Starting phenix.real_space_refine
on Sat May 17 06:52:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q6v_18199/05_2025/8q6v_18199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q6v_18199/05_2025/8q6v_18199.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q6v_18199/05_2025/8q6v_18199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q6v_18199/05_2025/8q6v_18199.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q6v_18199/05_2025/8q6v_18199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q6v_18199/05_2025/8q6v_18199.cif"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.015
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: 6
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      29      5.16       5
     C    5100      2.51       5
     N    1341      2.21       5
     O    1438      1.98       5
     H    7497      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15406
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 5714
          Classifications: {'peptide': 370}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 358}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 139
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 53
    Chain: "B"
      Number of atoms: 9691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 651, 9691
          Classifications: {'peptide': 651}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 49, 'TRANS': 601}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 306
          Unresolved non-hydrogen angles: 375
          Unresolved non-hydrogen dihedrals: 251
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 11, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 200
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.27, per 1000 atoms: 0.47
  Number of scatterers: 15406
  At special positions: 0
  Unit cell: (71.724, 86.736, 131.772, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      29     16.00
     Mg      1     11.99
     O    1438      8.00
     N    1341      7.00
     C    5100      6.00
     H    7497      1.00
    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: 4.40
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      47.0% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 55
    Processing helix  chain 'A' and resid 62 through 66
    Processing helix  chain 'A' and resid 70 through 73
    Processing helix  chain 'A' and resid 79 through 92
      removed outlier: 4.116A  pdb=" N   HIS A  92 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 114
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 161 through 175
      removed outlier: 3.776A  pdb=" N   GLY A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TYR A 169 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 191
      removed outlier: 3.881A  pdb=" N   ILE A 189 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 195
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 250 through 270
      removed outlier: 3.640A  pdb=" N   THR A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   HIS A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 306
    Processing helix  chain 'A' and resid 306 through 311
    Processing helix  chain 'A' and resid 311 through 328
      removed outlier: 3.692A  pdb=" N   GLU A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 372
    Processing helix  chain 'A' and resid 377 through 386
    Processing helix  chain 'B' and resid 4 through 14
      removed outlier: 3.940A  pdb=" N   ARG B   8 " --> pdb=" O   PRO B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 63
      Proline residue:  B  60  - end of helix
    Processing helix  chain 'B' and resid 72 through 92
    Processing helix  chain 'B' and resid 106 through 128
      removed outlier: 3.988A  pdb=" N   GLN B 112 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ALA B 115 " --> pdb=" O   ASN B 111 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG B 116 " --> pdb=" O   GLN B 112 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE B 126 " --> pdb=" O   ARG B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 161
      removed outlier: 3.529A  pdb=" N   THR B 161 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 185
      removed outlier: 4.090A  pdb=" N   ARG B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 189
    Processing helix  chain 'B' and resid 203 through 217
    Processing helix  chain 'B' and resid 235 through 244
      removed outlier: 3.934A  pdb=" N   HIS B 244 " --> pdb=" O   GLY B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 305
      removed outlier: 3.695A  pdb=" N   GLU B 299 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ALA B 303 " --> pdb=" O   GLU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 330
