REVERT: A  319 MET cc_start: 0.8291 (tpt) cc_final: 0.7877 (tpt)
REVERT: A  388 PHE cc_start: 0.7901 (t80) cc_final: 0.7503 (t80)
REVERT: A  637 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7209 (tm-30)
REVERT: A  663 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8416 (mt)
REVERT: A  682 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6412 (tp30)
REVERT: B   95 LYS cc_start: 0.8137 (tppt) cc_final: 0.7742 (ttpt)
REVERT: B   96 ASN cc_start: 0.7956 (p0) cc_final: 0.7537 (p0)
REVERT: B  115 LEU cc_start: 0.7962 (mt) cc_final: 0.7656 (mt)
REVERT: B  137 PHE cc_start: 0.8863 (t80) cc_final: 0.8400 (t80)
REVERT: B  166 ASP cc_start: 0.8212 (t0) cc_final: 0.7710 (t0)
REVERT: B  210 SER cc_start: 0.8437 (m) cc_final: 0.8071 (p)
REVERT: B  263 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7153 (t)
REVERT: B  319 MET cc_start: 0.8232 (tpt) cc_final: 0.7815 (tpt)
REVERT: B  338 LYS cc_start: 0.8720 (mttt) cc_final: 0.7582 (tptt)
REVERT: B  607 ASP cc_start: 0.7999 (t0) cc_final: 0.7448 (m-30)
REVERT: B  622 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8541 (m)
REVERT: B  663 LEU cc_start: 0.8518 (mt) cc_final: 0.8238 (mt)
REVERT: B  677 THR cc_start: 0.7395 (m) cc_final: 0.7008 (p)
REVERT: B  682 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6256 (tp30)
  outliers start: 29
  outliers final: 17
  residues processed: 232
  average time/residue: 0.2050
  time to fit residues: 66.1504
Evaluate side-chains
  216 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 196
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain B residue   77 ASN
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  101 CYS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  622 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 90 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0170
   chunk 103 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 86 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 346 GLN
** A 612 ASN ** 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 = 0.4612 r_free = 0.4612 target = 0.235721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.183190 restraints weight = 9345.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 2.13
r_work: 0.3961 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3823 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9098  Z= 0.204
  Angle     :  0.672   8.667  12278  Z= 0.332
  Chirality :  0.041   0.146   1370
  Planarity :  0.004   0.066   1500
  Dihedral  : 12.153  62.738   1452
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.29 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.25), residues: 1046
  helix: -0.33 (0.18), residues: 734
  sheet:  None (None), residues: 0
  loop : -1.92 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  92 
 HIS   0.007   0.002   HIS B  27 
 PHE   0.028   0.001   PHE A  65 
 TYR   0.021   0.002   TYR A 216 
 ARG   0.002   0.000   ARG A  69 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 0.924 
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   95 LYS cc_start: 0.8128 (tppt) cc_final: 0.7770 (ttpt)
REVERT: A  115 LEU cc_start: 0.8125 (mt) cc_final: 0.7698 (mt)
REVERT: A  119 GLU cc_start: 0.7959 (mm-30) cc_final: 0.6929 (tm-30)
REVERT: A  137 PHE cc_start: 0.8885 (t80) cc_final: 0.8438 (t80)
REVERT: A  166 ASP cc_start: 0.8128 (t0) cc_final: 0.7678 (t0)
REVERT: A  200 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7944 (ttp-170)
REVERT: A  210 SER cc_start: 0.8078 (m) cc_final: 0.7719 (p)
REVERT: A  319 MET cc_start: 0.8162 (tpt) cc_final: 0.7774 (tpt)
REVERT: A  388 PHE cc_start: 0.8022 (t80) cc_final: 0.7631 (t80)
REVERT: A  660 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5269 (tp)
REVERT: A  663 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8199 (mt)
REVERT: A  682 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6398 (tp30)
REVERT: B   95 LYS cc_start: 0.8095 (tppt) cc_final: 0.7674 (ttpt)
REVERT: B   96 ASN cc_start: 0.7846 (p0) cc_final: 0.7452 (p0)
