Starting phenix.real_space_refine
on Tue Feb 13 22:06:25 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsp_32763/02_2024/7wsp_32763.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsp_32763/02_2024/7wsp_32763.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsp_32763/02_2024/7wsp_32763.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsp_32763/02_2024/7wsp_32763.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsp_32763/02_2024/7wsp_32763.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsp_32763/02_2024/7wsp_32763.pdb"
  }
  resolution = 4.09
  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=   0.003 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4993      2.51       5
     N    1344      2.21       5
     O    1506      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  131": "NH1" <-> "NH2"
    Residue "C ARG   51": "NH1" <-> "NH2"
    Residue "D PHE  492": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 7883
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1076
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "C"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1128
          Classifications: {'peptide': 139}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 135}
    Chain: "B"
      Number of atoms: 2837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2837
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 339}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 2842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2842
          Classifications: {'peptide': 367}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 341}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 4.74, per 1000 atoms: 0.60
  Number of scatterers: 7883
  At special positions: 0
  Unit cell: (68.2, 104.5, 192.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1506      8.00
     N    1344      7.00
     C    4993      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 106 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS C 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 122 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 270 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS D 350 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 380 " - pdb=" SG  CYS B 439 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 487 " - pdb=" SG  CYS B 549 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 270 " - pdb=" SG  CYS D 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 380 " - pdb=" SG  CYS D 439 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 487 " - pdb=" SG  CYS D 549 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.08
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 21 sheets defined
      18.2% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 166
      removed outlier: 4.214A  pdb=" N   ARG A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   VAL A 158 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
      removed outlier: 3.913A  pdb=" N   LEU A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 117
      removed outlier: 3.846A  pdb=" N   ASN C 117 " --> pdb=" O   PHE C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 181
      removed outlier: 3.811A  pdb=" N   LYS C 152 " --> pdb=" O   LEU C 148 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      Proline residue:  C 176  - end of helix
    Processing helix  chain 'B' and resid 322 through 326
    Processing helix  chain 'B' and resid 427 through 434
      removed outlier: 3.992A  pdb=" N   TRP B 431 " --> pdb=" O   CYS B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 479
      removed outlier: 3.959A  pdb=" N   ASN B 478 " --> pdb=" O   ARG B 474 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 479 " --> pdb=" O   GLU B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 542
      removed outlier: 3.717A  pdb=" N   TRP B 541 " --> pdb=" O   SER B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 607
      removed outlier: 3.735A  pdb=" N   TRP B 584 " --> pdb=" O   PHE B 580 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE B 599 " --> pdb=" O   LEU B 595 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   TYR B 600 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   THR B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL B 604 " --> pdb=" O   TYR B 600 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 322 through 327
    Processing helix  chain 'D' and resid 368 through 374
      removed outlier: 4.135A  pdb=" N   LEU D 372 " --> pdb=" O   ALA D 368 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   THR D 373 " --> pdb=" O   SER D 369 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 480
    Processing helix  chain 'D' and resid 537 through 542
    Processing helix  chain 'D' and resid 575 through 607
      removed outlier: 3.989A  pdb=" N   THR D 605 " --> pdb=" O   SER D 601 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44
      removed outlier: 3.944A  pdb=" N   ARG A 124 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL A  44 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 83
      removed outlier: 4.016A  pdb=" N   GLU A  79 " --> pdb=" O   ARG A  68 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG A  68 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   TRP A  66 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   VAL A  64 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 103 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 49