    Processing helix  chain 'B' and resid 343 through 346
    Processing helix  chain 'B' and resid 347 through 359
    Processing helix  chain 'B' and resid 360 through 362
      No H-bonds generated for 'chain 'B' and resid 360 through 362'
    Processing helix  chain 'B' and resid 373 through 398
      removed outlier: 3.991A  pdb=" N   THR B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   GLY B 389 " --> pdb=" O   GLY B 385 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   ASP B 390 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 614
      removed outlier: 5.242A  pdb=" N   THR B 610 " --> pdb=" O   GLU B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 618
      No H-bonds generated for 'chain 'B' and resid 616 through 618'
    Processing helix  chain 'B' and resid 619 through 645
      removed outlier: 3.594A  pdb=" N   TYR B 642 " --> pdb=" O   VAL B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 664
      removed outlier: 3.592A  pdb=" N   PHE B 664 " --> pdb=" O   ALA B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 681 through 690
    Processing helix  chain 'B' and resid 691 through 698
      removed outlier: 4.438A  pdb=" N   HIS B 696 " --> pdb=" O   ALA B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 699 through 708
      removed outlier: 3.857A  pdb=" N   ARG B 703 " --> pdb=" O   PRO B 699 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LEU B 705 " --> pdb=" O   ILE B 701 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET B 706 " --> pdb=" O   PHE B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 717
    Processing helix  chain 'B' and resid 742 through 752
    Processing helix  chain 'B' and resid 753 through 757
    Processing helix  chain 'B' and resid 758 through 763
    Processing helix  chain 'B' and resid 780 through 789
    Processing helix  chain 'B' and resid 838 through 842
    Processing helix  chain 'B' and resid 873 through 882
    Processing helix  chain 'B' and resid 920 through 928
      removed outlier: 3.811A  pdb=" N   PHE B 925 " --> pdb=" O   TYR B 921 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   TYR B 926 " --> pdb=" O   ARG B 922 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8
      removed outlier: 4.803A  pdb=" N   PHE A 104 " --> pdb=" O   ILE A 137 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   GLU A 139 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE A 101 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   GLY A 219 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   THR A 103 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   GLU A 221 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY A  25 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ARG A 208 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   GLU A  23 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 177
      removed outlier: 6.806A  pdb=" N   ASN A  44 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   CYS A 224 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ARG A 275 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLY A 279 " --> pdb=" O   LYS A 243 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ILE A 276 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   GLU A 292 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   TYR A 278 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   VAL A 290 " --> pdb=" O   TYR A 278 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   PHE A 280 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68
    Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20
      removed outlier: 6.665A  pdb=" N   HIS B 227 " --> pdb=" O   LYS B 249 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   LEU B 251 " --> pdb=" O   HIS B 227 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE B 229 " --> pdb=" O   LEU B 251 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   CYS B 228 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ASN B  49 " --> pdb=" O   CYS B 228 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   TYR B 230 " --> pdb=" O   ASN B  49 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TYR B  51 " --> pdb=" O   TYR B 230 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   LEU B  47 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   VAL B  96 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ASN B  49 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   VAL B  98 " --> pdb=" O   ASN B  49 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   TYR B  51 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   GLN B 192 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LYS B  95 " --> pdb=" O   GLN B 192 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   ILE B 194 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU B  97 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 193 " --> pdb=" O   ILE B 774 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL B 771 " --> pdb=" O   TYR B 848 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 723 through 724