REVERT: B  115 LEU cc_start: 0.7994 (mt) cc_final: 0.7693 (mt)
REVERT: B  137 PHE cc_start: 0.8890 (t80) cc_final: 0.8452 (t80)
REVERT: B  166 ASP cc_start: 0.8253 (t0) cc_final: 0.7759 (t0)
REVERT: B  210 SER cc_start: 0.8165 (m) cc_final: 0.7875 (p)
REVERT: B  319 MET cc_start: 0.8162 (tpt) cc_final: 0.7793 (tpt)
REVERT: B  338 LYS cc_start: 0.8698 (mttt) cc_final: 0.7533 (tptp)
REVERT: B  607 ASP cc_start: 0.7876 (t0) cc_final: 0.7550 (m-30)
REVERT: B  682 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6247 (tp30)
  outliers start: 30
  outliers final: 18
  residues processed: 215
  average time/residue: 0.2074
  time to fit residues: 61.5136
Evaluate side-chains
  210 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  101 CYS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 71 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0970
   chunk 48 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 ASN ** 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 = 0.4622 r_free = 0.4622 target = 0.236845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.184191 restraints weight = 9435.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 2.17
r_work: 0.3978 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3841 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9098  Z= 0.192
  Angle     :  0.666  11.931  12278  Z= 0.327
  Chirality :  0.041   0.143   1370
  Planarity :  0.004   0.065   1500
  Dihedral  : 11.664  65.638   1452
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 14.84 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.26), residues: 1046
  helix:  0.02 (0.19), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.69 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  92 
 HIS   0.007   0.002   HIS B  27 
 PHE   0.017   0.001   PHE B 554 
 TYR   0.025   0.002   TYR B 107 
 ARG   0.002   0.000   ARG A 104 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 202
  time to evaluate  : 0.927 
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   33 LYS cc_start: 0.8512 (pptt) cc_final: 0.8208 (ptpp)
REVERT: A   95 LYS cc_start: 0.8150 (tppt) cc_final: 0.7826 (ttpt)
REVERT: A  115 LEU cc_start: 0.8130 (mt) cc_final: 0.7702 (mt)
REVERT: A  119 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7093 (tm-30)
REVERT: A  137 PHE cc_start: 0.8881 (t80) cc_final: 0.8420 (t80)
REVERT: A  151 ARG cc_start: 0.6976 (ttp-170) cc_final: 0.6263 (ptm160)
REVERT: A  166 ASP cc_start: 0.8172 (t0) cc_final: 0.7707 (t0)
REVERT: A  210 SER cc_start: 0.8098 (m) cc_final: 0.7724 (p)
REVERT: A  319 MET cc_start: 0.8130 (tpt) cc_final: 0.7761 (tpt)
REVERT: A  660 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.5063 (tp)
REVERT: A  663 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8208 (mt)
REVERT: B   95 LYS cc_start: 0.7976 (tppt) cc_final: 0.7614 (ttpt)
REVERT: B   96 ASN cc_start: 0.7805 (p0) cc_final: 0.7442 (p0)
REVERT: B  115 LEU cc_start: 0.7894 (mt) cc_final: 0.7601 (mt)
REVERT: B  137 PHE cc_start: 0.8868 (t80) cc_final: 0.8453 (t80)
REVERT: B  166 ASP cc_start: 0.8214 (t0) cc_final: 0.7760 (t0)
REVERT: B  210 SER cc_start: 0.8253 (m) cc_final: 0.7906 (p)
REVERT: B  306 ASP cc_start: 0.8786 (t0) cc_final: 0.8335 (t0)
REVERT: B  319 MET cc_start: 0.8015 (tpt) cc_final: 0.7677 (tpt)
REVERT: B  338 LYS cc_start: 0.8673 (mttt) cc_final: 0.7565 (tptp)
REVERT: B  387 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8004 (mp0)
REVERT: B  607 ASP cc_start: 0.7773 (t0) cc_final: 0.7535 (m-30)
REVERT: B  663 LEU cc_start: 0.8980 (mm) cc_final: 0.8683 (mt)
REVERT: B  682 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6233 (tp30)
  outliers start: 34
  outliers final: 19
  residues processed: 219
  average time/residue: 0.2014
  time to fit residues: 61.9494
Evaluate side-chains
  211 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain B residue   77 ASN
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  101 CYS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0470
