Starting phenix.real_space_refine
on Wed Mar 12 14:26:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q2z_13786/03_2025/7q2z_13786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q2z_13786/03_2025/7q2z_13786.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q2z_13786/03_2025/7q2z_13786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q2z_13786/03_2025/7q2z_13786.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q2z_13786/03_2025/7q2z_13786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q2z_13786/03_2025/7q2z_13786.cif"
  }
  resolution = 3.2
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      46      5.49       5
     S      32      5.16       5
     C    5130      2.51       5
     N    1403      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8258
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 6543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 812, 6543
          Classifications: {'peptide': 812}
          Link IDs: {'PTRANS': 19, 'TRANS': 792}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 772
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 460
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
    Chain: "G"
      Number of atoms: 483
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 483
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
  Time building chain proxies: 5.13, per 1000 atoms: 0.62
  Number of scatterers: 8258
  At special positions: 0
  Unit cell: (85.32, 109.08, 133.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P      46     15.00
     O    1647      8.00
     N    1403      7.00
     C    5130      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 860.4 milliseconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1754

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      19 base pairs and 41 stacking pairs defined.
    Time for finding SS restraints: 2.87
  Creating SS restraints...
    Processing helix  chain 'E' and resid 8 through 25
    Processing helix  chain 'E' and resid 32 through 49
    Processing helix  chain 'E' and resid 50 through 64
      removed outlier: 3.839A  pdb=" N   PHE E  54 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS E  64 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 99
      removed outlier: 3.547A  pdb=" N   ILE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL E  79 " --> pdb=" O   GLY E  75 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS E  80 " --> pdb=" O   ASP E  76 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLU E  92 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LEU E  93 " --> pdb=" O   LEU E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 107 through 123
    Processing helix  chain 'E' and resid 124 through 126
      No H-bonds generated for 'chain 'E' and resid 124 through 126'
    Processing helix  chain 'E' and resid 130 through 145
    Processing helix  chain 'E' and resid 152 through 167
    Processing helix  chain 'E' and resid 171 through 183
    Processing helix  chain 'E' and resid 206 through 217
      removed outlier: 3.972A  pdb=" N   GLN E 215 " --> pdb=" O   VAL E 211 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 219 through 229
      removed outlier: 3.548A  pdb=" N   ARG E 223 " --> pdb=" O   SER E 219 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 236 through 242
    Processing helix  chain 'E' and resid 243 through 246
    Processing helix  chain 'E' and resid 248 through 258
      removed outlier: 3.645A  pdb=" N   VAL E 255 " --> pdb=" O   ASN E 251 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   TYR E 256 " --> pdb=" O   ARG E 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 258 through 264
    Processing helix  chain 'E' and resid 265 through 269
    Processing helix  chain 'E' and resid 272 through 284
    Processing helix  chain 'E' and resid 288 through 301
      removed outlier: 3.589A  pdb=" N   ARG E 292 " --> pdb=" O   GLU E 288 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 301 through 306
    Processing helix  chain 'E' and resid 311 through 318
    Processing helix  chain 'E' and resid 325 through 337
      removed outlier: 3.994A  pdb=" N   GLU E 331 " --> pdb=" O   VAL E 327 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ALA E 332 " --> pdb=" O   LYS E 328 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 355 through 372
      removed outlier: 3.577A  pdb=" N   ASN E 372 " --> pdb=" O   TYR E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 374 through 381
      removed outlier: 3.607A  pdb=" N   LEU E 378 " --> pdb=" O   ILE E 374 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 384 through 401
      removed outlier: 3.563A  pdb=" N   GLU E 390 " --> pdb=" O   SER E 386 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TYR E 395 " --> pdb=" O   HIS E 391 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 431
      removed outlier: 4.090A  pdb=" N   ARG E 431 " --> pdb=" O   ILE E 427 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 436 through 452
      removed outlier: 3.634A  pdb=" N   ARG E 440 " --> pdb=" O   ASP E 436 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 457 through 471
    Processing helix  chain 'E' and resid 474 through 503
