Starting phenix.real_space_refine
on Sun Jun 15 15:40:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d3x_27167/06_2025/8d3x_27167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d3x_27167/06_2025/8d3x_27167.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d3x_27167/06_2025/8d3x_27167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d3x_27167/06_2025/8d3x_27167.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d3x_27167/06_2025/8d3x_27167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d3x_27167/06_2025/8d3x_27167.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9217 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      61      5.16       5
     C    6531      2.51       5
     N    1704      2.21       5
     O    1918      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.36s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10219
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2322
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264}
    Chain: "G"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 246
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
    Chain: "A"
      Number of atoms: 7646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 989, 7646
          Classifications: {'peptide': 989}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 41, 'TRANS': 947}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'MF4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.60, per 1000 atoms: 0.65
  Number of scatterers: 10219
  At special positions: 0
  Unit cell: (146.08, 106.24, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      61     16.00
     Mg      1     11.99
     F       4      9.00
     O    1918      8.00
     N    1704      7.00
     C    6531      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 213 " - pdb=" SG  CYS B 276 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 201 " - pdb=" SG  CYS A 239 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 9 sheets defined
      46.0% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'B' and resid 33 through 60
      removed outlier: 3.532A  pdb=" N   THR B  60 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 110
    Processing helix  chain 'B' and resid 152 through 156
      removed outlier: 3.734A  pdb=" N   TRP B 155 " --> pdb=" O   LYS B 152 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 58
      removed outlier: 3.525A  pdb=" N   LEU G  55 " --> pdb=" O   VAL G  51 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ILE G  56 " --> pdb=" O   GLY G  52 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU G  57 " --> pdb=" O   ILE G  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 3.630A  pdb=" N   TYR A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.917A  pdb=" N   ARG A  64 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 88
    Processing helix  chain 'A' and resid 91 through 109
    Processing helix  chain 'A' and resid 119 through 138
    Processing helix  chain 'A' and resid 146 through 151
      removed outlier: 3.618A  pdb=" N   GLU A 149 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER A 150 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   PHE A 151 " --> pdb=" O   MET A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 146 through 151'
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.918A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 304
    Processing helix  chain 'A' and resid 306 through 322
    Processing helix  chain 'A' and resid 326 through 343
      removed outlier: 3.870A  pdb=" N   THR A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL A 332 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG A 343 " --> pdb=" O   LYS A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 360
      removed outlier: 3.589A  pdb=" N   THR A 356 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLY A 358 " --> pdb=" O   VAL A 354 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER A 359 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 418
    Processing helix  chain 'A' and resid 431 through 435
      removed outlier: 3.726A  pdb=" N   ARG A 435 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 454
    Processing helix  chain 'A' and resid 456 through 464
    Processing helix  chain 'A' and resid 500 through 507
    Processing helix  chain 'A' and resid 521 through 537
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.580A  pdb=" N   ALA A 592 " --> pdb=" O   ALA A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 622
    Processing helix  chain 'A' and resid 630 through 638
    Processing helix  chain 'A' and resid 641 through 645
    Processing helix  chain 'A' and resid 646 through 650
    Processing helix  chain 'A' and resid 659 through 663
    Processing helix  chain 'A' and resid 664 through 675
    Processing helix  chain 'A' and resid 684 through 698
      removed outlier: 3.699A  pdb=" N   GLN A 698 " --> pdb=" O   GLY A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 718
    Processing helix  chain 'A' and resid 729 through 735
    Processing helix  chain 'A' and resid 744 through 772
      removed outlier: 3.870A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA A 767 " --> pdb=" O   LYS A 763 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   SER A 772 " --> pdb=" O   TYR A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 786
      Proline residue:  A 779  - end of helix
    Processing helix  chain 'A' and resid 794 through 804
      removed outlier: 3.520A  pdb=" N   LEU A 798 " --> pdb=" O   THR A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 812
