Starting phenix.real_space_refine
on Wed Feb 12 13:59:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q2z_13786/02_2025/7q2z_13786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q2z_13786/02_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_13786/02_2025/7q2z_13786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q2z_13786/02_2025/7q2z_13786.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q2z_13786/02_2025/7q2z_13786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q2z_13786/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.79, per 1000 atoms: 0.58
  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: 2.03
  Conformation dependent library (CDL) restraints added in 784.4 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: 2.82
  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: 2.76

  Time building geometry restraints manager: 2.36 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:             0.290
  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:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.730
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.720
-------------------------------------------------------------------------------
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  : 1.067 
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: 0.2934
  time to fit residues: 66.7691
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  : 0.968 
-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.165508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.124717 restraints weight = 9387.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.35
r_work: 0.3040 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
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  : 0.842 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6848 (ttmm) cc_final: 0.6398 (mptt)
REVERT: E  170 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7377 (ttm170)
REVERT: E  297 ARG cc_start: 0.8610 (tpt170) cc_final: 0.8314 (ttm-80)
REVERT: E  312 ILE cc_start: 0.8966 (mm) cc_final: 0.8693 (mm)
REVERT: E  344 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7350 (mt)
REVERT: E  466 ARG cc_start: 0.8473 (mtp85) cc_final: 0.7733 (mmm-85)
REVERT: E  496 LYS cc_start: 0.7681 (tttm) cc_final: 0.7376 (tttt)
REVERT: E  604 ASP cc_start: 0.8447 (p0) cc_final: 0.8216 (p0)
REVERT: E  641 MET cc_start: 0.8930 (mmt) cc_final: 0.8364 (mmt)
REVERT: E  646 MET cc_start: 0.8250 (mmm) cc_final: 0.8045 (mmp)
REVERT: E  688 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7377 (mmtm)
REVERT: E  823 LYS cc_start: 0.8361 (ptmt) cc_final: 0.8005 (ptmt)
REVERT: C  482 LYS cc_start: 0.7585 (mtmm) cc_final: 0.7134 (ptpt)
REVERT: C  510 THR cc_start: 0.8867 (m) cc_final: 0.8550 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 114
  average time/residue: 0.2615
  time to fit residues: 39.0276
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  : 0.867 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 29 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 93 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.158617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116975 restraints weight = 9501.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.35
r_work: 0.2957 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8488  Z= 0.332
  Angle     :  0.592   8.421  11657  Z= 0.318
  Chirality :  0.039   0.148   1348
  Planarity :  0.004   0.056   1325
  Dihedral  : 19.756 176.902   1516
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.49 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.23 %
    Favored  : 88.94 %
  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:  0.39 (0.28), residues: 888
  helix:  1.24 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop : -2.36 (0.34), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E 351 
 HIS   0.005   0.001   HIS E 274 
 PHE   0.021   0.002   PHE E 382 
 TYR   0.014   0.002   TYR E 366 
 ARG   0.004   0.001   ARG E 287 

*********************** 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
  118 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.935 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.7016 (ttmm) cc_final: 0.6409 (mptt)
REVERT: E   44 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7430 (mmtm)
REVERT: E   79 VAL cc_start: 0.8538 (m) cc_final: 0.8253 (t)
REVERT: E  107 GLU cc_start: 0.8160 (mp0) cc_final: 0.7597 (mp0)
REVERT: E  170 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7691 (ttm170)
REVERT: E  297 ARG cc_start: 0.8682 (tpt170) cc_final: 0.8350 (ttm-80)
REVERT: E  322 ARG cc_start: 0.8487 (ptm160) cc_final: 0.7855 (ptp90)
REVERT: E  344 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7646 (mt)
REVERT: E  377 MET cc_start: 0.8018 (ttm) cc_final: 0.7752 (ttt)
REVERT: E  466 ARG cc_start: 0.8500 (mtp85) cc_final: 0.7767 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7648 (tttm) cc_final: 0.7209 (tttt)
REVERT: E  688 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7369 (mmtm)
REVERT: E  823 LYS cc_start: 0.8360 (ptmt) cc_final: 0.7984 (ptmt)
REVERT: E  894 ASP cc_start: 0.7630 (m-30) cc_final: 0.7338 (m-30)
REVERT: C  482 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7152 (ptpt)
  outliers start: 15
  outliers final: 12
  residues processed: 112
  average time/residue: 0.2444
  time to fit residues: 36.3727
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  : 0.846 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 86 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 335 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.158265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.120724 restraints weight = 9300.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.26
r_work: 0.3074 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3119