      removed outlier: 4.091A  pdb=" N   PHE E 478 " --> pdb=" O   ASN E 474 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL E 479 " --> pdb=" O   GLU E 475 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR E 480 " --> pdb=" O   LYS E 476 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LYS E 502 " --> pdb=" O   GLU E 498 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ILE E 503 " --> pdb=" O   GLN E 499 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 571 through 587
      removed outlier: 3.767A  pdb=" N   TYR E 584 " --> pdb=" O   THR E 580 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET E 585 " --> pdb=" O   ARG E 581 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 596 through 606
      removed outlier: 3.614A  pdb=" N   ALA E 600 " --> pdb=" O   ASN E 596 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP E 604 " --> pdb=" O   ALA E 600 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 606 through 612
      removed outlier: 4.052A  pdb=" N   ARG E 612 " --> pdb=" O   THR E 608 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 615 through 631
    Processing helix  chain 'E' and resid 633 through 640
      removed outlier: 3.623A  pdb=" N   ALA E 637 " --> pdb=" O   ASP E 633 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 641 through 650
    Processing helix  chain 'E' and resid 652 through 670
    Processing helix  chain 'E' and resid 671 through 675
      removed outlier: 3.991A  pdb=" N   VAL E 674 " --> pdb=" O   GLY E 671 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL E 675 " --> pdb=" O   ASN E 672 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 671 through 675'
    Processing helix  chain 'E' and resid 682 through 696
      removed outlier: 4.023A  pdb=" N   LEU E 686 " --> pdb=" O   ASP E 682 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 699 through 716
      removed outlier: 3.527A  pdb=" N   ALA E 716 " --> pdb=" O   LYS E 712 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 721 through 733
      removed outlier: 3.995A  pdb=" N   PHE E 725 " --> pdb=" O   ASP E 721 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 735 through 739
      removed outlier: 3.613A  pdb=" N   SER E 738 " --> pdb=" O   PRO E 735 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   SER E 739 " --> pdb=" O   ILE E 736 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 735 through 739'
    Processing helix  chain 'E' and resid 740 through 758
      removed outlier: 3.576A  pdb=" N   VAL E 744 " --> pdb=" O   ASN E 740 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE E 749 " --> pdb=" O   GLN E 745 " (cutoff:3.500A)
      Proline residue:  E 752  - end of helix
      removed outlier: 4.121A  pdb=" N   HIS E 758 " --> pdb=" O   TYR E 754 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 758 through 785
      removed outlier: 3.736A  pdb=" N   THR E 768 " --> pdb=" O   ARG E 764 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   ALA E 770 " --> pdb=" O   SER E 766 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   ASP E 771 " --> pdb=" O   ARG E 767 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL E 778 " --> pdb=" O   LEU E 774 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU E 779 " --> pdb=" O   ARG E 775 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ASP E 781 " --> pdb=" O   CYS E 777 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 798 through 810
    Processing helix  chain 'E' and resid 811 through 815
      removed outlier: 3.855A  pdb=" N   LEU E 815 " --> pdb=" O   PRO E 812 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 820 through 824
      removed outlier: 4.244A  pdb=" N   LYS E 823 " --> pdb=" O   GLY E 820 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 827 through 839
      removed outlier: 3.738A  pdb=" N   PHE E 831 " --> pdb=" O   VAL E 827 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 840 through 842
      No H-bonds generated for 'chain 'E' and resid 840 through 842'
    Processing helix  chain 'E' and resid 844 through 854
      removed outlier: 3.901A  pdb=" N   LYS E 848 " --> pdb=" O   LYS E 844 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ASN E 854 " --> pdb=" O   MET E 850 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 866 through 882
    Processing helix  chain 'E' and resid 887 through 909
    Processing helix  chain 'C' and resid 388 through 398
    Processing helix  chain 'C' and resid 468 through 475
      removed outlier: 4.004A  pdb=" N   ASP C 472 " --> pdb=" O   ASP C 468 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 491
      removed outlier: 4.247A  pdb=" N   LYS C 491 " --> pdb=" O   LYS C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 505 through 511

    430 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      76 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      41 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2310
        1.34 -     1.45: 1458
        1.45 -     1.57: 4579
        1.57 -     1.69: 91
        1.69 -     1.81: 50
  Bond restraints: 8488
  Sorted by residual:
  bond pdb=" CB  PRO E 592 "
       pdb=" CG  PRO E 592 "
    ideal  model  delta    sigma   weight residual
    1.492  1.576 -0.084 5.00e-02 4.00e+02 2.83e+00
  bond pdb=" O3'  DA G  13 "
       pdb=" P    DA G  14 "