    Processing helix  chain 'A' and resid 818 through 824
      removed outlier: 3.827A  pdb=" N   ILE A 821 " --> pdb=" O   GLU A 818 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET A 822 " --> pdb=" O   SER A 819 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ARG A 824 " --> pdb=" O   ILE A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 836 through 845
      removed outlier: 3.577A  pdb=" N   SER A 841 " --> pdb=" O   GLU A 837 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   MET A 842 " --> pdb=" O   ARG A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 865
    Processing helix  chain 'A' and resid 876 through 881
    Processing helix  chain 'A' and resid 897 through 928
      removed outlier: 3.807A  pdb=" N   VAL A 904 " --> pdb=" O   GLN A 900 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA A 922 " --> pdb=" O   VAL A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 938
    Processing helix  chain 'A' and resid 941 through 959
      removed outlier: 3.838A  pdb=" N   ILE A 945 " --> pdb=" O   ASN A 941 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   PHE A 946 " --> pdb=" O   LYS A 942 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR A 952 " --> pdb=" O   LEU A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 969
    Processing helix  chain 'A' and resid 974 through 980
    Processing helix  chain 'A' and resid 981 through 1002
      removed outlier: 4.501A  pdb=" N   LEU A 987 " --> pdb=" O   PRO A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1012
    Processing sheet with id=AA1, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.567A  pdb=" N   THR B  78 " --> pdb=" O   LYS B 179 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90
      removed outlier: 5.852A  pdb=" N   ILE B  88 " --> pdb=" O   GLU B 300 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 299 " --> pdb=" O   ILE B 272 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ILE B 272 " --> pdb=" O   ILE B 299 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 227 through 230
    Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 171
      removed outlier: 5.133A  pdb=" N   LEU A 160 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU A 180 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   GLU A 241 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   GLY A 200 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   THR A 243 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ALA A 198 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   ARG A 245 " --> pdb=" O   ILE A 196 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ASP A 192 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 193 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348
      removed outlier: 6.194A  pdb=" N   GLY A 721 " --> pdb=" O   MET A 738 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   LEU A 740 " --> pdb=" O   GLY A 721 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ALA A 723 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   VAL A 702 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   VAL A 722 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL A 704 " --> pdb=" O   VAL A 722 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   MET A 724 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   GLY A 706 " --> pdb=" O   MET A 724 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ILE A 363 " --> pdb=" O   ILE A 604 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   VAL A 606 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   SER A 365 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   VAL A 603 " --> pdb=" O   ILE A 678 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   PHE A 680 " --> pdb=" O   VAL A 603 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   MET A 605 " --> pdb=" O   PHE A 680 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   CYS A 653 " --> pdb=" O   VAL A 679 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 389
      removed outlier: 3.536A  pdb=" N   HIS A 380 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TRP A 382 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 9.971A  pdb=" N   LEU A 573 " --> pdb=" O   TYR A 549 " (cutoff:3.500A)
      removed outlier: 9.089A  pdb=" N   TYR A 549 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   PHE A 575 " --> pdb=" O   HIS A 547 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   HIS A 547 " --> pdb=" O   PHE A 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLY A 577 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LEU A 480 " --> pdb=" O   ILE A 470 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA A 468 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 389
      removed outlier: 3.536A  pdb=" N   HIS A 380 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TRP A 382 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   PHE A 575 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ILE A 511 " --> pdb=" O   PHE A 575 " (cutoff:3.500A)
      removed outlier: 9.192A  pdb=" N   GLY A 577 " --> pdb=" O   ILE A 511 " (cutoff:3.500A)
      removed outlier: 11.521A  pdb=" N   LEU A 513 " --> pdb=" O   GLY A 577 " (cutoff:3.500A)
      removed outlier: 17.099A  pdb=" N   MET A 579 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 422 through 423
      removed outlier: 3.984A  pdb=" N   VAL A 422 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ALA A 438 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 888 through 889

    454 hydrogen bonds defined for protein.
