Starting phenix.real_space_refine
on Tue Feb 13 11:49:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/02_2024/7nrx_12552.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/02_2024/7nrx_12552.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/02_2024/7nrx_12552.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/02_2024/7nrx_12552.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/02_2024/7nrx_12552.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/02_2024/7nrx_12552.pdb"
  }
  resolution = 3.55
  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=   0.001 sd=   0.006
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      10      5.16       5
     C    3670      2.51       5
     N    1080      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "I GLU  342": "OE1" <-> "OE2"
    Residue "I ARG  379": "NH1" <-> "NH2"
    Residue "C GLU  342": "OE1" <-> "OE2"
    Residue "C ARG  379": "NH1" <-> "NH2"
    Residue "E GLU  342": "OE1" <-> "OE2"
    Residue "E ARG  379": "NH1" <-> "NH2"
    Residue "G GLU  342": "OE1" <-> "OE2"
    Residue "G ARG  379": "NH1" <-> "NH2"
    Residue "J GLU  342": "OE1" <-> "OE2"
    Residue "J ARG  379": "NH1" <-> "NH2"
  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: 5870
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "I"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "E"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "G"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "H"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "J"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Time building chain proxies: 3.53, per 1000 atoms: 0.60
  Number of scatterers: 5870
  At special positions: 0
  Unit cell: (132.25, 92, 44.85, 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      10     16.00
     O    1110      8.00
     N    1080      7.00
     C    3670      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  - 3.50
        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: 1.84
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 15 sheets defined
      0.0% alpha, 27.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.516A  pdb=" N   GLN A 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   TYR F 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   VAL A 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLN F 307 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   TYR H 310 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL F 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.668A  pdb=" N   VAL A 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL F 313 " --> pdb=" O   ASP H 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 322
      removed outlier: 6.472A  pdb=" N   LYS A 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   SER F 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   THR A 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   CYS F 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LYS A 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LYS F 317 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   SER H 320 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   THR F 319 " --> pdb=" O   SER H 320 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   CYS H 322 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LYS F 321 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 340
      removed outlier: 6.176A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 359 through 362
      removed outlier: 6.472A  pdb=" N   ASN B 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   HIS D 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ASN A 359 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   HIS B 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR A 361 " --> pdb=" O   HIS B 362 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 371 through 373
      removed outlier: 6.223A  pdb=" N   ILE A 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ILE F 371 " --> pdb=" O   GLU H 372 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 378
      removed outlier: 6.539A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU A 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 306 through 310
      removed outlier: 6.219A  pdb=" N   VAL C 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   VAL E 309 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE C 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   VAL I 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL C 309 " --> pdb=" O   VAL I 306 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE I 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.646A  pdb=" N   VAL I 313 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL G 313 " --> pdb=" O   ASP J 314 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 317 through 322
      removed outlier: 6.496A  pdb=" N   LYS I 317 " --> pdb=" O   VAL G 318 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   SER G 320 " --> pdb=" O   LYS I 317 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   THR I 319 " --> pdb=" O   SER G 320 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   CYS G 322 " --> pdb=" O   THR I 319 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   LYS I 321 " --> pdb=" O   CYS G 322 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LYS G 317 " --> pdb=" O   VAL J 318 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   SER J 320 " --> pdb=" O   LYS G 317 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR G 319 " --> pdb=" O   SER J 320 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   CYS J 322 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LYS G 321 " --> pdb=" O   CYS J 322 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 328 through 330
      removed outlier: 6.275A  pdb=" N   ILE C 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE I 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 336 through 339
      removed outlier: 6.553A  pdb=" N   VAL C 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL I 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 353 through 354
      removed outlier: 6.763A  pdb=" N   LYS I 353 " --> pdb=" O   ILE G 354 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LYS G 353 " --> pdb=" O   ILE J 354 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 359 through 362
      removed outlier: 6.760A  pdb=" N   ILE I 360 " --> pdb=" O   THR G 361 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE G 360 " --> pdb=" O   THR J 361 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 369 through 371
      removed outlier: 6.289A  pdb=" N   LYS C 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LYS I 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)

    84 hydrogen bonds defined for protein.