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 ASN ** 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 = 0.4620 r_free = 0.4620 target = 0.236583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.184077 restraints weight = 9426.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 2.23
r_work: 0.3985 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9098  Z= 0.203
  Angle     :  0.682  14.082  12278  Z= 0.329
  Chirality :  0.041   0.146   1370
  Planarity :  0.004   0.067   1500
  Dihedral  : 11.369  65.412   1452
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.96 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.26), residues: 1046
  helix:  0.24 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop : -1.62 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  92 
 HIS   0.007   0.002   HIS B  27 
 PHE   0.017   0.001   PHE B 554 
 TYR   0.022   0.002   TYR A 141 
 ARG   0.006   0.000   ARG A 200 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 200
  time to evaluate  : 0.971 
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   33 LYS cc_start: 0.8509 (pptt) cc_final: 0.8180 (ptpp)
REVERT: A   95 LYS cc_start: 0.8054 (tppt) cc_final: 0.7749 (ttpt)
REVERT: A  111 GLU cc_start: 0.7331 (tp30) cc_final: 0.7109 (tt0)
REVERT: A  114 TYR cc_start: 0.8030 (m-10) cc_final: 0.7807 (m-80)
REVERT: A  115 LEU cc_start: 0.8134 (mt) cc_final: 0.7760 (mt)
REVERT: A  119 GLU cc_start: 0.7899 (mm-30) cc_final: 0.6960 (tm-30)
REVERT: A  137 PHE cc_start: 0.8938 (t80) cc_final: 0.8510 (t80)
REVERT: A  142 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8144 (mt-10)
REVERT: A  151 ARG cc_start: 0.6965 (ttp-170) cc_final: 0.6284 (ptm160)
REVERT: A  166 ASP cc_start: 0.8315 (t0) cc_final: 0.7739 (t0)
REVERT: A  200 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7762 (ttp-170)
REVERT: A  210 SER cc_start: 0.8207 (m) cc_final: 0.7858 (p)
REVERT: A  213 LEU cc_start: 0.9125 (mm) cc_final: 0.8843 (mm)
REVERT: A  319 MET cc_start: 0.8085 (tpt) cc_final: 0.7754 (tpt)
REVERT: A  660 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4685 (tp)
REVERT: A  663 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8210 (mt)
REVERT: A  676 PHE cc_start: 0.7653 (m-10) cc_final: 0.7362 (m-10)
REVERT: B   96 ASN cc_start: 0.7833 (p0) cc_final: 0.7501 (p0)
REVERT: B  115 LEU cc_start: 0.7873 (mt) cc_final: 0.7587 (mt)
REVERT: B  137 PHE cc_start: 0.8813 (t80) cc_final: 0.8387 (t80)
REVERT: B  166 ASP cc_start: 0.8352 (t0) cc_final: 0.7797 (t0)
REVERT: B  210 SER cc_start: 0.8239 (m) cc_final: 0.7880 (p)
REVERT: B  306 ASP cc_start: 0.8726 (t0) cc_final: 0.8386 (t0)
REVERT: B  319 MET cc_start: 0.7980 (tpt) cc_final: 0.7632 (tpt)
REVERT: B  387 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7946 (mp0)
REVERT: B  663 LEU cc_start: 0.9068 (mm) cc_final: 0.8817 (mt)
REVERT: B  682 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6197 (tp30)
  outliers start: 27
  outliers final: 19
  residues processed: 214
  average time/residue: 0.2036
  time to fit residues: 61.5674
Evaluate side-chains
  212 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  101 CYS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0000
   chunk 76 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 86 optimal weight:    0.1980
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 ASN ** 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 = 0.4637 r_free = 0.4637 target = 0.239401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.188422 restraints weight = 9531.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 2.23
r_work: 0.4026 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3897 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9098  Z= 0.184
  Angle     :  0.669  11.467  12278  Z= 0.324
  Chirality :  0.041   0.205   1370
  Planarity :  0.005   0.066   1500
  Dihedral  : 10.701  59.489   1450
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.19 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.26), residues: 1046
  helix:  0.43 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop : -1.56 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  92 