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= 0.190
  Angle     :  0.493   6.941  11657  Z= 0.270
  Chirality :  0.035   0.120   1348
  Planarity :  0.004   0.051   1325
  Dihedral  : 19.544 176.783   1516
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.25 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.33 %
    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:  0.97 (0.29), residues: 888
  helix:  1.63 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop : -2.01 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 780 
 HIS   0.003   0.001   HIS E 394 
 PHE   0.015   0.001   PHE E 733 
 TYR   0.012   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
  111 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.913 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6973 (ttmm) cc_final: 0.6379 (mptt)
REVERT: E  107 GLU cc_start: 0.8215 (mp0) cc_final: 0.7899 (mp0)
REVERT: E  170 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7530 (ttm170)
REVERT: E  297 ARG cc_start: 0.8570 (tpt170) cc_final: 0.8267 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7431 (mt)
REVERT: E  377 MET cc_start: 0.7913 (ttm) cc_final: 0.7636 (ttt)
REVERT: E  466 ARG cc_start: 0.8495 (mtp85) cc_final: 0.7755 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7614 (tttm) cc_final: 0.7187 (tttt)
REVERT: E  603 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8189 (mtp)
REVERT: E  688 LYS cc_start: 0.7780 (mtmt) cc_final: 0.7352 (mmtm)
REVERT: E  823 LYS cc_start: 0.8403 (ptmt) cc_final: 0.8142 (ptmt)
REVERT: E  879 ILE cc_start: 0.7840 (mm) cc_final: 0.7252 (mm)
REVERT: E  897 ARG cc_start: 0.8248 (mtm180) cc_final: 0.8013 (mtm-85)
REVERT: C  482 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7206 (ptpt)
  outliers start: 15
  outliers final: 10
  residues processed: 107
  average time/residue: 0.2607
  time to fit residues: 37.0597
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  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  110 ILE
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
Chi-restraints excluded: chain C residue  509 ILE
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:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0470
   chunk 89 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.8120

-------------------------------------------------------------------------------
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 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 = 0.3819 r_free = 0.3819 target = 0.161331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120727 restraints weight = 9273.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.32
r_work: 0.3049 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8488  Z= 0.139
  Angle     :  0.448   5.980  11657  Z= 0.248
  Chirality :  0.034   0.106   1348
  Planarity :  0.003   0.051   1325
  Dihedral  : 19.467 177.148   1516
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.70 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.06 %
    Favored  : 87.36 %
  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:  1.50 (0.30), residues: 888
  helix:  2.00 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.73 (0.37), residues: 252

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   0.014   0.001   PHE C 523 
 TYR   0.012   0.001   TYR E 657 
 ARG   0.003   0.000   ARG E 793 

*********************** 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
  115 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: E   23 LYS cc_start: 0.6791 (ttmm) cc_final: 0.6243 (mptt)
REVERT: E  170 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7463 (ttm170)
REVERT: E  297 ARG cc_start: 0.8563 (tpt170) cc_final: 0.8301 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7384 (mt)
REVERT: E  377 MET cc_start: 0.7965 (ttm) cc_final: 0.7761 (ttt)
REVERT: E  379 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7346 (mp0)
REVERT: E  466 ARG cc_start: 0.8518 (mtp85) cc_final: 0.7793 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7576 (tttm) cc_final: 0.7153 (tttt)
REVERT: E  604 ASP cc_start: 0.8437 (p0) cc_final: 0.8151 (p0)
REVERT: E  688 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7331 (mmtm)
REVERT: E  879 ILE cc_start: 0.7685 (mm) cc_final: 0.7133 (mm)
REVERT: E  894 ASP cc_start: 0.7567 (m-30) cc_final: 0.7354 (m-30)
REVERT: E  897 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7971 (mtm-85)
  outliers start: 13
  outliers final: 9
  residues processed: 111
  average time/residue: 0.2435
  time to fit residues: 35.5494
Evaluate side-chains
  106 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
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
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:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 90 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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
E 804 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.160450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.121072 restraints weight = 9238.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 1.22
r_work: 0.3093 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.3189