    ideal  model  delta    sigma   weight residual
    1.607  1.585  0.022 1.50e-02 4.44e+03 2.21e+00
  bond pdb=" C3'  DT F   3 "
       pdb=" O3'  DT F   3 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.70e+00
  bond pdb=" O3'  DT F  11 "
       pdb=" P    DT F  12 "
    ideal  model  delta    sigma   weight residual
    1.607  1.590  0.017 1.50e-02 4.44e+03 1.28e+00
  bond pdb=" O3'  DT F  12 "
       pdb=" P    DT F  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.590  0.017 1.50e-02 4.44e+03 1.27e+00
  ... (remaining 8483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 11189
        1.07 -     2.14: 334
        2.14 -     3.21: 108
        3.21 -     4.28: 18
        4.28 -     5.35: 8
  Bond angle restraints: 11657
  Sorted by residual:
  angle pdb=" C4'  DA G  12 "
        pdb=" C3'  DA G  12 "
        pdb=" O3'  DA G  12 "
      ideal   model   delta    sigma   weight residual
     110.00  105.30    4.70 1.50e+00 4.44e-01 9.82e+00
  angle pdb=" C4'  DT F  13 "
        pdb=" O4'  DT F  13 "
        pdb=" C1'  DT F  13 "
      ideal   model   delta    sigma   weight residual
     109.70  105.97    3.73 1.50e+00 4.44e-01 6.18e+00
  angle pdb=" C4'  DT F  13 "
        pdb=" C3'  DT F  13 "
        pdb=" O3'  DT F  13 "
      ideal   model   delta    sigma   weight residual
     110.00  106.27    3.73 1.50e+00 4.44e-01 6.18e+00
  angle pdb=" CA  PRO E 592 "
        pdb=" N   PRO E 592 "
        pdb=" CD  PRO E 592 "
      ideal   model   delta    sigma   weight residual
     112.00  108.53    3.47 1.40e+00 5.10e-01 6.15e+00
  angle pdb=" N   GLU E 874 "
        pdb=" CA  GLU E 874 "
        pdb=" CB  GLU E 874 "
      ideal   model   delta    sigma   weight residual
     110.28  114.09   -3.81 1.55e+00 4.16e-01 6.03e+00
  ... (remaining 11652 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.83: 4817
       34.83 -    69.66: 279
       69.66 -   104.48: 11
      104.48 -   139.31: 0
      139.31 -   174.14: 1
  Dihedral angle restraints: 5108
    sinusoidal: 2435
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" C4'  DT F   3 "
           pdb=" C3'  DT F   3 "
           pdb=" O3'  DT F   3 "
           pdb=" P    DT F   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.86  174.14     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  ASP E 302 "
           pdb=" CB  ASP E 302 "
           pdb=" CG  ASP E 302 "
           pdb=" OD1 ASP E 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.83   56.83     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  ASP E 286 "
           pdb=" CB  ASP E 286 "
           pdb=" CG  ASP E 286 "
           pdb=" OD1 ASP E 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.99   52.99     1      2.00e+01 2.50e-03 9.55e+00
  ... (remaining 5105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 987
       0.034 -    0.067: 292
       0.067 -    0.101: 61
       0.101 -    0.135: 7
       0.135 -    0.168: 1
  Chirality restraints: 1348
  Sorted by residual:
  chirality pdb=" C3'  DA G  12 "
            pdb=" C4'  DA G  12 "
            pdb=" O3'  DA G  12 "
            pdb=" C2'  DA G  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.83    0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CA  PRO E 799 "
            pdb=" N   PRO E 799 "
            pdb=" C   PRO E 799 "
            pdb=" CB  PRO E 799 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.14e-01
  chirality pdb=" C4'  DT F  13 "
            pdb=" C5'  DT F  13 "
            pdb=" O4'  DT F  13 "
            pdb=" C3'  DT F  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.41   -0.11 2.00e-01 2.50e+01 3.10e-01
  ... (remaining 1345 not shown)

  Planarity restraints: 1325
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 591 "   -0.056 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO E 592 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO E 592 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO E 592 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 272 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO E 273 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO E 273 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E 273 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA G  13 "   -0.022 2.00e-02 2.50e+03   1.03e-02 2.91e+00
        pdb=" N9   DA G  13 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DA G  13 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA G  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DA G  13 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DA G  13 "   -0.009 2.00e-02 2.50e+03
        pdb=" N6   DA G  13 "    0.001 2.00e-02 2.50e+03
        pdb=" N1   DA G  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA G  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA G  13 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DA G  13 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1322 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1291
        2.76 -     3.30: 7672
        3.30 -     3.83: 13540
        3.83 -     4.37: 15544
        4.37 -     4.90: 26188
  Nonbonded interactions: 64235
  Sorted by model distance:
  nonbonded pdb=" O   SER E 601 "
            pdb=" OG1 THR E 605 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   PRO E 383 "