    343 hydrogen bonds defined for protein.
    939 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.35

  Time building geometry restraints manager: 5.17 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 7483
        1.12 -     1.30: 1312
        1.30 -     1.47: 3183
        1.47 -     1.65: 3585
        1.65 -     1.82: 44
  Bond restraints: 15607
  Sorted by residual:
  bond pdb=" N   ALA B 928 "
       pdb=" H   ALA B 928 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   LEU B 182 "
       pdb=" H   LEU B 182 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   ALA B 760 "
       pdb=" H   ALA B 760 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   VAL B 307 "
       pdb=" H   VAL B 307 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   ARG B 624 "
       pdb=" H   ARG B 624 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 15602 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.84: 24635
        2.84 -     5.68: 2725
        5.68 -     8.52: 752
        8.52 -    11.36: 6
       11.36 -    14.21: 14
  Bond angle restraints: 28132
  Sorted by residual:
  angle pdb=" C   GLY A 133 "
        pdb=" N   GLN A 134 "
        pdb=" CA  GLN A 134 "
      ideal   model   delta    sigma   weight residual
     121.75  132.46  -10.71 1.73e+00 3.34e-01 3.84e+01
  angle pdb=" C   PHE B 600 "
        pdb=" N   GLU B 601 "
        pdb=" CA  GLU B 601 "
      ideal   model   delta    sigma   weight residual
     120.58  127.24   -6.66 1.32e+00 5.74e-01 2.55e+01
  angle pdb=" OE1 GLN B 913 "
        pdb=" CD  GLN B 913 "
        pdb=" NE2 GLN B 913 "
      ideal   model   delta    sigma   weight residual
     122.60  117.65    4.95 1.00e+00 1.00e+00 2.45e+01
  angle pdb=" CB  HIS B 337 "
        pdb=" CG  HIS B 337 "
        pdb=" CD2 HIS B 337 "
      ideal   model   delta    sigma   weight residual
     131.20  124.85    6.35 1.30e+00 5.92e-01 2.38e+01
  angle pdb=" N   VAL B  96 "
        pdb=" CA  VAL B  96 "
        pdb=" C   VAL B  96 "
      ideal   model   delta    sigma   weight residual
     108.42  115.36   -6.94 1.43e+00 4.89e-01 2.36e+01
  ... (remaining 28127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 6845
       17.69 -    35.38: 407
       35.38 -    53.07: 105
       53.07 -    70.76: 110
       70.76 -    88.45: 7
  Dihedral angle restraints: 7474
    sinusoidal: 3874
      harmonic: 3600
  Sorted by residual:
  dihedral pdb=" CA  LEU A 353 "
           pdb=" C   LEU A 353 "
           pdb=" N   ARG A 354 "
           pdb=" CA  ARG A 354 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.63   27.37     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  PRO B 770 "
           pdb=" C   PRO B 770 "
           pdb=" N   VAL B 771 "
           pdb=" CA  VAL B 771 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.19   26.81     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  THR B 364 "
           pdb=" C   THR B 364 "
           pdb=" N   TYR B 365 "
           pdb=" CA  TYR B 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.87   26.13     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 7471 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 735
       0.072 -    0.144: 372
       0.144 -    0.216: 97
       0.216 -    0.288: 14
       0.288 -    0.360: 3
  Chirality restraints: 1221
  Sorted by residual:
  chirality pdb=" CA  HIS B 244 "
            pdb=" N   HIS B 244 "
            pdb=" C   HIS B 244 "
            pdb=" CB  HIS B 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CA  PRO B 836 "
            pdb=" N   PRO B 836 "
            pdb=" C   PRO B 836 "
            pdb=" CB  PRO B 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CA  LYS B 845 "
            pdb=" N   LYS B 845 "
            pdb=" C   LYS B 845 "
            pdb=" CB  LYS B 845 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 1218 not shown)

  Planarity restraints: 2382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 285 "    0.247 2.00e-02 2.50e+03   9.63e-02 2.78e+02
        pdb=" CG  TYR A 285 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 285 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 285 "   -0.092 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 285 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 285 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 285 "    0.024 2.00e-02 2.50e+03