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     :  0.466   6.362  11657  Z= 0.256
  Chirality :  0.034   0.115   1348
  Planarity :  0.003   0.049   1325
  Dihedral  : 19.461 177.116   1516
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.59 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.30 %
    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:  1.64 (0.29), residues: 888
  helix:  2.05 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop : -1.60 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 780 
 HIS   0.002   0.001   HIS E 394 
 PHE   0.014   0.001   PHE C 523 
 TYR   0.012   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
  109 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.872 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6254 (mptt)
REVERT: E  102 LYS cc_start: 0.5584 (mmtm) cc_final: 0.5342 (tttt)
REVERT: E  170 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7521 (ttm170)
REVERT: E  297 ARG cc_start: 0.8553 (tpt170) cc_final: 0.8285 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7480 (mt)
REVERT: E  379 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7334 (mp0)
REVERT: E  466 ARG cc_start: 0.8496 (mtp85) cc_final: 0.7783 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7554 (tttm) cc_final: 0.7114 (tttt)
REVERT: E  604 ASP cc_start: 0.8456 (p0) cc_final: 0.8156 (p0)
REVERT: E  688 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7414 (mmtm)
REVERT: E  793 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.8120 (mmt90)
REVERT: E  879 ILE cc_start: 0.7696 (mm) cc_final: 0.7140 (mm)
REVERT: E  894 ASP cc_start: 0.7679 (m-30) cc_final: 0.7419 (m-30)
REVERT: E  897 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7890 (mtm-85)
REVERT: C  482 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7229 (ptpt)
  outliers start: 13
  outliers final: 10
  residues processed: 106
  average time/residue: 0.2558
  time to fit residues: 35.5467
Evaluate side-chains
  104 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
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  614 THR
Chi-restraints excluded: chain C residue  494 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 85 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   chunk 73 optimal weight:    0.4980
   chunk 32 optimal weight:    0.0570
   chunk 88 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    2.2502

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

Flipped N/Q/H residues before XYZ refinement:
E 381 ASN
E 401 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.160115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.118870 restraints weight = 9319.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.30
r_work: 0.3009 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3365

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= 0.218
  Angle     :  0.505   7.009  11657  Z= 0.275
  Chirality :  0.036   0.128   1348
  Planarity :  0.004   0.050   1325
  Dihedral  : 19.517 177.247   1516
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.27 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.79 %
    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:  1.57 (0.29), residues: 888
  helix:  2.01 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop : -1.58 (0.37), residues: 253

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   0.013   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
  110 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.959 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6398 (mptt)
REVERT: E  102 LYS cc_start: 0.5452 (mmtm) cc_final: 0.4996 (tttp)
REVERT: E  170 ARG cc_start: 0.8256 (ttm170) cc_final: 0.7636 (ttm170)
REVERT: E  297 ARG cc_start: 0.8653 (tpt170) cc_final: 0.8356 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7578 (mt)
REVERT: E  379 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7407 (mp0)
REVERT: E  466 ARG cc_start: 0.8483 (mtp85) cc_final: 0.7756 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7587 (tttm) cc_final: 0.7134 (tttt)
REVERT: E  688 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7385 (mmtm)
REVERT: E  793 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.8131 (mmt90)
REVERT: E  879 ILE cc_start: 0.7714 (mm) cc_final: 0.7163 (mm)
REVERT: C  482 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7230 (ptpt)
  outliers start: 12
  outliers final: 10
  residues processed: 107
  average time/residue: 0.2603
  time to fit residues: 36.5138
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  : 0.866 
-------------------------------------------------------------------------------
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  614 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:    0.2980
   chunk 18 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    0.4980
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.160924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.121769 restraints weight = 9304.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.31
r_work: 0.3113 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8488  Z= 0.137
  Angle     :  0.448   7.539  11657  Z= 0.248
  Chirality :  0.034   0.119   1348
  Planarity :  0.003   0.048   1325
  Dihedral  : 19.407 177.158   1516
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.25 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.15 %
    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:  1.98 (0.30), residues: 888
  helix:  2.33 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.41 (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   0.011   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
  105 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.934 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6233 (mptt)
REVERT: E  102 LYS cc_start: 0.5427 (mmtm) cc_final: 0.5086 (tttp)
REVERT: E  170 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7423 (ttm170)
REVERT: E  297 ARG cc_start: 0.8524 (tpt170) cc_final: 0.8259 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7402 (mt)
REVERT: E  379 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7484 (mp0)
REVERT: E  466 ARG cc_start: 0.8507 (mtp85) cc_final: 0.7797 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7647 (tttm) cc_final: 0.7211 (tttt)
REVERT: E  603 MET cc_start: 0.8461 (mtp) cc_final: 0.8185 (ttm)
REVERT: E  604 ASP cc_start: 0.8386 (p0) cc_final: 0.8096 (p0)
REVERT: E  688 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7393 (mmtm)
REVERT: E  879 ILE cc_start: 0.7597 (mm) cc_final: 0.7074 (mm)
REVERT: C  482 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7278 (ptpt)
  outliers start: 10
  outliers final: 7
  residues processed: 102
  average time/residue: 0.2358
  time to fit residues: 32.0778
Evaluate side-chains
  101 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
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  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:    8.9990
   chunk 53 optimal weight:    0.0470
   chunk 45 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0050
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3594 r_free = 0.3594 target = 0.144387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.101634 restraints weight = 9482.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.34
r_work: 0.3075 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.3322