            pdb=" OH  TYR E 432 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ASP E 782 "
            pdb=" OG  SER E 786 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ASP E 319 "
            pdb=" N   SER E 321 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OE1 GLN E  22 "
            pdb=" NE2 GLN E  25 "
     model   vdw
     2.306 3.120
  ... (remaining 64230 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.480
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
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      :  0.002   0.084   8488  Z= 0.159
  Angle     :  0.483   5.347  11657  Z= 0.282
  Chirality :  0.033   0.168   1348
  Planarity :  0.004   0.083   1325
  Dihedral  : 18.984 174.140   3354
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.53 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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: -1.44 (0.26), residues: 888
  helix: -0.12 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -2.95 (0.31), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  57 
 HIS   0.003   0.001   HIS E 394 
 PHE   0.009   0.001   PHE E 360 
 TYR   0.009   0.001   TYR E 168 
 ARG   0.004   0.000   ARG E 775 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.921 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.7039 (ttmm) cc_final: 0.6707 (mptt)
REVERT: E   69 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7530 (tttm)
REVERT: E  312 ILE cc_start: 0.8625 (mm) cc_final: 0.8179 (mm)
REVERT: E  434 TYR cc_start: 0.8136 (m-80) cc_final: 0.7042 (m-10)
REVERT: E  466 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7048 (mmm-85)
REVERT: E  488 ASP cc_start: 0.6882 (m-30) cc_final: 0.6598 (m-30)
REVERT: E  496 LYS cc_start: 0.7749 (tttm) cc_final: 0.7548 (tttt)
REVERT: E  697 ASN cc_start: 0.7293 (t0) cc_final: 0.7077 (t0)
REVERT: E  838 ILE cc_start: 0.8424 (mt) cc_final: 0.8172 (pt)
REVERT: C  482 LYS cc_start: 0.7247 (mtmm) cc_final: 0.6785 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.3091
  time to fit residues: 70.7329
Evaluate side-chains
  99 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 71 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0070
   chunk 48 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.9804

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

Flipped N/Q/H residues before XYZ refinement:
** E  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  48 GLN
E 305 ASN
E 381 ASN
E 391 HIS
C 489 ASN
C 492 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.163018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.122671 restraints weight = 9261.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.34
r_work: 0.3061 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8488  Z= 0.211
  Angle     :  0.525   7.046  11657  Z= 0.286
  Chirality :  0.036   0.115   1348
  Planarity :  0.004   0.059   1325
  Dihedral  : 19.699 175.225   1516
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.48 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  7.41 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.12 (0.28), residues: 888
  helix:  1.02 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.44 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 408 
 HIS   0.003   0.001   HIS E 274 
 PHE   0.017   0.001   PHE E 733 
 TYR   0.010   0.001   TYR E 657 
 ARG   0.004   0.001   ARG E 793 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.975 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6854 (ttmm) cc_final: 0.6405 (mptt)
REVERT: E  170 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7383 (ttm170)
REVERT: E  297 ARG cc_start: 0.8614 (tpt170) cc_final: 0.8318 (ttm-80)
REVERT: E  312 ILE cc_start: 0.8975 (mm) cc_final: 0.8703 (mm)
REVERT: E  344 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7352 (mt)
REVERT: E  466 ARG cc_start: 0.8481 (mtp85) cc_final: 0.7743 (mmm-85)
REVERT: E  496 LYS cc_start: 0.7689 (tttm) cc_final: 0.7384 (tttt)
REVERT: E  604 ASP cc_start: 0.8455 (p0) cc_final: 0.8224 (p0)
REVERT: E  641 MET cc_start: 0.8925 (mmt) cc_final: 0.8359 (mmt)
REVERT: E  646 MET cc_start: 0.8244 (mmm) cc_final: 0.8037 (mmp)
REVERT: E  688 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7389 (mmtm)
REVERT: E  823 LYS cc_start: 0.8369 (ptmt) cc_final: 0.8016 (ptmt)
REVERT: C  482 LYS cc_start: 0.7600 (mtmm) cc_final: 0.7150 (ptpt)
REVERT: C  510 THR cc_start: 0.8875 (m) cc_final: 0.8556 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 114
  average time/residue: 0.2689
  time to fit residues: 40.2457
Evaluate side-chains
  101 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  110 ILE
Chi-restraints excluded: chain E residue  147 ASN
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  594 THR
Chi-restraints excluded: chain E residue  888 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 93 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** E  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 147 ASN
E 335 GLN
E 737 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.160217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.118751 restraints weight = 9539.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.36
r_work: 0.2982 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8488  Z= 0.258