 HIS   0.007   0.002   HIS B  27 
 PHE   0.017   0.001   PHE A 554 
 TYR   0.021   0.002   TYR A 141 
 ARG   0.004   0.000   ARG A 200 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7137 (mm-30)
REVERT: A  137 PHE cc_start: 0.8843 (t80) cc_final: 0.8403 (t80)
REVERT: A  142 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8131 (mt-10)
REVERT: A  151 ARG cc_start: 0.6832 (ttp-170) cc_final: 0.6244 (ptm160)
REVERT: A  166 ASP cc_start: 0.8202 (t0) cc_final: 0.7754 (t0)
REVERT: A  200 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7727 (ttp-170)
REVERT: A  210 SER cc_start: 0.8173 (m) cc_final: 0.7828 (p)
REVERT: A  213 LEU cc_start: 0.9037 (mm) cc_final: 0.8775 (mm)
REVERT: A  272 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8685 (mm)
REVERT: A  319 MET cc_start: 0.7917 (tpt) cc_final: 0.7636 (tpt)
REVERT: B   96 ASN cc_start: 0.7739 (p0) cc_final: 0.7440 (p0)
REVERT: B  115 LEU cc_start: 0.7843 (mt) cc_final: 0.7560 (mt)
REVERT: B  137 PHE cc_start: 0.8787 (t80) cc_final: 0.8410 (t80)
REVERT: B  166 ASP cc_start: 0.8261 (t0) cc_final: 0.7816 (t0)
REVERT: B  210 SER cc_start: 0.8402 (m) cc_final: 0.8097 (p)
REVERT: B  306 ASP cc_start: 0.8528 (t0) cc_final: 0.8298 (t0)
REVERT: B  319 MET cc_start: 0.7968 (tpt) cc_final: 0.7640 (tpt)
REVERT: B  335 ASP cc_start: 0.6935 (m-30) cc_final: 0.6009 (t70)
REVERT: B  663 LEU cc_start: 0.9090 (mm) cc_final: 0.8826 (mp)
REVERT: B  682 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6137 (tp30)
  outliers start: 25
  outliers final: 13
  residues processed: 215
  average time/residue: 0.1903
  time to fit residues: 57.8365
Evaluate side-chains
  208 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 194
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.236479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.185960 restraints weight = 9438.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 1.98
r_work: 0.3998 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3875 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9098  Z= 0.253
  Angle     :  0.717  11.203  12278  Z= 0.348
  Chirality :  0.043   0.192   1370
  Planarity :  0.005   0.066   1500
  Dihedral  : 10.989  59.717   1450
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.86 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.26), residues: 1046
  helix:  0.42 (0.19), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.49 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  92 
 HIS   0.008   0.003   HIS A  27 
 PHE   0.023   0.001   PHE B 554 
 TYR   0.023   0.002   TYR B 141 
 ARG   0.006   0.000   ARG B  69 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 0.905 
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  119 GLU cc_start: 0.7776 (mm-30) cc_final: 0.6957 (mm-30)
REVERT: A  137 PHE cc_start: 0.8817 (t80) cc_final: 0.8354 (t80)
REVERT: A  151 ARG cc_start: 0.6898 (ttp-170) cc_final: 0.6291 (ptm160)
REVERT: A  166 ASP cc_start: 0.8224 (t0) cc_final: 0.7767 (t0)
REVERT: A  200 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7715 (ttp-170)
REVERT: A  210 SER cc_start: 0.8133 (m) cc_final: 0.7752 (p)
REVERT: A  213 LEU cc_start: 0.9048 (mm) cc_final: 0.8791 (mm)
REVERT: A  319 MET cc_start: 0.8024 (tpt) cc_final: 0.7769 (tpt)
REVERT: A  660 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.4596 (tp)
REVERT: B   96 ASN cc_start: 0.7859 (p0) cc_final: 0.7620 (p0)
REVERT: B  115 LEU cc_start: 0.7867 (mt) cc_final: 0.7590 (mt)
REVERT: B  137 PHE cc_start: 0.8811 (t80) cc_final: 0.8405 (t80)
REVERT: B  166 ASP cc_start: 0.8306 (t0) cc_final: 0.7822 (t0)
REVERT: B  210 SER cc_start: 0.8329 (m) cc_final: 0.8080 (p)
REVERT: B  306 ASP cc_start: 0.8624 (t0) cc_final: 0.8310 (t0)
REVERT: B  319 MET cc_start: 0.7930 (tpt) cc_final: 0.7611 (tpt)
REVERT: B  663 LEU cc_start: 0.9131 (mm) cc_final: 0.8801 (mp)
REVERT: B  682 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6287 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 204
  average time/residue: 0.2067