    1299 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: 3.53

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3338
        1.35 -     1.47: 2328
        1.47 -     1.59: 4667
        1.59 -     1.71: 1
        1.71 -     1.82: 94
  Bond restraints: 10428
  Sorted by residual:
  bond pdb=" CB  PRO A 519 "
       pdb=" CG  PRO A 519 "
    ideal  model  delta    sigma   weight residual
    1.492  1.615 -0.123 5.00e-02 4.00e+02 6.05e+00
  bond pdb=" F3  MF4 A2101 "
       pdb="MG   MF4 A2101 "
    ideal  model  delta    sigma   weight residual
    1.837  1.788  0.049 2.00e-02 2.50e+03 6.05e+00
  bond pdb=" F2  MF4 A2101 "
       pdb="MG   MF4 A2101 "
    ideal  model  delta    sigma   weight residual
    1.836  1.788  0.048 2.00e-02 2.50e+03 5.82e+00
  bond pdb=" F1  MF4 A2101 "
       pdb="MG   MF4 A2101 "
    ideal  model  delta    sigma   weight residual
    1.836  1.789  0.047 2.00e-02 2.50e+03 5.52e+00
  bond pdb=" F4  MF4 A2101 "
       pdb="MG   MF4 A2101 "
    ideal  model  delta    sigma   weight residual
    1.836  1.789  0.047 2.00e-02 2.50e+03 5.50e+00
  ... (remaining 10423 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.64: 14121
        6.64 -    13.29: 7
       13.29 -    19.93: 2
       19.93 -    26.57: 0
       26.57 -    33.21: 1
  Bond angle restraints: 14131
  Sorted by residual:
  angle pdb=" N   TYR G  32 "
        pdb=" CA  TYR G  32 "
        pdb=" C   TYR G  32 "
      ideal   model   delta    sigma   weight residual
     108.20   74.99   33.21 1.71e+00 3.42e-01 3.77e+02
  angle pdb=" C   TYR G  32 "
        pdb=" CA  TYR G  32 "
        pdb=" CB  TYR G  32 "
      ideal   model   delta    sigma   weight residual
     110.78   91.27   19.51 1.60e+00 3.91e-01 1.49e+02
  angle pdb=" N   ASP G  33 "
        pdb=" CA  ASP G  33 "
        pdb=" C   ASP G  33 "
      ideal   model   delta    sigma   weight residual
     110.80  126.71  -15.91 2.13e+00 2.20e-01 5.58e+01
  angle pdb=" CA  PRO A 983 "
        pdb=" N   PRO A 983 "
        pdb=" CD  PRO A 983 "
      ideal   model   delta    sigma   weight residual
     112.00  102.85    9.15 1.40e+00 5.10e-01 4.27e+01
  angle pdb=" CA  PRO A 519 "
        pdb=" N   PRO A 519 "
        pdb=" CD  PRO A 519 "
      ideal   model   delta    sigma   weight residual
     112.00  103.32    8.68 1.40e+00 5.10e-01 3.84e+01
  ... (remaining 14126 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5603
       17.99 -    35.98: 558
       35.98 -    53.98: 96
       53.98 -    71.97: 17
       71.97 -    89.96: 9
  Dihedral angle restraints: 6283
    sinusoidal: 2530
      harmonic: 3753
  Sorted by residual:
  dihedral pdb=" C   TYR G  32 "
           pdb=" N   TYR G  32 "
           pdb=" CA  TYR G  32 "
           pdb=" CB  TYR G  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -85.73  -36.87     0      2.50e+00 1.60e-01 2.17e+02
  dihedral pdb=" N   ASP G  33 "
           pdb=" C   ASP G  33 "
           pdb=" CA  ASP G  33 "
           pdb=" CB  ASP G  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  154.71  -31.91     0      2.50e+00 1.60e-01 1.63e+02
  dihedral pdb=" C   ASP G  33 "
           pdb=" N   ASP G  33 "
           pdb=" CA  ASP G  33 "
           pdb=" CB  ASP G  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -152.40   29.80     0      2.50e+00 1.60e-01 1.42e+02
  ... (remaining 6280 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.283: 1596
       0.283 -    0.565: 1
       0.565 -    0.848: 0
       0.848 -    1.130: 0
       1.130 -    1.413: 1
  Chirality restraints: 1598
  Sorted by residual:
  chirality pdb=" CA  ASP G  33 "
            pdb=" N   ASP G  33 "
            pdb=" C   ASP G  33 "
            pdb=" CB  ASP G  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.10    1.41 2.00e-01 2.50e+01 4.99e+01
  chirality pdb=" CA  TYR G  32 "
            pdb=" N   TYR G  32 "
            pdb=" C   TYR G  32 "
            pdb=" CB  TYR G  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.05   -0.54 2.00e-01 2.50e+01 7.38e+00
  chirality pdb=" CA  PRO A 983 "
            pdb=" N   PRO A 983 "
            pdb=" C   PRO A 983 "
            pdb=" CB  PRO A 983 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.57e-01
  ... (remaining 1595 not shown)

  Planarity restraints: 1824
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 982 "   -0.073 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO A 983 "    0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO A 983 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 983 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 825 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.76e+00
        pdb=" N   PRO A 826 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 826 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 826 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  71 "    0.174 9.50e-02 1.11e+02   7.79e-02 3.73e+00