    249 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: 1.39

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1836
        1.33 -     1.45: 820
        1.45 -     1.57: 3294
        1.57 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 5960
  Sorted by residual:
  bond pdb=" CG1 ILE J 354 "
       pdb=" CD1 ILE J 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.377  0.136 3.90e-02 6.57e+02 1.22e+01
  bond pdb=" CG1 ILE G 354 "
       pdb=" CD1 ILE G 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.377  0.136 3.90e-02 6.57e+02 1.21e+01
  bond pdb=" CG1 ILE C 354 "
       pdb=" CD1 ILE C 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.378  0.135 3.90e-02 6.57e+02 1.20e+01
  bond pdb=" CG1 ILE I 354 "
       pdb=" CD1 ILE I 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.378  0.135 3.90e-02 6.57e+02 1.20e+01
  bond pdb=" CG1 ILE E 354 "
       pdb=" CD1 ILE E 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.378  0.135 3.90e-02 6.57e+02 1.20e+01
  ... (remaining 5955 not shown)

  Histogram of bond angle deviations from ideal:
      102.21 -   108.08: 471
      108.08 -   113.95: 3185
      113.95 -   119.81: 1644
      119.81 -   125.68: 2610
      125.68 -   131.54: 60
  Bond angle restraints: 7970
  Sorted by residual:
  angle pdb=" CA  LYS B 311 "
        pdb=" CB  LYS B 311 "
        pdb=" CG  LYS B 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.62   -9.52 2.00e+00 2.50e-01 2.26e+01
  angle pdb=" CA  LYS H 311 "
        pdb=" CB  LYS H 311 "
        pdb=" CG  LYS H 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.61   -9.51 2.00e+00 2.50e-01 2.26e+01
  angle pdb=" CA  LYS D 311 "
        pdb=" CB  LYS D 311 "
        pdb=" CG  LYS D 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.58   -9.48 2.00e+00 2.50e-01 2.25e+01
  angle pdb=" CA  LYS F 311 "
        pdb=" CB  LYS F 311 "
        pdb=" CG  LYS F 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.57   -9.47 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" CA  LYS A 311 "
        pdb=" CB  LYS A 311 "
        pdb=" CG  LYS A 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.51   -9.41 2.00e+00 2.50e-01 2.21e+01
  ... (remaining 7965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.37: 3186
       14.37 -    28.74: 329
       28.74 -    43.12: 100
       43.12 -    57.49: 10
       57.49 -    71.86: 5
  Dihedral angle restraints: 3630
    sinusoidal: 1520
      harmonic: 2110
  Sorted by residual:
  dihedral pdb=" CA  LYS F 347 "
           pdb=" C   LYS F 347 "
           pdb=" N   ASP F 348 "
           pdb=" CA  ASP F 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.66  -26.34     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  LYS D 347 "
           pdb=" C   LYS D 347 "
           pdb=" N   ASP D 348 "
           pdb=" CA  ASP D 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.68  -26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  LYS H 347 "
           pdb=" C   LYS H 347 "
           pdb=" N   ASP H 348 "
           pdb=" CA  ASP H 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.70  -26.30     0      5.00e+00 4.00e-02 2.77e+01
  ... (remaining 3627 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.144: 845
       0.144 -    0.289: 35
       0.289 -    0.433: 5
       0.433 -    0.577: 0
       0.577 -    0.722: 5
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" CB  VAL H 306 "
            pdb=" CA  VAL H 306 "
            pdb=" CG1 VAL H 306 "
            pdb=" CG2 VAL H 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.30e+01
  chirality pdb=" CB  VAL A 306 "
            pdb=" CA  VAL A 306 "
            pdb=" CG1 VAL A 306 "
            pdb=" CG2 VAL A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.29e+01
  chirality pdb=" CB  VAL B 306 "
            pdb=" CA  VAL B 306 "
            pdb=" CG1 VAL B 306 "
            pdb=" CG2 VAL B 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.29e+01
  ... (remaining 887 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 363 "    0.064 5.00e-02 4.00e+02   9.65e-02 1.49e+01
        pdb=" N   PRO D 364 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO D 364 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO D 364 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 363 "    0.064 5.00e-02 4.00e+02   9.63e-02 1.48e+01