      removed outlier: 3.558A  pdb=" N   VAL C  61 " --> pdb=" O   ILE C 109 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE C 109 " --> pdb=" O   VAL C  61 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU C 107 " --> pdb=" O   MET C  63 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA C 105 " --> pdb=" O   CYS C  65 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU C 104 " --> pdb=" O   ASN C 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 56
      removed outlier: 6.485A  pdb=" N   ILE C  53 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   MET C 143 " --> pdb=" O   ILE C  53 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ARG C  55 " --> pdb=" O   MET C 143 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88
      removed outlier: 3.802A  pdb=" N   TRP C  78 " --> pdb=" O   GLN C  87 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 251 through 252
      removed outlier: 4.186A  pdb=" N   ILE B 269 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS B 270 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER B 316 " --> pdb=" O   CYS B 270 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA B 272 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL B 314 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   TYR B 312 " --> pdb=" O   GLY B 274 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 252
      removed outlier: 4.186A  pdb=" N   ILE B 269 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS B 270 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER B 316 " --> pdb=" O   CYS B 270 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA B 272 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL B 314 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   TYR B 312 " --> pdb=" O   GLY B 274 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 290
      removed outlier: 3.520A  pdb=" N   CYS B 333 " --> pdb=" O   GLN B 344 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 381 through 385
      removed outlier: 3.599A  pdb=" N   VAL B 382 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 384 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 396
      removed outlier: 3.794A  pdb=" N   THR B 440 " --> pdb=" O   SER B 394 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 466 through 470
      removed outlier: 3.608A  pdb=" N   ASP B 466 " --> pdb=" O   THR B 490 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR B 490 " --> pdb=" O   ASP B 466 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR B 486 " --> pdb=" O   LEU B 470 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER B 532 " --> pdb=" O   CYS B 487 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL B 489 " --> pdb=" O   ALA B 530 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   TYR B 528 " --> pdb=" O   GLY B 491 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 506 through 507
      removed outlier: 3.798A  pdb=" N   GLN B 503 " --> pdb=" O   GLN B 506 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN B 500 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 252
      removed outlier: 4.122A  pdb=" N   THR D 273 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ILE D 269 " --> pdb=" O   PHE D 252 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   ILE D 269 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU D 318 " --> pdb=" O   ILE D 269 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   GLN D 271 " --> pdb=" O   SER D 316 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   SER D 316 " --> pdb=" O   GLN D 271 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   THR D 273 " --> pdb=" O   VAL D 314 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL D 314 " --> pdb=" O   THR D 273 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 248 through 252
      removed outlier: 4.122A  pdb=" N   THR D 273 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ILE D 269 " --> pdb=" O   PHE D 252 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   ILE D 269 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU D 318 " --> pdb=" O   ILE D 269 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   GLN D 271 " --> pdb=" O   SER D 316 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   SER D 316 " --> pdb=" O   GLN D 271 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   THR D 273 " --> pdb=" O   VAL D 314 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL D 314 " --> pdb=" O   THR D 273 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 266
    Processing sheet with id=AB7, first strand: chain 'D' and resid 281 through 283
      removed outlier: 3.587A  pdb=" N   HIS D 337 " --> pdb=" O   LEU D 340 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 331 through 332
    Processing sheet with id=AB9, first strand: chain 'D' and resid 360 through 362
      removed outlier: 3.564A  pdb=" N   GLY D 422 " --> pdb=" O   CYS D 380 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 392 through 396
    Processing sheet with id=AC2, first strand: chain 'D' and resid 466 through 470
      removed outlier: 3.526A  pdb=" N   ASP D 466 " --> pdb=" O   THR D 490 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU D 488 " --> pdb=" O   TYR D 468 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR D 486 " --> pdb=" O   LEU D 470 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   TYR D 528 " --> pdb=" O   GLY D 491 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 501 through 502

    245 hydrogen bonds defined for protein.