        pdb=" NE  ARG B  71 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  71 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  71 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  71 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1821 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.17: 5
        2.17 -     2.86: 3631
        2.86 -     3.54: 14825
        3.54 -     4.22: 22382
        4.22 -     4.90: 39449
  Nonbonded interactions: 80292
  Sorted by model distance:
  nonbonded pdb=" CZ  PHE A  90 "
            pdb=" CG1 VAL A 322 "
     model   vdw
     1.492 3.760
  nonbonded pdb=" O   GLU B 165 "
            pdb=" OG1 THR B 166 "
     model   vdw
     1.982 3.040
  nonbonded pdb=" CE1 PHE A  90 "
            pdb=" CG1 VAL A 322 "
     model   vdw
     2.051 3.760
  nonbonded pdb=" O   SER A  91 "
            pdb=" N   LEU A  94 "
     model   vdw
     2.058 3.120
  nonbonded pdb=" O   SER A  91 "
            pdb=" N   LEU A  93 "
     model   vdw
     2.080 3.120
  ... (remaining 80287 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.360
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.070
  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:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
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      :  0.003   0.123  10431  Z= 0.139
  Angle     :  0.695  33.213  14137  Z= 0.383
  Chirality :  0.056   1.413   1598
  Planarity :  0.005   0.105   1824
  Dihedral  : 14.473  89.962   3866
  Min Nonbonded Distance : 1.492

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.39 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.71 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.23), residues: 1299
  helix:  0.87 (0.23), residues: 537
  sheet: -1.53 (0.40), residues: 150
  loop : -1.04 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 896 
 HIS   0.010   0.001   HIS A 413 
 PHE   0.021   0.001   PHE A 136 
 TYR   0.012   0.001   TYR G  34 
 ARG   0.004   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14590 (  448)
  hydrogen bonds       : angle       6.36363 ( 1299)
  SS BOND              : bond        0.00384 (    3)
  SS BOND              : angle       2.75106 (    6)
  covalent geometry    : bond        0.00330 (10428)
  covalent geometry    : angle       0.69296 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 197
  time to evaluate  : 1.089 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7865 (tt) cc_final: 0.7617 (tt)
REVERT: A  215 GLN cc_start: 0.7439 (mm110) cc_final: 0.7064 (mm110)
REVERT: A  360 THR cc_start: 0.8891 (p) cc_final: 0.8671 (p)
REVERT: A  409 VAL cc_start: 0.8641 (m) cc_final: 0.8209 (t)
REVERT: A  419 ASN cc_start: 0.7179 (m110) cc_final: 0.6794 (m-40)
REVERT: A  457 VAL cc_start: 0.8729 (t) cc_final: 0.8124 (m)
REVERT: A  724 MET cc_start: 0.8665 (mmt) cc_final: 0.8244 (mmt)
  outliers start: 3
  outliers final: 1
  residues processed: 200
  average time/residue: 0.1747
  time to fit residues: 53.7332
Evaluate side-chains
  147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 97 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 61 optimal weight:    3.9990
   chunk 75 optimal weight:   20.0000
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
A 464 ASN
A 518 GLN
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 932 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.133159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.104675 restraints weight = 18800.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.107184 restraints weight = 11225.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.108964 restraints weight = 7797.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10431  Z= 0.126
  Angle     :  0.543   7.027  14137  Z= 0.286
  Chirality :  0.041   0.146   1598
  Planarity :  0.004   0.049   1824
  Dihedral  :  4.081  21.513   1404
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.23), residues: 1299
  helix:  0.93 (0.23), residues: 552
  sheet: -1.45 (0.39), residues: 157
  loop : -0.87 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  79 
 HIS   0.006   0.001   HIS A  34 
 PHE   0.030   0.001   PHE A  90 
 TYR   0.013   0.001   TYR G  32 
 ARG   0.003   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (  448)
  hydrogen bonds       : angle       4.95586 ( 1299)
  SS BOND              : bond        0.00416 (    3)
  SS BOND              : angle       1.83320 (    6)
  covalent geometry    : bond        0.00287 (10428)
  covalent geometry    : angle       0.54195 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.080 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7918 (tt) cc_final: 0.7696 (tt)
REVERT: A  215 GLN cc_start: 0.7257 (mm110) cc_final: 0.6942 (mm110)
REVERT: A  324 GLU cc_start: 0.7485 (mp0) cc_final: 0.7218 (mp0)
REVERT: A  355 GLU cc_start: 0.8058 (tp30) cc_final: 0.7705 (tp30)
REVERT: A  360 THR cc_start: 0.8861 (p) cc_final: 0.8613 (p)
REVERT: A  409 VAL cc_start: 0.8627 (m) cc_final: 0.8361 (t)