  time to fit residues: 59.0313
Evaluate side-chains
  204 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  101 CYS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 ASN ** 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 = 0.4627 r_free = 0.4627 target = 0.238327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.187772 restraints weight = 9363.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 2.00
r_work: 0.4016 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3887 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9098  Z= 0.215
  Angle     :  0.696  10.974  12278  Z= 0.339
  Chirality :  0.042   0.186   1370
  Planarity :  0.005   0.065   1500
  Dihedral  : 10.675  59.880   1450
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.75 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.26), residues: 1046
  helix:  0.49 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -1.48 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  92 
 HIS   0.008   0.003   HIS A  27 
 PHE   0.018   0.001   PHE B 554 
 TYR   0.040   0.002   TYR A 305 
 ARG   0.006   0.000   ARG B  69 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 198
  time to evaluate  : 0.950 
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  119 GLU cc_start: 0.7745 (mm-30) cc_final: 0.6892 (mm-30)
REVERT: A  137 PHE cc_start: 0.8856 (t80) cc_final: 0.8426 (t80)
REVERT: A  166 ASP cc_start: 0.8261 (t0) cc_final: 0.7792 (t0)
REVERT: A  200 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7687 (ttp-170)
REVERT: A  210 SER cc_start: 0.8146 (m) cc_final: 0.7738 (p)
REVERT: A  213 LEU cc_start: 0.9040 (mm) cc_final: 0.8778 (mm)
REVERT: A  319 MET cc_start: 0.7997 (tpt) cc_final: 0.7749 (tpt)
REVERT: A  632 TRP cc_start: 0.8646 (p-90) cc_final: 0.7939 (p-90)
REVERT: A  660 ILE cc_start: 0.5061 (OUTLIER) cc_final: 0.4503 (tp)
REVERT: B   67 PHE cc_start: 0.7443 (m-80) cc_final: 0.6917 (m-80)
REVERT: B   96 ASN cc_start: 0.7759 (p0) cc_final: 0.7458 (p0)
REVERT: B  115 LEU cc_start: 0.7811 (mt) cc_final: 0.7542 (mt)
REVERT: B  137 PHE cc_start: 0.8781 (t80) cc_final: 0.8361 (t80)
REVERT: B  166 ASP cc_start: 0.8301 (t0) cc_final: 0.7822 (t0)
REVERT: B  210 SER cc_start: 0.8056 (m) cc_final: 0.7795 (p)
REVERT: B  306 ASP cc_start: 0.8614 (t0) cc_final: 0.8277 (t0)
REVERT: B  319 MET cc_start: 0.7902 (tpt) cc_final: 0.7572 (tpt)
REVERT: B  663 LEU cc_start: 0.9083 (mm) cc_final: 0.8848 (mt)
REVERT: B  682 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6247 (tm-30)
  outliers start: 16
  outliers final: 14
  residues processed: 210
  average time/residue: 0.2007
  time to fit residues: 59.0592
Evaluate side-chains
  206 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 191
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 CYS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  659 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 80 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 ASN ** 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 = 0.4628 r_free = 0.4628 target = 0.238298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.187509 restraints weight = 9376.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 2.20
r_work: 0.4007 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3877 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9098  Z= 0.216
  Angle     :  0.708  12.201  12278  Z= 0.342
  Chirality :  0.042   0.176   1370
  Planarity :  0.005   0.064   1500
  Dihedral  : 10.637  59.687   1450
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.42 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.26), residues: 1046
  helix:  0.49 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -1.43 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  92 
 HIS   0.008   0.003   HIS A  27 
 PHE   0.022   0.001   PHE B 388 
 TYR   0.045   0.002   TYR A 305 
 ARG   0.009   0.000   ARG B  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5411.00 seconds
wall clock time: 96 minutes 16.43 seconds (5776.43 seconds total)