        pdb=" N   PRO B 364 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO B 364 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 364 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 363 "    0.064 5.00e-02 4.00e+02   9.62e-02 1.48e+01
        pdb=" N   PRO H 364 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO H 364 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO H 364 "    0.052 5.00e-02 4.00e+02
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1897
        2.87 -     3.37: 4466
        3.37 -     3.88: 9908
        3.88 -     4.39: 10017
        4.39 -     4.90: 21866
  Nonbonded interactions: 48154
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU G 372 "
            pdb=" OD2 ASP J 314 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" OE2 GLU I 372 "
            pdb=" OD2 ASP G 314 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" OD2 ASP C 314 "
            pdb=" OE2 GLU E 372 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" OD2 ASP I 314 "
            pdb=" OE2 GLU C 372 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" NZ  LYS A 353 "
            pdb=" OD2 ASP A 358 "
     model   vdw
     2.418 2.520
  ... (remaining 48149 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             1.000
  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:          3.760
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     19.120
  Find NCS groups from input model:        0.410
  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:             0.010
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
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      :  0.010   0.136   5960  Z= 0.671
  Angle     :  1.201   9.516   7970  Z= 0.703
  Chirality :  0.092   0.722    890
  Planarity :  0.011   0.097   1020
  Dihedral  : 12.756  71.859   2290
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  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: -3.60 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 330 
 PHE   0.010   0.004   PHE A 346 
 TYR   0.046   0.008   TYR B 310 
 ARG   0.002   0.000   ARG G 349 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7824 (mmmm)
REVERT: B  353 LYS cc_start: 0.9030 (ttmt) cc_final: 0.7549 (mttt)
REVERT: C  349 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6261 (ttm-80)
REVERT: D  331 LYS cc_start: 0.8878 (mttt) cc_final: 0.8044 (mmtt)
REVERT: D  353 LYS cc_start: 0.9030 (ttmt) cc_final: 0.7607 (mttp)
REVERT: E  311 LYS cc_start: 0.8841 (mttt) cc_final: 0.8107 (mmmt)
REVERT: E  349 ARG cc_start: 0.7475 (mtt180) cc_final: 0.6298 (mmt-90)
REVERT: E  350 VAL cc_start: 0.9052 (m) cc_final: 0.8797 (t)
REVERT: E  353 LYS cc_start: 0.8666 (ttmt) cc_final: 0.6971 (mttp)
REVERT: E  369 LYS cc_start: 0.8180 (mttt) cc_final: 0.7568 (mmmt)
REVERT: E  375 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8174 (mtpt)
REVERT: F  353 LYS cc_start: 0.8931 (ttmt) cc_final: 0.7524 (mttt)
REVERT: G  320 SER cc_start: 0.9176 (t) cc_final: 0.8700 (m)
REVERT: G  327 ASN cc_start: 0.8562 (m-40) cc_final: 0.8314 (m110)
REVERT: G  353 LYS cc_start: 0.8422 (ttmt) cc_final: 0.6875 (mttp)
REVERT: G  369 LYS cc_start: 0.8304 (mttt) cc_final: 0.7882 (mtmt)
REVERT: G  375 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8155 (mtpp)
REVERT: G  377 THR cc_start: 0.9122 (m) cc_final: 0.8706 (m)
REVERT: H  331 LYS cc_start: 0.8824 (mttt) cc_final: 0.8609 (mttp)
REVERT: H  347 LYS cc_start: 0.8478 (mmmm) cc_final: 0.6930 (pptt)
REVERT: H  353 LYS cc_start: 0.9184 (ttmt) cc_final: 0.7600 (mttp)
REVERT: H  379 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6521 (pmt-80)
REVERT: J  320 SER cc_start: 0.9069 (t) cc_final: 0.8857 (m)
REVERT: J  343 LYS cc_start: 0.7997 (tptt) cc_final: 0.7553 (pptt)
REVERT: J  375 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8253 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.2534
  time to fit residues: 77.1913
Evaluate side-chains
  192 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    3.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5960  Z= 0.318
  Angle     :  0.628   4.758   7970  Z= 0.324
  Chirality :  0.049   0.135    890
  Planarity :  0.006   0.058   1020
  Dihedral  :  5.504  20.661    790
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.58 %
    Favored  : 84.63 %