  Angle     :  0.547   7.879  11657  Z= 0.295
  Chirality :  0.037   0.133   1348
  Planarity :  0.004   0.054   1325
  Dihedral  : 19.573 176.807   1516
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.38 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.75 %
    Favored  : 89.43 %
  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:  0.58 (0.29), residues: 888
  helix:  1.40 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop : -2.33 (0.34), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP E 351 
 HIS   0.004   0.001   HIS E 274 
 PHE   0.019   0.002   PHE E 382 
 TYR   0.013   0.001   TYR E 366 
 ARG   0.003   0.001   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.785 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.7004 (ttmm) cc_final: 0.6421 (mptt)
REVERT: E   44 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7410 (mmtm)
REVERT: E  107 GLU cc_start: 0.8179 (mp0) cc_final: 0.7654 (mp0)
REVERT: E  170 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7611 (ttm170)
REVERT: E  297 ARG cc_start: 0.8670 (tpt170) cc_final: 0.8354 (ttm-80)
REVERT: E  322 ARG cc_start: 0.8401 (ptm160) cc_final: 0.8024 (ptp-170)
REVERT: E  344 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7604 (mt)
REVERT: E  377 MET cc_start: 0.8019 (ttm) cc_final: 0.7748 (ttt)
REVERT: E  466 ARG cc_start: 0.8502 (mtp85) cc_final: 0.7771 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7607 (tttm) cc_final: 0.7192 (tttt)
REVERT: E  603 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8319 (mtp)
REVERT: E  688 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7363 (mmtm)
REVERT: E  823 LYS cc_start: 0.8363 (ptmt) cc_final: 0.7968 (ptmt)
REVERT: E  894 ASP cc_start: 0.7660 (m-30) cc_final: 0.7413 (m-30)
REVERT: C  482 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7109 (ptpt)
  outliers start: 15
  outliers final: 12
  residues processed: 110
  average time/residue: 0.2474
  time to fit residues: 36.2736
Evaluate side-chains
  103 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  110 ILE
Chi-restraints excluded: chain E residue  147 ASN
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  594 THR
Chi-restraints excluded: chain E residue  603 MET
Chi-restraints excluded: chain E residue  614 THR
Chi-restraints excluded: chain E residue  838 ILE
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** E  42 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 = 0.3807 r_free = 0.3807 target = 0.160174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.119313 restraints weight = 9305.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.33
r_work: 0.3050 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8488  Z= 0.162
  Angle     :  0.472   6.569  11657  Z= 0.260
  Chirality :  0.034   0.115   1348
  Planarity :  0.003   0.051   1325
  Dihedral  : 19.454 176.655   1516
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.03 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  9.84 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.29), residues: 888
  helix:  1.76 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.93 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 780 
 HIS   0.003   0.001   HIS E 394 
 PHE   0.014   0.001   PHE C 523 
 TYR   0.011   0.001   TYR E 657 
 ARG   0.003   0.000   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.861 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6933 (ttmm) cc_final: 0.6363 (mptt)
REVERT: E  170 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7506 (ttm-80)
REVERT: E  297 ARG cc_start: 0.8573 (tpt170) cc_final: 0.8288 (ttm-80)
REVERT: E  322 ARG cc_start: 0.8421 (ptm160) cc_final: 0.8156 (ptp-170)
REVERT: E  344 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7403 (mt)
REVERT: E  377 MET cc_start: 0.7940 (ttm) cc_final: 0.7674 (ttt)
REVERT: E  466 ARG cc_start: 0.8504 (mtp85) cc_final: 0.7746 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7580 (tttm) cc_final: 0.7212 (tttt)
REVERT: E  603 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8177 (mtp)
REVERT: E  604 ASP cc_start: 0.8462 (p0) cc_final: 0.8136 (p0)
REVERT: E  688 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7337 (mmtm)
REVERT: E  823 LYS cc_start: 0.8381 (ptmt) cc_final: 0.8094 (ptmt)
REVERT: E  879 ILE cc_start: 0.7797 (mm) cc_final: 0.7209 (mm)
REVERT: C  482 LYS cc_start: 0.7782 (mtmm) cc_final: 0.7184 (ptpt)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2575
  time to fit residues: 36.3007
Evaluate side-chains
  98 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  413 PHE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  603 MET
Chi-restraints excluded: chain E residue  614 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 50 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 86 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
E  48 GLN
E 147 ASN
E 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.159132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.120513 restraints weight = 9189.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.25
r_work: 0.3083 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8488  Z= 0.200
  Angle     :  0.494   6.780  11657  Z= 0.270
  Chirality :  0.035   0.126   1348