        pdb=" OH  TYR A 285 "    0.153 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 285 "   -0.045 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 285 "   -0.067 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 285 "   -0.022 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 285 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 803 "    0.144 2.00e-02 2.50e+03   1.35e-01 2.75e+02
        pdb=" CD  GLN B 803 "   -0.049 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 803 "   -0.088 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 803 "   -0.122 2.00e-02 2.50e+03
        pdb="HE21 GLN B 803 "   -0.112 2.00e-02 2.50e+03
        pdb="HE22 GLN B 803 "    0.227 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  42 "   -0.120 2.00e-02 2.50e+03   1.17e-01 2.04e+02
        pdb=" CG  ASN A  42 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  42 "    0.075 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  42 "    0.117 2.00e-02 2.50e+03
        pdb="HD21 ASN A  42 "    0.093 2.00e-02 2.50e+03
        pdb="HD22 ASN A  42 "   -0.195 2.00e-02 2.50e+03
  ... (remaining 2379 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 980
        2.20 -     2.80: 27098
        2.80 -     3.40: 42155
        3.40 -     4.00: 54827
        4.00 -     4.60: 80294
  Nonbonded interactions: 205354
  Sorted by model distance:
  nonbonded pdb=" HH  TYR B 657 "
            pdb=" OD2 ASP B 724 "
     model   vdw
     1.596 2.450
  nonbonded pdb=" O   ILE A 251 "
            pdb=" HG1 THR A 254 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OD1 ASP A  58 "
            pdb=" HG  SER A  60 "
     model   vdw
     1.617 2.450
  nonbonded pdb=" OE2 GLU A  23 "
            pdb=" HG  SER A 205 "
     model   vdw
     1.621 2.450
  nonbonded pdb=" HH  TYR B 221 "
            pdb=" OE1 GLU B 245 "
     model   vdw
     1.627 2.450
  ... (remaining 205349 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.260
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     36.250
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
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      :  0.012   0.044   8110  Z= 0.699
  Angle     :  1.713  10.714  11033  Z= 1.155
  Chirality :  0.087   0.360   1221
  Planarity :  0.015   0.124   1429
  Dihedral  : 13.171  88.451   2888
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  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: -1.06 (0.25), residues: 1003
  helix: -0.80 (0.23), residues: 381
  sheet: -0.00 (0.46), residues: 114
  loop : -0.67 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.113   0.022   TRP B 355 
 HIS   0.009   0.002   HIS A 338 
 PHE   0.062   0.011   PHE A 344 
 TYR   0.215   0.022   TYR A 285 
 ARG   0.010   0.001   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16837 (  343)
  hydrogen bonds       : angle       7.31462 (  939)
  covalent geometry    : bond        0.01181 ( 8110)
  covalent geometry    : angle       1.71293 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  159 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 MET cc_start: 0.5389 (mtt) cc_final: 0.5123 (mtp)
REVERT: B   87 VAL cc_start: 0.9185 (t) cc_final: 0.8704 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.4596
  time to fit residues: 95.9019
Evaluate side-chains
  90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 132 ASN
B 192 GLN
B 793 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.072265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.057006 restraints weight = 78819.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 5.07
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8110  Z= 0.143
  Angle     :  0.653   6.179  11033  Z= 0.352
  Chirality :  0.043   0.161   1221
  Planarity :  0.004   0.037   1429
  Dihedral  :  6.456  70.053   1104
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.22 %
    Favored  : 91.78 %
  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: -0.10 (0.26), residues: 1003
  helix:  0.55 (0.25), residues: 388
  sheet: -0.55 (0.41), residues: 128
  loop : -0.32 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 291 
 HIS   0.004   0.001   HIS A 199 
 PHE   0.019   0.002   PHE A 344 
 TYR   0.024   0.002   TYR A 285 
 ARG   0.004   0.001   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05345 (  343)
  hydrogen bonds       : angle       5.55161 (  939)
  covalent geometry    : bond        0.00314 ( 8110)
  covalent geometry    : angle       0.65334 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  102 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ARG cc_start: 0.8271 (mtt90) cc_final: 0.8022 (mtt90)
REVERT: A  267 GLN cc_start: 0.9394 (tt0) cc_final: 0.8764 (tp-100)