    642 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: 2.31

  Time building geometry restraints manager: 3.32 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2477
        1.34 -     1.46: 1954
        1.46 -     1.59: 3589
        1.59 -     1.71: 0
        1.71 -     1.84: 56
  Bond restraints: 8076
  Sorted by residual:
  bond pdb=" C   VAL D 351 "
       pdb=" N   PRO D 352 "
    ideal  model  delta    sigma   weight residual
    1.330  1.366 -0.036 1.19e-02 7.06e+03 8.96e+00
  bond pdb=" CA  TYR D 468 "
       pdb=" CB  TYR D 468 "
    ideal  model  delta    sigma   weight residual
    1.527  1.477  0.050 1.75e-02 3.27e+03 8.08e+00
  bond pdb=" CB  TRP C  47 "
       pdb=" CG  TRP C  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.431  0.067 3.10e-02 1.04e+03 4.63e+00
  bond pdb=" CB  VAL C 142 "
       pdb=" CG2 VAL C 142 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.77e+00
  bond pdb=" CB  PHE D 594 "
       pdb=" CG  PHE D 594 "
    ideal  model  delta    sigma   weight residual
    1.502  1.459  0.043 2.30e-02 1.89e+03 3.46e+00
  ... (remaining 8071 not shown)

  Histogram of bond angle deviations from ideal:
       97.71 -   104.98: 212
      104.98 -   112.24: 3993
      112.24 -   119.50: 2719
      119.50 -   126.76: 3931
      126.76 -   134.02: 150
  Bond angle restraints: 11005
  Sorted by residual:
  angle pdb=" C   ASP A 135 "
        pdb=" N   MET A 136 "
        pdb=" CA  MET A 136 "
      ideal   model   delta    sigma   weight residual
     121.54  132.17  -10.63 1.91e+00 2.74e-01 3.10e+01
  angle pdb=" C   GLU D 545 "
        pdb=" N   THR D 546 "
        pdb=" CA  THR D 546 "
      ideal   model   delta    sigma   weight residual
     121.54  131.29   -9.75 1.91e+00 2.74e-01 2.61e+01
  angle pdb=" N   VAL A 158 "
        pdb=" CA  VAL A 158 "
        pdb=" C   VAL A 158 "
      ideal   model   delta    sigma   weight residual
     108.88  119.79  -10.91 2.16e+00 2.14e-01 2.55e+01
  angle pdb=" N   GLU B 570 "
        pdb=" CA  GLU B 570 "
        pdb=" C   GLU B 570 "
      ideal   model   delta    sigma   weight residual
     110.80  100.66   10.14 2.13e+00 2.20e-01 2.27e+01
  angle pdb=" C   LEU A  70 "
        pdb=" N   HIS A  71 "
        pdb=" CA  HIS A  71 "
      ideal   model   delta    sigma   weight residual
     121.19  128.51   -7.32 1.59e+00 3.96e-01 2.12e+01
  ... (remaining 11000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.52: 4494
       15.52 -    31.04: 283
       31.04 -    46.56: 76
       46.56 -    62.07: 6
       62.07 -    77.59: 2
  Dihedral angle restraints: 4861
    sinusoidal: 1937
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" CA  VAL D 351 "
           pdb=" C   VAL D 351 "
           pdb=" N   PRO D 352 "
           pdb=" CA  PRO D 352 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.04  -48.96     0      5.00e+00 4.00e-02 9.59e+01
  dihedral pdb=" CA  GLN A 127 "
           pdb=" C   GLN A 127 "
           pdb=" N   PRO A 128 "
           pdb=" CA  PRO A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.05  -43.95     0      5.00e+00 4.00e-02 7.73e+01
  dihedral pdb=" CA  GLU B 577 "
           pdb=" C   GLU B 577 "
           pdb=" N   GLU B 578 "
           pdb=" CA  GLU B 578 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.80  -39.20     0      5.00e+00 4.00e-02 6.15e+01
  ... (remaining 4858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1073
       0.089 -    0.179: 168
       0.179 -    0.268: 12
       0.268 -    0.358: 0
       0.358 -    0.447: 1
  Chirality restraints: 1254
  Sorted by residual:
  chirality pdb=" CB  ILE B 358 "
            pdb=" CA  ILE B 358 "
            pdb=" CG1 ILE B 358 "
            pdb=" CG2 ILE B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.45 2.00e-01 2.50e+01 5.00e+00
  chirality pdb=" CB  VAL B 497 "
            pdb=" CA  VAL B 497 "
            pdb=" CG1 VAL B 497 "
            pdb=" CG2 VAL B 497 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A  38 "
            pdb=" CA  VAL A  38 "
            pdb=" CG1 VAL A  38 "
            pdb=" CG2 VAL A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1251 not shown)

  Planarity restraints: 1419
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 509 "   -0.052 5.00e-02 4.00e+02   7.81e-02 9.76e+00