  Planarity :  0.004   0.051   1325
  Dihedral  : 19.544 177.046   1516
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.93 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.45 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.29), residues: 888
  helix:  1.79 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -1.80 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 780 
 HIS   0.003   0.001   HIS E 274 
 PHE   0.013   0.001   PHE C 523 
 TYR   0.012   0.001   TYR E 366 
 ARG   0.003   0.000   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.803 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6963 (ttmm) cc_final: 0.6387 (mptt)
REVERT: E  170 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7511 (ttm170)
REVERT: E  297 ARG cc_start: 0.8582 (tpt170) cc_final: 0.8286 (ttm-80)
REVERT: E  322 ARG cc_start: 0.8386 (ptm160) cc_final: 0.8151 (ptp-170)
REVERT: E  344 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7477 (mt)
REVERT: E  379 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7336 (mp0)
REVERT: E  466 ARG cc_start: 0.8427 (mtp85) cc_final: 0.7723 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7624 (tttm) cc_final: 0.7209 (tttt)
REVERT: E  603 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8146 (mtp)
REVERT: E  604 ASP cc_start: 0.8445 (p0) cc_final: 0.8140 (p0)
REVERT: E  688 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7325 (mmtm)
REVERT: E  879 ILE cc_start: 0.7792 (mm) cc_final: 0.7215 (mm)
REVERT: C  482 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7218 (ptpt)
  outliers start: 14
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2377
  time to fit residues: 32.7281
Evaluate side-chains
  102 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 ASN
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  379 GLU
Chi-restraints excluded: chain E residue  413 PHE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  603 MET
Chi-restraints excluded: chain E residue  614 THR
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
E 335 GLN
E 381 ASN
E 804 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.160104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.119205 restraints weight = 9256.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.32
r_work: 0.3050 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8488  Z= 0.152
  Angle     :  0.458   6.495  11657  Z= 0.253
  Chirality :  0.034   0.113   1348
  Planarity :  0.003   0.049   1325
  Dihedral  : 19.460 177.102   1516
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.25 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.54 %
    Favored  : 86.88 %
  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:  1.57 (0.30), residues: 888
  helix:  2.00 (0.21), residues: 639
  sheet:  None (None), residues: 0
  loop : -1.62 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 780 
 HIS   0.002   0.001   HIS E 394 
 PHE   0.016   0.001   PHE C 523 
 TYR   0.011   0.001   TYR E 657 
 ARG   0.003   0.000   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
REVERT: E   23 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6260 (mptt)
REVERT: E  170 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7460 (ttm170)
REVERT: E  297 ARG cc_start: 0.8603 (tpt170) cc_final: 0.8327 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7465 (mt)
REVERT: E  379 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7388 (mp0)
REVERT: E  466 ARG cc_start: 0.8507 (mtp85) cc_final: 0.7782 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7580 (tttm) cc_final: 0.7157 (tttt)
REVERT: E  604 ASP cc_start: 0.8461 (p0) cc_final: 0.8103 (p0)
REVERT: E  688 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7373 (mmtm)
REVERT: E  793 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.8156 (mmt90)
REVERT: E  879 ILE cc_start: 0.7648 (mm) cc_final: 0.7099 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 104
  average time/residue: 0.2494
  time to fit residues: 34.1940
Evaluate side-chains
  103 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  379 GLU
Chi-restraints excluded: chain E residue  413 PHE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  614 THR
Chi-restraints excluded: chain C residue  494 THR
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 85 optimal weight:    0.3980
   chunk 28 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 73 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    2.0386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.160373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.119053 restraints weight = 9317.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.31
r_work: 0.3017 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8488  Z= 0.203
  Angle     :  0.493   6.363  11657  Z= 0.269
  Chirality :  0.035   0.128   1348
  Planarity :  0.004   0.049   1325
  Dihedral  : 19.526 177.155   1516
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.93 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.66 %
    Favored  : 86.88 %
  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:  1.55 (0.29), residues: 888
  helix:  2.03 (0.21), residues: 631
  sheet:  None (None), residues: 0
  loop : -1.64 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 780 
 HIS   0.003   0.001   HIS E 274 