REVERT: B   54 MET cc_start: 0.9567 (tpt) cc_final: 0.9348 (tpp)
REVERT: B  349 ASP cc_start: 0.9416 (p0) cc_final: 0.9193 (p0)
REVERT: B  640 MET cc_start: 0.8970 (ttm) cc_final: 0.8568 (ttp)
REVERT: B  842 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9085 (mm)
REVERT: B  912 THR cc_start: 0.9374 (m) cc_final: 0.8875 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 100
  average time/residue: 0.4052
  time to fit residues: 56.4674
Evaluate side-chains
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  268 CYS
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  842 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 56 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 63 optimal weight:    0.5980
   chunk 89 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    1.6382

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

Flipped N/Q/H residues before XYZ refinement:
B 206 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.072194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.056511 restraints weight = 79587.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 5.11
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8110  Z= 0.129
  Angle     :  0.558   5.495  11033  Z= 0.295
  Chirality :  0.041   0.151   1221
  Planarity :  0.004   0.041   1429
  Dihedral  :  5.676  66.434   1104
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  8.84 %
    Favored  : 90.78 %
  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:  0.42 (0.27), residues: 1003
  helix:  1.24 (0.26), residues: 388
  sheet: -0.57 (0.40), residues: 129
  loop : -0.17 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 291 
 HIS   0.003   0.001   HIS B 396 
 PHE   0.022   0.001   PHE A 131 
 TYR   0.018   0.001   TYR A 285 
 ARG   0.004   0.001   ARG B 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  343)
  hydrogen bonds       : angle       5.01575 (  939)
  covalent geometry    : bond        0.00286 ( 8110)
  covalent geometry    : angle       0.55764 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.9419 (tt0) cc_final: 0.8646 (tp-100)
REVERT: B   76 MET cc_start: 0.8734 (mtp) cc_final: 0.8378 (mtt)
REVERT: B  349 ASP cc_start: 0.9390 (p0) cc_final: 0.9179 (p0)
REVERT: B  706 MET cc_start: 0.8571 (mtp) cc_final: 0.7868 (mtp)
REVERT: B  912 THR cc_start: 0.9409 (m) cc_final: 0.8965 (t)
  outliers start: 3
  outliers final: 2
  residues processed: 84
  average time/residue: 0.4129
  time to fit residues: 48.7471
Evaluate side-chains
  72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  638 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 96 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.068910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.053660 restraints weight = 81895.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 5.00
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.092   8110  Z= 0.286
  Angle     :  0.623   4.725  11033  Z= 0.339
  Chirality :  0.042   0.161   1221
  Planarity :  0.004   0.039   1429
  Dihedral  :  5.725  68.998   1104
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.34 %
    Favored  : 88.29 %
  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:  0.06 (0.26), residues: 1003
  helix:  1.12 (0.26), residues: 384
  sheet: -0.92 (0.40), residues: 128
  loop : -0.48 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 306 
 HIS   0.006   0.001   HIS B 396 
 PHE   0.011   0.001   PHE B 596 
 TYR   0.025   0.002   TYR A 285 
 ARG   0.009   0.001   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  343)
  hydrogen bonds       : angle       5.27125 (  939)
  covalent geometry    : bond        0.00617 ( 8110)
  covalent geometry    : angle       0.62331 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7830 (mtt90)
REVERT: B   76 MET cc_start: 0.8891 (mtp) cc_final: 0.8564 (mtt)
REVERT: B  640 MET cc_start: 0.9039 (ttt) cc_final: 0.8692 (ttp)
REVERT: B  912 THR cc_start: 0.9436 (m) cc_final: 0.9074 (t)
  outliers start: 11
  outliers final: 10
  residues processed: 76
  average time/residue: 0.3755
  time to fit residues: 40.5609
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  638 VAL
Chi-restraints excluded: chain B residue  771 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0010
   chunk 98 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.3190

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.070998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.055619 restraints weight = 81034.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 5.06
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8110  Z= 0.111
  Angle     :  0.529   4.921  11033  Z= 0.275
  Chirality :  0.040   0.146   1221
  Planarity :  0.004   0.034   1429