        pdb=" N   PRO B 510 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO B 510 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 510 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 577 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.48e+00
        pdb=" C   GLU B 577 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLU B 577 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU B 578 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 413 "   -0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO D 414 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO D 414 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D 414 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1416 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1021
        2.75 -     3.29: 7339
        3.29 -     3.82: 12572
        3.82 -     4.36: 13578
        4.36 -     4.90: 23414
  Nonbonded interactions: 57924
  Sorted by model distance:
  nonbonded pdb=" O   THR D 546 "
            pdb=" OG1 THR D 564 "
     model   vdw
     2.212 2.440
  nonbonded pdb=" O   PHE D 599 "
            pdb=" OG1 THR D 603 "
     model   vdw
     2.234 2.440
  nonbonded pdb=" OG1 THR B 396 "
            pdb=" OG1 THR B 438 "
     model   vdw
     2.263 2.440
  nonbonded pdb=" O   MET B 502 "
            pdb=" OG1 THR B 548 "
     model   vdw
     2.268 2.440
  nonbonded pdb=" O   LEU D 583 "
            pdb=" OG1 THR D 586 "
     model   vdw
     2.272 2.440
  ... (remaining 57919 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 242 through 352 or (resid 353 through 355 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 356 through 357 or (resid 358  \ 
and (name N or name CA or name C or name O or name CB )) or resid 359 through 60 \ 
7))
  selection = (chain 'D' and (resid 242 through 255 or (resid 256 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 257 through 348 or (resid 349 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 350 through 607))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          4.010
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     25.640
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.040
  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:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.085   8076  Z= 0.529
  Angle     :  1.115  10.908  11005  Z= 0.600
  Chirality :  0.062   0.447   1254
  Planarity :  0.008   0.078   1419
  Dihedral  : 10.989  77.592   2933
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 13.19 %
    Favored  : 86.61 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.75 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.43 %

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: -4.84 (0.21), residues: 1001
  helix: -3.07 (0.27), residues: 156
  sheet: -3.04 (0.30), residues: 240
  loop : -3.48 (0.21), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP D 541 
 HIS   0.013   0.003   HIS A  71 
 PHE   0.026   0.003   PHE C 145 
 TYR   0.037   0.004   TYR C  66 
 ARG   0.006   0.001   ARG B 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.996 
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: C   96 MET cc_start: 0.7860 (mtt) cc_final: 0.7251 (mtt)
REVERT: B  502 MET cc_start: 0.7947 (mmm) cc_final: 0.7654 (mtm)
REVERT: D  395 TRP cc_start: 0.8311 (m100) cc_final: 0.7553 (m100)
REVERT: D  513 TYR cc_start: 0.7339 (p90) cc_final: 0.6647 (p90)
  outliers start: 6
  outliers final: 2
  residues processed: 147
  average time/residue: 0.2127
  time to fit residues: 41.8600
Evaluate side-chains
  81 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 29 optimal weight:   20.0000
   chunk 46 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 406 HIS
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 271 GLN
D 343 GLN
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8076  Z= 0.231
  Angle     :  0.730   9.149  11005  Z= 0.380
  Chirality :  0.046   0.185   1254
  Planarity :  0.006   0.059   1419
  Dihedral  :  6.664  32.683   1074
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.19 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.11 %

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: -3.98 (0.24), residues: 1001
  helix: -1.30 (0.36), residues: 171
  sheet: -2.60 (0.31), residues: 256