 PHE   0.013   0.001   PHE C 523 
 TYR   0.012   0.001   TYR E 366 
 ARG   0.004   0.000   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.830 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6932 (ttmm) cc_final: 0.6292 (mptt)
REVERT: E   44 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7322 (mmtm)
REVERT: E  102 LYS cc_start: 0.5482 (mmtm) cc_final: 0.5019 (tttp)
REVERT: E  170 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7578 (ttm170)
REVERT: E  297 ARG cc_start: 0.8658 (tpt170) cc_final: 0.8363 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7504 (mt)
REVERT: E  379 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7435 (mp0)
REVERT: E  466 ARG cc_start: 0.8502 (mtp85) cc_final: 0.7774 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7628 (tttm) cc_final: 0.7189 (tttt)
REVERT: E  688 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7382 (mmtm)
REVERT: E  793 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.8143 (mmt90)
REVERT: E  879 ILE cc_start: 0.7756 (mm) cc_final: 0.7212 (mm)
REVERT: C  482 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7269 (ptpt)
  outliers start: 12
  outliers final: 10
  residues processed: 102
  average time/residue: 0.2327
  time to fit residues: 31.9217
Evaluate side-chains
  102 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  379 GLU
Chi-restraints excluded: chain E residue  413 PHE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  614 THR
Chi-restraints excluded: chain C residue  494 THR
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
E 147 ASN
E 335 GLN
E 401 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.159975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.119151 restraints weight = 9286.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.32
r_work: 0.3051 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8488  Z= 0.150
  Angle     :  0.456   6.320  11657  Z= 0.252
  Chirality :  0.034   0.121   1348
  Planarity :  0.003   0.048   1325
  Dihedral  : 19.434 177.010   1516
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.25 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.94 %
    Favored  : 87.12 %
  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:  1.85 (0.29), residues: 888
  helix:  2.24 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.49 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 780 
 HIS   0.002   0.000   HIS E 394 
 PHE   0.015   0.001   PHE C 523 
 TYR   0.012   0.001   TYR E 657 
 ARG   0.004   0.000   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.882 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6263 (mptt)
REVERT: E   44 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7359 (mmtm)
REVERT: E  102 LYS cc_start: 0.5470 (mmtm) cc_final: 0.5033 (tttp)
REVERT: E  170 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7491 (ttm170)
REVERT: E  297 ARG cc_start: 0.8551 (tpt170) cc_final: 0.8286 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7415 (mt)
REVERT: E  379 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7419 (mp0)
REVERT: E  466 ARG cc_start: 0.8514 (mtp85) cc_final: 0.7795 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7612 (tttm) cc_final: 0.7161 (tttt)
REVERT: E  603 MET cc_start: 0.8519 (mtp) cc_final: 0.8151 (ttm)
REVERT: E  604 ASP cc_start: 0.8444 (p0) cc_final: 0.8158 (p0)
REVERT: E  688 LYS cc_start: 0.7672 (mtmt) cc_final: 0.7337 (mmtm)
REVERT: E  793 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8132 (mmt90)
REVERT: E  879 ILE cc_start: 0.7626 (mm) cc_final: 0.7105 (mm)
REVERT: C  482 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7265 (ptpt)
  outliers start: 16
  outliers final: 12
  residues processed: 106
  average time/residue: 0.2367
  time to fit residues: 33.7375
Evaluate side-chains
  107 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 ASN
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  233 ASP
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  379 GLU
Chi-restraints excluded: chain E residue  413 PHE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  614 THR
Chi-restraints excluded: chain C residue  494 THR
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0980
   chunk 45 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
E 335 GLN
E 401 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.161530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.122286 restraints weight = 9369.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.34
r_work: 0.3122 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8488  Z= 0.133
  Angle     :  0.446   5.857  11657  Z= 0.247
  Chirality :  0.034   0.118   1348
  Planarity :  0.003   0.046   1325
  Dihedral  : 19.390 176.957   1516
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.48 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.30 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.30), residues: 888
  helix:  2.43 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.34 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 780 
 HIS   0.002   0.000   HIS E 394 
 PHE   0.016   0.001   PHE C 523 
 TYR   0.011   0.001   TYR E 657 
 ARG   0.004   0.000   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.907 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6811 (ttmm) cc_final: 0.6239 (mptt)