  Dihedral  :  5.305  65.701   1104
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.34 %
    Favored  : 88.67 %
  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:  0.52 (0.27), residues: 1003
  helix:  1.60 (0.26), residues: 389
  sheet: -0.85 (0.41), residues: 128
  loop : -0.28 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 291 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.020   0.001   PHE A 131 
 TYR   0.017   0.001   TYR B 717 
 ARG   0.003   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  343)
  hydrogen bonds       : angle       4.82598 (  939)
  covalent geometry    : bond        0.00248 ( 8110)
  covalent geometry    : angle       0.52862 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.9450 (tt0) cc_final: 0.8846 (tp-100)
REVERT: A  278 TYR cc_start: 0.8522 (m-80) cc_final: 0.8196 (m-80)
REVERT: B   76 MET cc_start: 0.8805 (mtp) cc_final: 0.8451 (mtt)
REVERT: B  640 MET cc_start: 0.9030 (ttt) cc_final: 0.8697 (ttp)
REVERT: B  706 MET cc_start: 0.8276 (mtp) cc_final: 0.8014 (mmm)
REVERT: B  717 TYR cc_start: 0.8084 (m-80) cc_final: 0.7862 (m-80)
REVERT: B  912 THR cc_start: 0.9416 (m) cc_final: 0.9014 (t)
  outliers start: 8
  outliers final: 7
  residues processed: 75
  average time/residue: 0.4290
  time to fit residues: 45.8509
Evaluate side-chains
  77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  638 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 804 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.068805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.053583 restraints weight = 82496.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 5.03
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   8110  Z= 0.227
  Angle     :  0.568   4.524  11033  Z= 0.303
  Chirality :  0.040   0.156   1221
  Planarity :  0.004   0.037   1429
  Dihedral  :  5.309  65.273   1104
  Min Nonbonded Distance : 1.786

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.83 %
    Favored  : 87.92 %
  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:  0.31 (0.27), residues: 1003
  helix:  1.49 (0.26), residues: 391
  sheet: -1.00 (0.41), residues: 128
  loop : -0.45 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 306 
 HIS   0.005   0.001   HIS B 383 
 PHE   0.019   0.001   PHE A 131 
 TYR   0.021   0.002   TYR A 285 
 ARG   0.007   0.001   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  343)
  hydrogen bonds       : angle       4.98332 (  939)
  covalent geometry    : bond        0.00492 ( 8110)
  covalent geometry    : angle       0.56849 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 TYR cc_start: 0.8600 (m-80) cc_final: 0.8306 (m-80)
REVERT: B   76 MET cc_start: 0.8875 (mtp) cc_final: 0.8523 (mtt)
REVERT: B  349 ASP cc_start: 0.9378 (p0) cc_final: 0.9172 (p0)
REVERT: B  640 MET cc_start: 0.9055 (ttt) cc_final: 0.8718 (ttp)
REVERT: B  706 MET cc_start: 0.8202 (mtp) cc_final: 0.7998 (mmm)
REVERT: B  717 TYR cc_start: 0.8332 (m-80) cc_final: 0.8066 (m-80)
REVERT: B  912 THR cc_start: 0.9433 (m) cc_final: 0.9074 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 0.3635
  time to fit residues: 40.4327
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  638 VAL
Chi-restraints excluded: chain B residue  771 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 100 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B 685 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.070850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.055503 restraints weight = 81053.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 5.07
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8110  Z= 0.101
  Angle     :  0.509   5.434  11033  Z= 0.262
  Chirality :  0.040   0.143   1221
  Planarity :  0.003   0.035   1429
  Dihedral  :  4.987  60.146   1104
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.08 %
    Favored  : 88.04 %
  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:  0.74 (0.27), residues: 1003
  helix:  1.90 (0.27), residues: 391
  sheet: -0.84 (0.42), residues: 128
  loop : -0.24 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 291 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.017   0.001   PHE A 131 
 TYR   0.013   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (  343)
  hydrogen bonds       : angle       4.66844 (  939)
  covalent geometry    : bond        0.00234 ( 8110)
  covalent geometry    : angle       0.50897 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.9427 (tt0) cc_final: 0.8790 (tp-100)
REVERT: A  278 TYR cc_start: 0.8544 (m-80) cc_final: 0.8304 (m-80)
REVERT: B   76 MET cc_start: 0.8836 (mtp) cc_final: 0.8492 (mtt)
REVERT: B  349 ASP cc_start: 0.9359 (p0) cc_final: 0.9088 (p0)
REVERT: B  640 MET cc_start: 0.9042 (ttt) cc_final: 0.8701 (ttp)