  loop : -3.21 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 584 
 HIS   0.005   0.001   HIS B 406 
 PHE   0.016   0.001   PHE D 580 
 TYR   0.015   0.001   TYR C  66 
 ARG   0.006   0.001   ARG D 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.987 
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  144 ILE cc_start: 0.8580 (mm) cc_final: 0.8377 (mm)
REVERT: A  148 GLU cc_start: 0.7881 (tt0) cc_final: 0.7640 (tt0)
REVERT: C   96 MET cc_start: 0.7439 (mtt) cc_final: 0.7191 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2085
  time to fit residues: 30.7861
Evaluate side-chains
  69 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0070
   chunk 60 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   chunk 79 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 71 optimal weight:   10.0000
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 HIS
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 531 HIS
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 343 GLN
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8076  Z= 0.173
  Angle     :  0.662   7.958  11005  Z= 0.339
  Chirality :  0.044   0.167   1254
  Planarity :  0.005   0.049   1419
  Dihedral  :  5.912  29.900   1074
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -3.41 (0.25), residues: 1001
  helix: -0.63 (0.36), residues: 171
  sheet: -2.24 (0.31), residues: 257
  loop : -2.90 (0.24), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 584 
 HIS   0.003   0.001   HIS A  71 
 PHE   0.019   0.001   PHE D 580 
 TYR   0.013   0.001   TYR B 388 
 ARG   0.006   0.000   ARG D 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.020 
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  148 GLU cc_start: 0.8014 (tt0) cc_final: 0.6749 (tt0)
REVERT: C   67 MET cc_start: 0.6113 (pmm) cc_final: 0.5811 (pmm)
REVERT: C   96 MET cc_start: 0.7379 (mtt) cc_final: 0.7122 (mtt)
REVERT: C  165 GLN cc_start: 0.9103 (tt0) cc_final: 0.8746 (tt0)
REVERT: B  503 GLN cc_start: 0.7791 (pp30) cc_final: 0.7153 (pt0)
REVERT: D  513 TYR cc_start: 0.7209 (p90) cc_final: 0.6829 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1906
  time to fit residues: 28.5450
Evaluate side-chains
  77 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 HIS
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8076  Z= 0.192
  Angle     :  0.644   9.317  11005  Z= 0.330
  Chirality :  0.043   0.148   1254
  Planarity :  0.005   0.047   1419
  Dihedral  :  5.600  28.161   1074
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -3.00 (0.25), residues: 1001
  helix: -0.08 (0.38), residues: 171
  sheet: -1.94 (0.32), residues: 256
  loop : -2.73 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 584 
 HIS   0.004   0.001   HIS B 406 
 PHE   0.023   0.001   PHE B 594 
 TYR   0.017   0.001   TYR C  66 
 ARG   0.004   0.000   ARG D 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.904 
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  131 ARG cc_start: 0.7047 (tmm-80) cc_final: 0.6481 (tmt170)
REVERT: A  148 GLU cc_start: 0.7878 (tt0) cc_final: 0.7520 (tt0)
REVERT: C   67 MET cc_start: 0.6575 (pmm) cc_final: 0.6281 (pmm)
REVERT: B  406 HIS cc_start: 0.6934 (p90) cc_final: 0.6709 (p-80)
REVERT: D  599 PHE cc_start: 0.8737 (t80) cc_final: 0.8495 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2015
  time to fit residues: 26.4059
Evaluate side-chains
  68 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0570
   chunk 23 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B 443 HIS
** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8076  Z= 0.160
  Angle     :  0.630   8.295  11005  Z= 0.323
  Chirality :  0.044   0.238   1254
  Planarity :  0.004   0.049   1419
  Dihedral  :  5.320  26.809   1074
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.68 (0.26), residues: 1001
  helix:  0.17 (0.38), residues: 172
  sheet: -1.65 (0.33), residues: 249
  loop : -2.56 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 584 
 HIS   0.003   0.001   HIS A  71 
 PHE   0.018   0.001   PHE B 594 
 TYR   0.010   0.001   TYR C  66 
 ARG   0.005   0.000   ARG D 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.983 
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  131 ARG cc_start: 0.7198 (tmm-80) cc_final: 0.6568 (tmt170)