REVERT: A  460 MET cc_start: 0.8108 (mmp) cc_final: 0.7633 (tpt)
REVERT: A  968 LEU cc_start: 0.8989 (tp) cc_final: 0.8744 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1649
  time to fit residues: 50.1409
Evaluate side-chains
  140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 39 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0270
   chunk 96 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    2.0842

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.131012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.102537 restraints weight = 19020.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.105095 restraints weight = 11277.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.106859 restraints weight = 7782.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  10431  Z= 0.156
  Angle     :  0.564   7.145  14137  Z= 0.293
  Chirality :  0.042   0.138   1598
  Planarity :  0.004   0.046   1824
  Dihedral  :  4.163  22.573   1404
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.23), residues: 1299
  helix:  0.93 (0.23), residues: 548
  sheet: -1.70 (0.39), residues: 151
  loop : -0.94 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 307 
 HIS   0.007   0.001   HIS A 909 
 PHE   0.027   0.001   PHE A 423 
 TYR   0.012   0.001   TYR B 204 
 ARG   0.004   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03712 (  448)
  hydrogen bonds       : angle       4.70581 ( 1299)
  SS BOND              : bond        0.00268 (    3)
  SS BOND              : angle       2.30529 (    6)
  covalent geometry    : bond        0.00362 (10428)
  covalent geometry    : angle       0.56166 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.472 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7889 (tt) cc_final: 0.7669 (tt)
REVERT: B   79 GLN cc_start: 0.6977 (pt0) cc_final: 0.6757 (pt0)
REVERT: A  136 PHE cc_start: 0.8556 (t80) cc_final: 0.8120 (t80)
REVERT: A  215 GLN cc_start: 0.7222 (mm110) cc_final: 0.6932 (mm110)
REVERT: A  355 GLU cc_start: 0.7906 (tp30) cc_final: 0.7588 (tp30)
REVERT: A  360 THR cc_start: 0.8828 (p) cc_final: 0.8481 (p)
REVERT: A  409 VAL cc_start: 0.8576 (m) cc_final: 0.8202 (t)
REVERT: A  419 ASN cc_start: 0.7081 (m110) cc_final: 0.6661 (m110)
REVERT: A  889 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7587 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2432
  time to fit residues: 75.7590
Evaluate side-chains
  143 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 79 optimal weight:   10.0000
   chunk 121 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0970
   chunk 4 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 119 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.132918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.104900 restraints weight = 18724.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107514 restraints weight = 11065.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.109280 restraints weight = 7624.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10431  Z= 0.112
  Angle     :  0.533   6.864  14137  Z= 0.276
  Chirality :  0.040   0.142   1598
  Planarity :  0.004   0.077   1824
  Dihedral  :  4.068  21.598   1404
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.23), residues: 1299
  helix:  0.98 (0.23), residues: 554
  sheet: -1.51 (0.40), residues: 150
  loop : -0.96 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 896 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.028   0.001   PHE A 423 
 TYR   0.020   0.001   TYR B 204 
 ARG   0.002   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03363 (  448)
  hydrogen bonds       : angle       4.55085 ( 1299)
  SS BOND              : bond        0.00572 (    3)
  SS BOND              : angle       2.15806 (    6)
  covalent geometry    : bond        0.00260 (10428)
  covalent geometry    : angle       0.53129 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ILE cc_start: 0.7853 (tt) cc_final: 0.7603 (tt)
REVERT: B   79 GLN cc_start: 0.6938 (pt0) cc_final: 0.6720 (pt0)
REVERT: B  202 MET cc_start: 0.3777 (tpt) cc_final: 0.3185 (ttt)
REVERT: A  136 PHE cc_start: 0.8561 (t80) cc_final: 0.8177 (t80)
REVERT: A  215 GLN cc_start: 0.7231 (mm110) cc_final: 0.6906 (mm110)
REVERT: A  324 GLU cc_start: 0.7576 (mp0) cc_final: 0.7303 (mp0)
REVERT: A  355 GLU cc_start: 0.7928 (tp30) cc_final: 0.7547 (tp30)
REVERT: A  360 THR cc_start: 0.8726 (p) cc_final: 0.8489 (p)
REVERT: A  409 VAL cc_start: 0.8546 (m) cc_final: 0.8214 (t)
REVERT: A  419 ASN cc_start: 0.7051 (m110) cc_final: 0.6798 (m110)
REVERT: A  460 MET cc_start: 0.8146 (mmp) cc_final: 0.7725 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1831
  time to fit residues: 58.3584
Evaluate side-chains
  144 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 125 optimal weight:    0.0870
   chunk 115 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0040
   chunk 128 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.0176