REVERT: E  102 LYS cc_start: 0.5392 (mmtm) cc_final: 0.5017 (tttp)
REVERT: E  170 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7430 (ttm170)
REVERT: E  297 ARG cc_start: 0.8513 (tpt170) cc_final: 0.8252 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7355 (mt)
REVERT: E  379 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7374 (mp0)
REVERT: E  466 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7776 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7603 (tttm) cc_final: 0.7155 (tttt)
REVERT: E  603 MET cc_start: 0.8430 (mtp) cc_final: 0.8164 (ttm)
REVERT: E  604 ASP cc_start: 0.8438 (p0) cc_final: 0.8157 (p0)
REVERT: E  688 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7385 (mmtm)
REVERT: E  879 ILE cc_start: 0.7623 (mm) cc_final: 0.7087 (mm)
REVERT: E  909 GLU cc_start: 0.7271 (tm-30) cc_final: 0.7060 (tm-30)
REVERT: C  482 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7254 (ptpt)
  outliers start: 12
  outliers final: 10
  residues processed: 107
  average time/residue: 0.2464
  time to fit residues: 35.4416
Evaluate side-chains
  108 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  233 ASP
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  379 GLU
Chi-restraints excluded: chain E residue  413 PHE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain C residue  494 THR
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 79 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
E 147 ASN
E 335 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.155794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.114590 restraints weight = 9207.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.30
r_work: 0.2993 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8488  Z= 0.282
  Angle     :  0.547   8.668  11657  Z= 0.295
  Chirality :  0.038   0.139   1348
  Planarity :  0.004   0.048   1325
  Dihedral  : 19.577 177.414   1516
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.15 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.66 %
    Favored  : 86.76 %
  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:  1.62 (0.29), residues: 888
  helix:  2.05 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop : -1.50 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 402 
 HIS   0.004   0.001   HIS E 401 
 PHE   0.015   0.002   PHE C 523 
 TYR   0.013   0.002   TYR E 366 
 ARG   0.003   0.000   ARG E  32 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.903 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.7091 (ttmm) cc_final: 0.6458 (mptt)
REVERT: E   44 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7316 (mmtm)
REVERT: E  102 LYS cc_start: 0.5442 (mmtm) cc_final: 0.4787 (tttp)
REVERT: E  170 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7662 (ttm170)
REVERT: E  297 ARG cc_start: 0.8612 (tpt170) cc_final: 0.8289 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7578 (mt)
REVERT: E  379 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7411 (mp0)
REVERT: E  466 ARG cc_start: 0.8458 (mtp85) cc_final: 0.7732 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7588 (tttm) cc_final: 0.7141 (tttt)
REVERT: E  688 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7441 (mmtm)
REVERT: E  879 ILE cc_start: 0.7771 (mm) cc_final: 0.7242 (mm)
REVERT: E  909 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7223 (tm-30)
REVERT: C  482 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7250 (ptpt)
  outliers start: 13
  outliers final: 11
  residues processed: 103
  average time/residue: 0.2363
  time to fit residues: 32.7538
Evaluate side-chains
  104 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  233 ASP
Chi-restraints excluded: chain E residue  290 SER
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  379 GLU
Chi-restraints excluded: chain E residue  413 PHE
Chi-restraints excluded: chain E residue  432 TYR
Chi-restraints excluded: chain E residue  438 VAL
Chi-restraints excluded: chain E residue  455 THR
Chi-restraints excluded: chain E residue  614 THR
Chi-restraints excluded: chain C residue  494 THR
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0970
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E 335 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.142221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.105491 restraints weight = 9472.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.20
r_work: 0.3158 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8488  Z= 0.145
  Angle     :  0.463   8.121  11657  Z= 0.256
  Chirality :  0.034   0.118   1348
  Planarity :  0.003   0.046   1325
  Dihedral  : 19.412 177.552   1516
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.80 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.79 %
    Favored  : 86.63 %
  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:  1.99 (0.29), residues: 888
  helix:  2.31 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.34 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 780 
 HIS   0.003   0.001   HIS E 401 
 PHE   0.015   0.001   PHE C 523 
 TYR   0.010   0.001   TYR E 657 
 ARG   0.003   0.000   ARG E  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4418.96 seconds
wall clock time: 76 minutes 23.22 seconds (4583.22 seconds total)