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= 0.131
  Angle     :  0.437   8.272  11657  Z= 0.242
  Chirality :  0.033   0.117   1348
  Planarity :  0.003   0.048   1325
  Dihedral  : 19.346 177.120   1516
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.82 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.27 %
    Favored  : 86.39 %
  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:  2.27 (0.30), residues: 888
  helix:  2.49 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.21 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 780 
 HIS   0.002   0.000   HIS E 394 
 PHE   0.015   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
  108 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.856 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6739 (ttmm) cc_final: 0.6137 (mptt)
REVERT: E   44 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7304 (mmtm)
REVERT: E  102 LYS cc_start: 0.5404 (mmtm) cc_final: 0.5023 (tttp)
REVERT: E  170 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7470 (ttm170)
REVERT: E  297 ARG cc_start: 0.8575 (tpt170) cc_final: 0.8302 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7319 (mt)
REVERT: E  379 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7268 (mp0)
REVERT: E  466 ARG cc_start: 0.8504 (mtp85) cc_final: 0.7792 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7577 (tttm) cc_final: 0.7124 (tttt)
REVERT: E  603 MET cc_start: 0.8542 (mtp) cc_final: 0.8327 (ttp)
REVERT: E  688 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7377 (mmtm)
REVERT: E  691 TYR cc_start: 0.8629 (m-80) cc_final: 0.8386 (m-80)
REVERT: E  823 LYS cc_start: 0.8438 (ptmt) cc_final: 0.8147 (ptmt)
REVERT: E  879 ILE cc_start: 0.7578 (mm) cc_final: 0.7035 (mm)
REVERT: C  397 ASN cc_start: 0.8357 (m110) cc_final: 0.8146 (m-40)
REVERT: C  482 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7219 (ptpt)
  outliers start: 11
  outliers final: 7
  residues processed: 105
  average time/residue: 0.2533
  time to fit residues: 35.5839
Evaluate side-chains
  99 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
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  509 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 5 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.3804 r_free = 0.3804 target = 0.160145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120672 restraints weight = 9219.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.22
r_work: 0.3063 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8488  Z= 0.184
  Angle     :  0.488   7.318  11657  Z= 0.267
  Chirality :  0.035   0.121   1348
  Planarity :  0.003   0.048   1325
  Dihedral  : 19.397 177.336   1516
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.70 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.39 %
    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:  2.13 (0.29), residues: 888
  helix:  2.39 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop : -1.25 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 780 
 HIS   0.004   0.001   HIS E 401 
 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 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
  101 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.809 
Fit side-chains
REVERT: E   23 LYS cc_start: 0.6829 (ttmm) cc_final: 0.6244 (mptt)
REVERT: E   44 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7308 (mmtm)
REVERT: E  102 LYS cc_start: 0.5335 (mmtm) cc_final: 0.4948 (tttp)
REVERT: E  170 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7505 (ttm170)
REVERT: E  297 ARG cc_start: 0.8563 (tpt170) cc_final: 0.8261 (ttm-80)
REVERT: E  344 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7426 (mt)
REVERT: E  379 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7453 (mp0)
REVERT: E  466 ARG cc_start: 0.8475 (mtp85) cc_final: 0.7769 (mtm-85)
REVERT: E  496 LYS cc_start: 0.7568 (tttm) cc_final: 0.7114 (tttt)
REVERT: E  603 MET cc_start: 0.8520 (mtp) cc_final: 0.8245 (ttp)
REVERT: E  688 LYS cc_start: 0.7653 (mtmt) cc_final: 0.7419 (mmtm)
REVERT: E  823 LYS cc_start: 0.8461 (ptmt) cc_final: 0.8183 (ptmt)
REVERT: E  879 ILE cc_start: 0.7667 (mm) cc_final: 0.7136 (mm)
REVERT: C  482 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7259 (ptpt)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.2389
  time to fit residues: 31.9720
Evaluate side-chains
  100 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain E residue  379 GLU
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  509 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.160624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.121236 restraints weight = 9289.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.21
r_work: 0.3052 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3429

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= 0.165
  Angle     :  0.471   7.087  11657  Z= 0.260
  Chirality :  0.035   0.119   1348
  Planarity :  0.003   0.047   1325
  Dihedral  : 19.377 177.615   1516
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.48 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.39 %
    Favored  : 86.51 %
  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:  2.17 (0.30), residues: 888
  helix:  2.42 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.21 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 780 
 HIS   0.002   0.001   HIS E 274 
 PHE   0.016   0.001   PHE C 523 
 TYR   0.012   0.001   TYR E 657 
 ARG   0.004   0.000   ARG E  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4437.29 seconds
wall clock time: 79 minutes 14.02 seconds (4754.02 seconds total)