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

Flipped N/Q/H residues before XYZ refinement:
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.135282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.106783 restraints weight = 18720.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.109317 restraints weight = 11264.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.111042 restraints weight = 7875.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10431  Z= 0.113
  Angle     :  0.541   6.745  14137  Z= 0.280
  Chirality :  0.040   0.140   1598
  Planarity :  0.004   0.062   1824
  Dihedral  :  4.040  21.601   1404
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.23), residues: 1299
  helix:  0.97 (0.23), residues: 557
  sheet: -1.43 (0.40), residues: 146
  loop : -0.92 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 896 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.020   0.001   PHE A  90 
 TYR   0.016   0.001   TYR B 204 
 ARG   0.002   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (  448)
  hydrogen bonds       : angle       4.49332 ( 1299)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       2.67506 (    6)
  covalent geometry    : bond        0.00265 (10428)
  covalent geometry    : angle       0.53880 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ILE cc_start: 0.7837 (tt) cc_final: 0.7600 (tt)
REVERT: A  215 GLN cc_start: 0.7196 (mm110) cc_final: 0.6931 (mm110)
REVERT: A  355 GLU cc_start: 0.7852 (tp30) cc_final: 0.7449 (tp30)
REVERT: A  360 THR cc_start: 0.8658 (p) cc_final: 0.8421 (p)
REVERT: A  409 VAL cc_start: 0.8560 (m) cc_final: 0.8242 (t)
REVERT: A  460 MET cc_start: 0.8097 (mmp) cc_final: 0.7678 (tpt)
REVERT: A  859 TYR cc_start: 0.9218 (t80) cc_final: 0.8907 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1743
  time to fit residues: 54.2431
Evaluate side-chains
  145 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 79 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0470
   chunk 112 optimal weight:    4.9990
   chunk 49 optimal weight:    0.4980
   chunk 115 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.136356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107969 restraints weight = 18973.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.110516 restraints weight = 11336.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112278 restraints weight = 7847.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10431  Z= 0.104
  Angle     :  0.537   7.125  14137  Z= 0.279
  Chirality :  0.040   0.141   1598
  Planarity :  0.004   0.054   1824
  Dihedral  :  3.986  23.255   1404
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.23), residues: 1299
  helix:  1.00 (0.23), residues: 558
  sheet: -1.39 (0.40), residues: 151
  loop : -0.90 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 155 
 HIS   0.002   0.001   HIS A  34 
 PHE   0.016   0.001   PHE B 263 
 TYR   0.015   0.001   TYR B 204 
 ARG   0.002   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03244 (  448)
  hydrogen bonds       : angle       4.43940 ( 1299)
  SS BOND              : bond        0.00340 (    3)
  SS BOND              : angle       2.52423 (    6)
  covalent geometry    : bond        0.00235 (10428)
  covalent geometry    : angle       0.53473 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.296 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7813 (tt) cc_final: 0.7581 (tt)
REVERT: B  202 MET cc_start: 0.3532 (tpt) cc_final: 0.2966 (ttt)
REVERT: B  212 GLN cc_start: 0.6806 (mm-40) cc_final: 0.6545 (mm-40)
REVERT: A  215 GLN cc_start: 0.7134 (mm110) cc_final: 0.6911 (mm110)
REVERT: A  324 GLU cc_start: 0.7420 (mp0) cc_final: 0.7117 (mp0)
REVERT: A  355 GLU cc_start: 0.7780 (tp30) cc_final: 0.7364 (tp30)
REVERT: A  460 MET cc_start: 0.8098 (mmp) cc_final: 0.7810 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2273
  time to fit residues: 69.0824
Evaluate side-chains
  146 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 113 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0970
   chunk 95 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 321 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.136336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107929 restraints weight = 19074.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.110488 restraints weight = 11430.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112257 restraints weight = 7935.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10431  Z= 0.104
  Angle     :  0.535   7.434  14137  Z= 0.277
  Chirality :  0.041   0.215   1598
  Planarity :  0.004   0.054   1824
  Dihedral  :  3.963  21.100   1404
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.24), residues: 1299
  helix:  1.10 (0.23), residues: 556
  sheet: -1.33 (0.41), residues: 151
  loop : -0.86 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 155 
 HIS   0.009   0.001   HIS A 413 
 PHE   0.013   0.001   PHE A  90 