REVERT: C   67 MET cc_start: 0.6543 (pmm) cc_final: 0.6247 (pmm)
REVERT: C  165 GLN cc_start: 0.8952 (tt0) cc_final: 0.8678 (tt0)
REVERT: D  330 MET cc_start: 0.8275 (tpp) cc_final: 0.8016 (tpp)
REVERT: D  599 PHE cc_start: 0.8689 (t80) cc_final: 0.8386 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1963
  time to fit residues: 27.8696
Evaluate side-chains
  70 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 94 optimal weight:    0.0670
   chunk 78 optimal weight:    0.4980
   chunk 43 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   chunk 31 optimal weight:   40.0000
   chunk 49 optimal weight:    0.0570
   chunk 91 optimal weight:    0.0470
   overall best weight:    0.7336

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 531 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8076  Z= 0.164
  Angle     :  0.620   8.441  11005  Z= 0.318
  Chirality :  0.043   0.249   1254
  Planarity :  0.004   0.044   1419
  Dihedral  :  5.193  26.740   1074
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.48 (0.26), residues: 1001
  helix:  0.44 (0.38), residues: 172
  sheet: -1.40 (0.33), residues: 257
  loop : -2.53 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 584 
 HIS   0.005   0.001   HIS D 443 
 PHE   0.018   0.001   PHE B 594 
 TYR   0.010   0.001   TYR C  66 
 ARG   0.007   0.000   ARG B 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.882 
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  131 ARG cc_start: 0.7217 (tmm-80) cc_final: 0.6357 (tmt170)
REVERT: A  144 ILE cc_start: 0.8616 (mm) cc_final: 0.8410 (mm)
REVERT: C   67 MET cc_start: 0.6508 (pmm) cc_final: 0.6228 (pmm)
REVERT: C  163 MET cc_start: 0.9047 (mmp) cc_final: 0.8703 (tmm)
REVERT: C  165 GLN cc_start: 0.8953 (tt0) cc_final: 0.8615 (tt0)
REVERT: B  446 LEU cc_start: 0.7994 (tp) cc_final: 0.7749 (tp)
REVERT: D  330 MET cc_start: 0.8367 (tpp) cc_final: 0.8134 (tpp)
REVERT: D  599 PHE cc_start: 0.8680 (t80) cc_final: 0.8344 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2129
  time to fit residues: 27.9707
Evaluate side-chains
  70 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:   20.0000
   chunk 53 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0470
   overall best weight:    1.3684

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8076  Z= 0.204
  Angle     :  0.642   9.360  11005  Z= 0.328
  Chirality :  0.044   0.209   1254
  Planarity :  0.005   0.047   1419
  Dihedral  :  5.224  26.521   1074
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.39 (0.26), residues: 1001
  helix:  0.71 (0.39), residues: 174
  sheet: -1.38 (0.32), residues: 263
  loop : -2.55 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 541 
 HIS   0.006   0.001   HIS A  71 
 PHE   0.022   0.001   PHE B 594 
 TYR   0.020   0.002   TYR B 388 
 ARG   0.005   0.000   ARG B 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.021 
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  131 ARG cc_start: 0.7298 (tmm-80) cc_final: 0.6403 (tmt170)
REVERT: A  144 ILE cc_start: 0.8722 (mm) cc_final: 0.8498 (mm)
REVERT: C  163 MET cc_start: 0.9003 (mmp) cc_final: 0.8725 (tmm)
REVERT: C  165 GLN cc_start: 0.8907 (tt0) cc_final: 0.8577 (tt0)
REVERT: B  446 LEU cc_start: 0.8080 (tp) cc_final: 0.7818 (tp)
REVERT: D  599 PHE cc_start: 0.8722 (t80) cc_final: 0.8363 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.2066
  time to fit residues: 27.6669
Evaluate side-chains
  69 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    0.0020
   chunk 56 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 64 optimal weight:   20.0000
   chunk 46 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0570
   chunk 74 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.5308

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8076  Z= 0.152
  Angle     :  0.616   9.059  11005  Z= 0.311
  Chirality :  0.043   0.194   1254
  Planarity :  0.005   0.052   1419
  Dihedral  :  5.037  25.892   1074
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.12 (0.27), residues: 1001
  helix:  0.90 (0.39), residues: 174
  sheet: -1.09 (0.33), residues: 259
  loop : -2.42 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 584 
 HIS   0.003   0.001   HIS A  71 
 PHE   0.017   0.001   PHE B 594 
 TYR   0.013   0.001   TYR B 388 