  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: -3.54 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.010   0.001   PHE D 378 
 TYR   0.005   0.001   TYR E 310 
 ARG   0.002   0.001   ARG I 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 190
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7903 (mp0) cc_final: 0.7587 (mp0)
REVERT: I  327 ASN cc_start: 0.8677 (m110) cc_final: 0.8433 (m-40)
REVERT: I  353 LYS cc_start: 0.8270 (ttmt) cc_final: 0.6804 (mttp)
REVERT: B  380 GLU cc_start: 0.5897 (tm-30) cc_final: 0.5305 (tm-30)
REVERT: C  349 ARG cc_start: 0.6897 (mtt180) cc_final: 0.6155 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7922 (mttt) cc_final: 0.7494 (mtpt)
REVERT: D  331 LYS cc_start: 0.8970 (mttt) cc_final: 0.8203 (mmtt)
REVERT: E  349 ARG cc_start: 0.7233 (mtt180) cc_final: 0.5913 (mmt-90)
REVERT: F  311 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8432 (mtpt)
REVERT: G  368 ASN cc_start: 0.9339 (m-40) cc_final: 0.8949 (m110)
REVERT: G  369 LYS cc_start: 0.7904 (mttt) cc_final: 0.7572 (mtmt)
REVERT: G  375 LYS cc_start: 0.8496 (ttmt) cc_final: 0.7980 (mtpp)
REVERT: J  354 ILE cc_start: 0.8963 (mm) cc_final: 0.8650 (mp)
REVERT: J  375 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8193 (ttmm)
  outliers start: 12
  outliers final: 10
  residues processed: 197
  average time/residue: 0.2120
  time to fit residues: 52.0260
Evaluate side-chains
  177 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 167
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 52 optimal weight:   30.0000
   chunk 43 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 63 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5960  Z= 0.258
  Angle     :  0.585   5.695   7970  Z= 0.298
  Chirality :  0.049   0.125    890
  Planarity :  0.005   0.049   1020
  Dihedral  :  5.119  21.212    790
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.01 %
    Favored  : 80.00 %
  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: -3.46 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.007   0.001   PHE B 378 
 TYR   0.022   0.002   TYR F 310 
 ARG   0.004   0.000   ARG I 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: I  327 ASN cc_start: 0.8727 (m110) cc_final: 0.8462 (m-40)
REVERT: B  311 LYS cc_start: 0.8617 (tttt) cc_final: 0.8096 (ttmm)
REVERT: B  347 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8040 (mmmm)
REVERT: C  349 ARG cc_start: 0.6860 (mtt180) cc_final: 0.6251 (ttm-80)
REVERT: E  348 ASP cc_start: 0.8068 (t0) cc_final: 0.7866 (t70)
REVERT: E  349 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6087 (mmt-90)
REVERT: F  311 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8464 (mtpt)
REVERT: G  320 SER cc_start: 0.9318 (t) cc_final: 0.8625 (m)
REVERT: H  328 ILE cc_start: 0.9264 (mm) cc_final: 0.9056 (mt)
REVERT: J  354 ILE cc_start: 0.8972 (mm) cc_final: 0.8771 (mm)
REVERT: J  375 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8193 (ttmm)
  outliers start: 20
  outliers final: 19
  residues processed: 183
  average time/residue: 0.1815
  time to fit residues: 42.7741
Evaluate side-chains
  177 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  368 ASN
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0470
   chunk 67 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 18 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    1.7282

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5960  Z= 0.183
  Angle     :  0.548   5.397   7970  Z= 0.279
  Chirality :  0.048   0.122    890
  Planarity :  0.004   0.044   1020
  Dihedral  :  4.752  18.561    790
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.10 %
    Favored  : 77.76 %
  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: -3.38 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.009   0.001   PHE I 346 
 TYR   0.020   0.002   TYR F 310 
 ARG   0.003   0.000   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.727 
Fit side-chains
REVERT: B  311 LYS cc_start: 0.8670 (tttt) cc_final: 0.8131 (ttmm)
REVERT: B  347 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8065 (mmmm)
REVERT: C  349 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6209 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7813 (mttt) cc_final: 0.7324 (mtmt)
REVERT: D  331 LYS cc_start: 0.8923 (mttt) cc_final: 0.8048 (mmpt)