 TYR   0.020   0.001   TYR A 105 
 ARG   0.003   0.000   ARG A 877 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03109 (  448)
  hydrogen bonds       : angle       4.39854 ( 1299)
  SS BOND              : bond        0.00454 (    3)
  SS BOND              : angle       1.89102 (    6)
  covalent geometry    : bond        0.00237 (10428)
  covalent geometry    : angle       0.53392 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.296 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7836 (tt) cc_final: 0.7584 (tt)
REVERT: A  105 TYR cc_start: 0.8649 (t80) cc_final: 0.8371 (t80)
REVERT: A  215 GLN cc_start: 0.7152 (mm110) cc_final: 0.6920 (mm110)
REVERT: A  355 GLU cc_start: 0.7770 (tp30) cc_final: 0.7391 (tp30)
REVERT: A  460 MET cc_start: 0.8099 (mmp) cc_final: 0.7814 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2157
  time to fit residues: 65.8281
Evaluate side-chains
  144 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 125 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 93 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 98 optimal weight:    0.2980
   chunk 86 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
G  31 HIS
A 321 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 413 HIS
A 419 ASN
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.134364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.105792 restraints weight = 18969.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.108334 restraints weight = 11373.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.109944 restraints weight = 7903.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10431  Z= 0.115
  Angle     :  0.546   7.577  14137  Z= 0.282
  Chirality :  0.041   0.140   1598
  Planarity :  0.004   0.051   1824
  Dihedral  :  3.970  21.380   1404
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.23), residues: 1299
  helix:  1.18 (0.23), residues: 547
  sheet: -1.33 (0.42), residues: 146
  loop : -0.93 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 155 
 HIS   0.008   0.001   HIS A 413 
 PHE   0.015   0.001   PHE A  90 
 TYR   0.015   0.001   TYR A 105 
 ARG   0.003   0.000   ARG A 877 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03169 (  448)
  hydrogen bonds       : angle       4.40203 ( 1299)
  SS BOND              : bond        0.00392 (    3)
  SS BOND              : angle       1.97489 (    6)
  covalent geometry    : bond        0.00266 (10428)
  covalent geometry    : angle       0.54475 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.145 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7863 (tt) cc_final: 0.7579 (tt)
REVERT: B   79 GLN cc_start: 0.6814 (pt0) cc_final: 0.6552 (pt0)
REVERT: B  202 MET cc_start: 0.3572 (tpt) cc_final: 0.3025 (ttt)
REVERT: A  105 TYR cc_start: 0.8684 (t80) cc_final: 0.8397 (t80)
REVERT: A  136 PHE cc_start: 0.8459 (t80) cc_final: 0.8049 (t80)
REVERT: A  215 GLN cc_start: 0.7218 (mm110) cc_final: 0.6932 (mm110)
REVERT: A  324 GLU cc_start: 0.7496 (mp0) cc_final: 0.7251 (mp0)
REVERT: A  355 GLU cc_start: 0.7903 (tp30) cc_final: 0.7506 (tp30)
REVERT: A  360 THR cc_start: 0.8723 (p) cc_final: 0.8489 (p)
REVERT: A  409 VAL cc_start: 0.8378 (t) cc_final: 0.8027 (t)
REVERT: A  460 MET cc_start: 0.8171 (mmp) cc_final: 0.7789 (tmm)
REVERT: A  889 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7553 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1726
  time to fit residues: 54.2217
Evaluate side-chains
  151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 108 optimal weight:    0.6980
   chunk 128 optimal weight:    0.0570
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 123 optimal weight:    0.4980
   chunk 110 optimal weight:    0.0670
   chunk 87 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
A 321 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 734 GLN
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.136211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.107811 restraints weight = 19049.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110419 restraints weight = 11360.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.112020 restraints weight = 7870.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10431  Z= 0.103
  Angle     :  0.548   7.963  14137  Z= 0.281
  Chirality :  0.040   0.140   1598
  Planarity :  0.004   0.046   1824
  Dihedral  :  3.917  20.037   1404
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.23), residues: 1299
  helix:  1.25 (0.23), residues: 546
  sheet: -0.97 (0.44), residues: 136
  loop : -0.94 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 155 
 HIS   0.003   0.001   HIS A 413 
 PHE   0.021   0.001   PHE A  90 
 TYR   0.013   0.001   TYR A 105 
 ARG   0.002   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03048 (  448)
  hydrogen bonds       : angle       4.35390 ( 1299)
  SS BOND              : bond        0.00386 (    3)
  SS BOND              : angle       1.97666 (    6)