 ARG   0.008   0.000   ARG A 126 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7241 (tmm-80) cc_final: 0.6456 (tmt170)
REVERT: A  144 ILE cc_start: 0.8740 (mm) cc_final: 0.8523 (mm)
REVERT: C  163 MET cc_start: 0.8963 (mmp) cc_final: 0.8708 (tmm)
REVERT: B  446 LEU cc_start: 0.8051 (tp) cc_final: 0.7835 (tp)
REVERT: D  599 PHE cc_start: 0.8725 (t80) cc_final: 0.8379 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1888
  time to fit residues: 24.4012
Evaluate side-chains
  71 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 88 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 69 optimal weight:   40.0000
   chunk 27 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.099   8076  Z= 0.233
  Angle     :  0.651   8.338  11005  Z= 0.332
  Chirality :  0.044   0.197   1254
  Planarity :  0.004   0.047   1419
  Dihedral  :  5.116  25.641   1074
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.14 (0.27), residues: 1001
  helix:  1.04 (0.40), residues: 174
  sheet: -1.22 (0.33), residues: 270
  loop : -2.44 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 584 
 HIS   0.006   0.001   HIS A  71 
 PHE   0.021   0.001   PHE B 594 
 TYR   0.015   0.001   TYR C  66 
 ARG   0.004   0.000   ARG D 359 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7368 (tmm-80) cc_final: 0.6541 (tmt170)
REVERT: A  144 ILE cc_start: 0.8705 (mm) cc_final: 0.8452 (mm)
REVERT: C  163 MET cc_start: 0.8948 (mmp) cc_final: 0.8726 (tmm)
REVERT: B  446 LEU cc_start: 0.8133 (tp) cc_final: 0.7889 (tp)
REVERT: D  599 PHE cc_start: 0.8780 (t80) cc_final: 0.8445 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1896
  time to fit residues: 24.6689
Evaluate side-chains
  70 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8076  Z= 0.199
  Angle     :  0.639  10.362  11005  Z= 0.325
  Chirality :  0.043   0.184   1254
  Planarity :  0.004   0.044   1419
  Dihedral  :  5.055  24.350   1074
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.49 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.11 (0.27), residues: 1001
  helix:  1.05 (0.40), residues: 174
  sheet: -1.08 (0.35), residues: 238
  loop : -2.43 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP D 584 
 HIS   0.004   0.001   HIS A  71 
 PHE   0.020   0.001   PHE B 594 
 TYR   0.012   0.001   TYR C  66 
 ARG   0.004   0.000   ARG A 126 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7350 (tmm-80) cc_final: 0.6512 (tmt170)
REVERT: A  144 ILE cc_start: 0.8727 (mm) cc_final: 0.8475 (mm)
REVERT: C  165 GLN cc_start: 0.8702 (tt0) cc_final: 0.8501 (tt0)
REVERT: B  446 LEU cc_start: 0.8147 (tp) cc_final: 0.7914 (tp)
REVERT: D  599 PHE cc_start: 0.8766 (t80) cc_final: 0.8449 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1836
  time to fit residues: 23.2870
Evaluate side-chains
  65 residues out of total 892 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 71 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 32 optimal weight:   30.0000
   chunk 79 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 68 optimal weight:   10.0000
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 165 GLN
** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.126687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.083527 restraints weight = 22230.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.084328 restraints weight = 16174.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.084177 restraints weight = 12086.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8076  Z= 0.317
  Angle     :  0.707   8.299  11005  Z= 0.364
  Chirality :  0.045   0.227   1254
  Planarity :  0.005   0.047   1419
  Dihedral  :  5.435  26.170   1074
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.49 %
    Favored  : 87.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    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: -2.21 (0.26), residues: 1001
  helix:  0.99 (0.39), residues: 174
  sheet: -1.20 (0.35), residues: 238
  loop : -2.48 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 584 
 HIS   0.005   0.001   HIS D 531 
 PHE   0.022   0.002   PHE B 594 
 TYR   0.018   0.002   TYR D 547 
 ARG   0.006   0.001   ARG A 126 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1726.10 seconds
wall clock time: 32 minutes 10.31 seconds (1930.31 seconds total)