REVERT: D  345 ASP cc_start: 0.8137 (t0) cc_final: 0.7862 (t0)
REVERT: E  348 ASP cc_start: 0.8195 (t0) cc_final: 0.7816 (t0)
REVERT: F  311 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8448 (mtpt)
REVERT: F  328 ILE cc_start: 0.9446 (mm) cc_final: 0.9109 (mt)
REVERT: F  342 GLU cc_start: 0.8036 (mp0) cc_final: 0.7717 (mp0)
REVERT: G  320 SER cc_start: 0.9285 (t) cc_final: 0.8584 (m)
REVERT: H  347 LYS cc_start: 0.8288 (mmmm) cc_final: 0.6862 (pttp)
REVERT: J  354 ILE cc_start: 0.8970 (mm) cc_final: 0.8754 (mm)
REVERT: J  375 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8165 (ttmm)
  outliers start: 21
  outliers final: 20
  residues processed: 192
  average time/residue: 0.1878
  time to fit residues: 45.7917
Evaluate side-chains
  185 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  316 SER
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 46 optimal weight:    9.9990
   chunk 34 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    4.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   5960  Z= 0.372
  Angle     :  0.623   4.498   7970  Z= 0.324
  Chirality :  0.050   0.142    890
  Planarity :  0.004   0.046   1020
  Dihedral  :  5.137  20.920    790
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 20.30 %
    Favored  : 75.97 %
  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: -3.35 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.011   0.002   PHE G 346 
 TYR   0.025   0.002   TYR F 310 
 ARG   0.003   0.001   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 173
  time to evaluate  : 0.731 
Fit side-chains
REVERT: I  327 ASN cc_start: 0.8678 (m110) cc_final: 0.8426 (m110)
REVERT: B  311 LYS cc_start: 0.8713 (tttt) cc_final: 0.8229 (ttmm)
REVERT: B  317 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7922 (mtpt)
REVERT: B  325 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8615 (tt)
REVERT: C  349 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6104 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7818 (mttt) cc_final: 0.7361 (mtpt)
REVERT: D  331 LYS cc_start: 0.8987 (mttt) cc_final: 0.8136 (mmtt)
REVERT: E  379 ARG cc_start: 0.4578 (mmp-170) cc_final: 0.4333 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8540 (mtpt)
REVERT: H  341 SER cc_start: 0.8886 (m) cc_final: 0.8584 (m)
  outliers start: 25
  outliers final: 23
  residues processed: 190
  average time/residue: 0.1873
  time to fit residues: 45.4656
Evaluate side-chains
  194 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 170
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  368 ASN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  368 ASN
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  316 SER
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 67 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5960  Z= 0.326
  Angle     :  0.614   6.322   7970  Z= 0.316
  Chirality :  0.050   0.131    890
  Planarity :  0.004   0.045   1020
  Dihedral  :  5.070  19.413    790
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.69 %
    Favored  : 73.43 %
  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: -3.38 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.009   0.002   PHE I 346 
 TYR   0.023   0.002   TYR F 310 
 ARG   0.003   0.000   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9196 (mp) cc_final: 0.8985 (mp)
REVERT: A  342 GLU cc_start: 0.8187 (mp0) cc_final: 0.7438 (mp0)
REVERT: I  327 ASN cc_start: 0.8668 (m110) cc_final: 0.8432 (m110)
REVERT: B  311 LYS cc_start: 0.8730 (tttt) cc_final: 0.8253 (ttmm)
REVERT: B  317 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7385 (mttt)
REVERT: B  325 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8519 (tt)
REVERT: C  349 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6070 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7870 (mttt) cc_final: 0.7355 (mtpt)
REVERT: D  331 LYS cc_start: 0.8993 (mttt) cc_final: 0.8133 (mmtt)
REVERT: D  340 LYS cc_start: 0.8763 (mptt) cc_final: 0.8420 (mmtp)
REVERT: D  343 LYS cc_start: 0.8387 (ttmm) cc_final: 0.7178 (tppt)
REVERT: E  379 ARG cc_start: 0.4716 (mmp-170) cc_final: 0.4446 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8482 (mtpt)
REVERT: G  320 SER cc_start: 0.9354 (t) cc_final: 0.8641 (m)
  outliers start: 26
  outliers final: 25