  covalent geometry    : bond        0.00233 (10428)
  covalent geometry    : angle       0.54632 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.126 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7822 (tt) cc_final: 0.7537 (tt)
REVERT: B  202 MET cc_start: 0.3739 (tpt) cc_final: 0.3249 (ttt)
REVERT: A  105 TYR cc_start: 0.8680 (t80) cc_final: 0.8403 (t80)
REVERT: A  136 PHE cc_start: 0.8411 (t80) cc_final: 0.8059 (t80)
REVERT: A  215 GLN cc_start: 0.7217 (mm110) cc_final: 0.6956 (mm110)
REVERT: A  355 GLU cc_start: 0.7908 (tp30) cc_final: 0.7566 (tp30)
REVERT: A  360 THR cc_start: 0.8616 (p) cc_final: 0.8359 (p)
REVERT: A  460 MET cc_start: 0.8124 (mmp) cc_final: 0.7771 (tmm)
REVERT: A  889 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7589 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1737
  time to fit residues: 54.8991
Evaluate side-chains
  151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 98 optimal weight:    0.0970
   chunk 45 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0070
   chunk 86 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 58 optimal weight:    0.9990
   chunk 115 optimal weight:    0.5980
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
G  31 HIS
A 321 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.136706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.108390 restraints weight = 18960.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111008 restraints weight = 11410.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.112812 restraints weight = 7895.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10431  Z= 0.104
  Angle     :  0.548   7.219  14137  Z= 0.281
  Chirality :  0.040   0.140   1598
  Planarity :  0.004   0.045   1824
  Dihedral  :  3.898  19.907   1404
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.24), residues: 1299
  helix:  1.26 (0.23), residues: 546
  sheet: -0.84 (0.45), residues: 135
  loop : -0.93 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 382 
 HIS   0.002   0.001   HIS A 199 
 PHE   0.024   0.001   PHE A  90 
 TYR   0.014   0.001   TYR A 105 
 ARG   0.004   0.000   ARG A 343 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03020 (  448)
  hydrogen bonds       : angle       4.32193 ( 1299)
  SS BOND              : bond        0.00457 (    3)
  SS BOND              : angle       2.14753 (    6)
  covalent geometry    : bond        0.00235 (10428)
  covalent geometry    : angle       0.54598 (14131)

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.224 
Fit side-chains
REVERT: B   41 ILE cc_start: 0.7849 (tt) cc_final: 0.7569 (tt)
REVERT: B  165 GLU cc_start: 0.5959 (pt0) cc_final: 0.5639 (pt0)
REVERT: B  202 MET cc_start: 0.3726 (tpt) cc_final: 0.3280 (ttt)
REVERT: A  105 TYR cc_start: 0.8674 (t80) cc_final: 0.8406 (t80)
REVERT: A  136 PHE cc_start: 0.8329 (t80) cc_final: 0.7850 (t80)
REVERT: A  215 GLN cc_start: 0.7217 (mm110) cc_final: 0.6923 (mm110)
REVERT: A  355 GLU cc_start: 0.7902 (tp30) cc_final: 0.7529 (tp30)
REVERT: A  360 THR cc_start: 0.8548 (p) cc_final: 0.8290 (p)
REVERT: A  460 MET cc_start: 0.8120 (mmp) cc_final: 0.7786 (tmm)
REVERT: A  889 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7622 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1727
  time to fit residues: 54.8246
Evaluate side-chains
  154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 127 optimal weight:    0.6980
   chunk 72 optimal weight:    8.9990
   chunk 121 optimal weight:    0.9990
   chunk 115 optimal weight:    6.9990
   chunk 126 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 24 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.133642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.105547 restraints weight = 19024.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108081 restraints weight = 11318.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.109851 restraints weight = 7814.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10431  Z= 0.125
  Angle     :  0.564   7.049  14137  Z= 0.291
  Chirality :  0.041   0.140   1598
  Planarity :  0.004   0.050   1824
  Dihedral  :  3.963  21.276   1404
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.23), residues: 1299
  helix:  1.08 (0.23), residues: 552
  sheet: -1.23 (0.43), residues: 145
  loop : -0.94 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 896 
 HIS   0.004   0.001   HIS A 909 
 PHE   0.027   0.001   PHE A  90 
 TYR   0.015   0.001   TYR B 204 
 ARG   0.004   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (  448)
  hydrogen bonds       : angle       4.30020 ( 1299)
  SS BOND              : bond        0.00304 (    3)
  SS BOND              : angle       1.80946 (    6)
  covalent geometry    : bond        0.00296 (10428)
  covalent geometry    : angle       0.56283 (14131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4226.73 seconds
wall clock time: 76 minutes 54.65 seconds (4614.65 seconds total)