  residues processed: 191
  average time/residue: 0.1903
  time to fit residues: 46.1205
Evaluate side-chains
  195 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 169
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  368 ASN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  368 ASN
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  316 SER
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5960  Z= 0.291
  Angle     :  0.600   6.583   7970  Z= 0.309
  Chirality :  0.049   0.128    890
  Planarity :  0.004   0.044   1020
  Dihedral  :  4.962  19.494    790
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.99 %
    Favored  : 73.13 %
  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: -3.34 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.012   0.002   PHE I 346 
 TYR   0.023   0.002   TYR F 310 
 ARG   0.007   0.001   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9205 (mp) cc_final: 0.8991 (mp)
REVERT: I  327 ASN cc_start: 0.8652 (m110) cc_final: 0.8384 (m-40)
REVERT: B  311 LYS cc_start: 0.8724 (tttt) cc_final: 0.8236 (ttmm)
REVERT: B  317 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7324 (mttt)
REVERT: B  325 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8518 (tt)
REVERT: C  349 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6066 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7788 (mttt) cc_final: 0.7247 (mtmt)
REVERT: D  331 LYS cc_start: 0.8985 (mttt) cc_final: 0.8111 (mmpt)
REVERT: D  340 LYS cc_start: 0.8616 (mptt) cc_final: 0.8337 (mmtp)
REVERT: D  343 LYS cc_start: 0.8417 (ttmm) cc_final: 0.7295 (tppt)
REVERT: D  344 LEU cc_start: 0.9200 (mp) cc_final: 0.8981 (mp)
REVERT: D  353 LYS cc_start: 0.8869 (tttt) cc_final: 0.8663 (tttm)
REVERT: E  349 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6132 (mmt-90)
REVERT: E  379 ARG cc_start: 0.4653 (mmp-170) cc_final: 0.4387 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8484 (mtpt)
REVERT: G  320 SER cc_start: 0.9353 (t) cc_final: 0.8640 (m)
  outliers start: 26
  outliers final: 24
  residues processed: 184
  average time/residue: 0.1997
  time to fit residues: 46.2008
Evaluate side-chains
  191 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  368 ASN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  368 ASN
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  316 SER
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 61 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
D 329 HIS
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN
H 330 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   5960  Z= 0.483
  Angle     :  0.698   6.913   7970  Z= 0.364
  Chirality :  0.052   0.170    890
  Planarity :  0.005   0.045   1020
  Dihedral  :  5.366  20.162    790
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 24.33 %
    Favored  : 71.64 %
  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: -3.41 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.014   0.002   PHE B 378 
 TYR   0.027   0.003   TYR F 310 
 ARG   0.006   0.001   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 0.650 
Fit side-chains
REVERT: I  327 ASN cc_start: 0.8690 (m110) cc_final: 0.8461 (m110)
REVERT: B  311 LYS cc_start: 0.8771 (tttt) cc_final: 0.8305 (ttmm)
REVERT: C  349 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6018 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7854 (mttt) cc_final: 0.7427 (mtpt)
REVERT: D  331 LYS cc_start: 0.8998 (mttt) cc_final: 0.8155 (mmtt)
REVERT: D  343 LYS cc_start: 0.8415 (ttmm) cc_final: 0.7153 (tppt)
REVERT: E  349 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6103 (mmt-90)
REVERT: F  311 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8717 (mtpt)
  outliers start: 27
  outliers final: 24
  residues processed: 191
  average time/residue: 0.1909
  time to fit residues: 46.0501
Evaluate side-chains
  196 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain I residue  316 SER
Chi-restraints excluded: chain I residue  368 ASN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  368 ASN
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5960  Z= 0.268
  Angle     :  0.615   8.789   7970  Z= 0.314
  Chirality :  0.050   0.125    890
  Planarity :  0.004   0.044   1020
  Dihedral  :  5.023  20.210    790
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 24.78 %
    Favored  : 71.64 %
  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: -3.36 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.009   0.002   PHE J 346 
 TYR   0.020   0.002   TYR F 310 
 ARG   0.004   0.001   ARG A 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.730 
Fit side-chains
REVERT: I  327 ASN cc_start: 0.8661 (m110) cc_final: 0.8412 (m110)
REVERT: B  311 LYS cc_start: 0.8738 (tttt) cc_final: 0.8257 (ttmm)
REVERT: C  349 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6012 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7810 (mttt) cc_final: 0.7287 (mtpt)
REVERT: D  331 LYS cc_start: 0.8972 (mttt) cc_final: 0.8115 (mmtt)
REVERT: D  343 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7280 (tppt)
REVERT: E  349 ARG cc_start: 0.7349 (mtt180) cc_final: 0.5893 (mmt-90)
REVERT: F  311 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8497 (mtpt)
REVERT: H  347 LYS cc_start: 0.8418 (mmmm) cc_final: 0.6999 (pttp)
REVERT: J  354 ILE cc_start: 0.9026 (mm) cc_final: 0.8822 (mp)
  outliers start: 24
  outliers final: 22
  residues processed: 180
  average time/residue: 0.2031
  time to fit residues: 45.8556
Evaluate side-chains
  185 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain I residue  316 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 59 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 51 optimal weight:    0.5980
   chunk 8 optimal weight:   10.0000
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5960  Z= 0.302
  Angle     :  0.624   6.518   7970  Z= 0.322
  Chirality :  0.050   0.129    890
  Planarity :  0.004   0.044   1020
  Dihedral  :  4.979  18.997    790
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 25.37 %
    Favored  : 71.64 %
  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: -3.33 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.014   0.002   PHE G 346 
 TYR   0.022   0.002   TYR F 310 
 ARG   0.005   0.001   ARG A 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9195 (mp) cc_final: 0.8995 (mp)
REVERT: I  327 ASN cc_start: 0.8668 (m110) cc_final: 0.8408 (m-40)
REVERT: B  311 LYS cc_start: 0.8831 (tttt) cc_final: 0.8364 (ttmm)
REVERT: B  317 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7432 (mttt)
REVERT: C  349 ARG cc_start: 0.7115 (mtt180) cc_final: 0.5962 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7765 (mttt) cc_final: 0.7243 (mtpt)
REVERT: D  331 LYS cc_start: 0.8976 (mttt) cc_final: 0.8084 (mmpt)
REVERT: D  343 LYS cc_start: 0.8345 (ttmm) cc_final: 0.7325 (tppt)
REVERT: E  349 ARG cc_start: 0.7394 (mtt180) cc_final: 0.5950 (mmt-90)
REVERT: F  311 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8550 (mtpt)
REVERT: G  320 SER cc_start: 0.9315 (t) cc_final: 0.8585 (m)
REVERT: H  347 LYS cc_start: 0.8403 (mmmm) cc_final: 0.6913 (pttp)
REVERT: J  354 ILE cc_start: 0.9014 (mm) cc_final: 0.8804 (mp)
  outliers start: 20
  outliers final: 20
  residues processed: 175
  average time/residue: 0.1917
  time to fit residues: 42.4185
Evaluate side-chains
  183 residues out of total 670 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain I residue  316 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  368 ASN
Chi-restraints excluded: chain J residue  368 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 10 optimal weight:   30.0000
   chunk 48 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.100949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.079489 restraints weight = 9841.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.081862 restraints weight = 4407.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.083324 restraints weight = 2636.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049   5960  Z= 0.535
  Angle     :  0.730   6.273   7970  Z= 0.381
  Chirality :  0.053   0.166    890
  Planarity :  0.005   0.045   1020
  Dihedral  :  5.478  21.496    790
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.93 %
    Favored  : 71.64 %
  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: -3.46 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 330 
 PHE   0.016   0.003   PHE G 346 
 TYR   0.027   0.003   TYR F 310 
 ARG   0.005   0.001   ARG A 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1561.39 seconds
wall clock time: 29 minutes 24.76 seconds (1764.76 seconds total)