REVERT: B  687 MET cc_start: 0.9700 (mmm) cc_final: 0.9228 (mmm)
REVERT: B  706 MET cc_start: 0.8120 (mtp) cc_final: 0.7398 (mmm)
REVERT: B  717 TYR cc_start: 0.8297 (m-80) cc_final: 0.7769 (m-80)
REVERT: B  912 THR cc_start: 0.9421 (m) cc_final: 0.9030 (t)
  outliers start: 7
  outliers final: 6
  residues processed: 76
  average time/residue: 0.3662
  time to fit residues: 40.0510
Evaluate side-chains
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  638 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    0.5980
   chunk 96 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.070755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.055514 restraints weight = 80494.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 5.04
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8110  Z= 0.112
  Angle     :  0.504   5.109  11033  Z= 0.259
  Chirality :  0.040   0.142   1221
  Planarity :  0.004   0.044   1429
  Dihedral  :  4.768  53.577   1104
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 11.71 %
    Favored  : 87.55 %
  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:  0.81 (0.28), residues: 1003
  helix:  2.03 (0.27), residues: 392
  sheet: -0.92 (0.41), residues: 129
  loop : -0.24 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.002   0.001   HIS B 383 
 PHE   0.016   0.001   PHE A 348 
 TYR   0.013   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  343)
  hydrogen bonds       : angle       4.56463 (  939)
  covalent geometry    : bond        0.00257 ( 8110)
  covalent geometry    : angle       0.50449 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.9410 (tt0) cc_final: 0.8406 (tp-100)
REVERT: A  278 TYR cc_start: 0.8567 (m-80) cc_final: 0.8342 (m-80)
REVERT: B   76 MET cc_start: 0.8846 (mtp) cc_final: 0.8503 (mtt)
REVERT: B  349 ASP cc_start: 0.9346 (p0) cc_final: 0.9096 (p0)
REVERT: B  687 MET cc_start: 0.9700 (mmm) cc_final: 0.9181 (mmm)
REVERT: B  706 MET cc_start: 0.8117 (mtp) cc_final: 0.7637 (mmm)
REVERT: B  717 TYR cc_start: 0.8354 (m-80) cc_final: 0.7908 (m-80)
REVERT: B  780 ASN cc_start: 0.9399 (m-40) cc_final: 0.9068 (t0)
REVERT: B  912 THR cc_start: 0.9423 (m) cc_final: 0.9035 (t)
  outliers start: 6
  outliers final: 5
  residues processed: 79
  average time/residue: 0.3614
  time to fit residues: 41.4826
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  638 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B 796 ASN ** 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 = 0.3387 r_free = 0.3387 target = 0.070181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.054939 restraints weight = 81585.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 5.04
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8110  Z= 0.152
  Angle     :  0.518   5.324  11033  Z= 0.269
  Chirality :  0.040   0.143   1221
  Planarity :  0.004   0.035   1429
  Dihedral  :  4.714  49.892   1104
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 11.96 %
    Favored  : 87.30 %
  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:  0.73 (0.27), residues: 1003
  helix:  2.00 (0.27), residues: 392
  sheet: -0.97 (0.41), residues: 131
  loop : -0.32 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 382 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.011   0.001   PHE A 131 
 TYR   0.015   0.001   TYR A 285 
 ARG   0.004   0.000   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03378 (  343)
  hydrogen bonds       : angle       4.60443 (  939)
  covalent geometry    : bond        0.00336 ( 8110)
  covalent geometry    : angle       0.51812 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 TYR cc_start: 0.8632 (m-80) cc_final: 0.8419 (m-80)
REVERT: B   76 MET cc_start: 0.8880 (mtp) cc_final: 0.8527 (mtt)
REVERT: B  640 MET cc_start: 0.9062 (ttt) cc_final: 0.8721 (ttp)
REVERT: B  687 MET cc_start: 0.9698 (mmm) cc_final: 0.9185 (mmm)
REVERT: B  706 MET cc_start: 0.8132 (mtp) cc_final: 0.7658 (mmm)
REVERT: B  717 TYR cc_start: 0.8413 (m-80) cc_final: 0.7963 (m-80)
REVERT: B  912 THR cc_start: 0.9427 (m) cc_final: 0.9049 (t)
  outliers start: 6
  outliers final: 6
  residues processed: 73
  average time/residue: 0.3960
  time to fit residues: 42.7598
Evaluate side-chains
  77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  638 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 58 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 796 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.071156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.055849 restraints weight = 80824.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 5.09
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8110  Z= 0.099
  Angle     :  0.501   5.411  11033  Z= 0.256
  Chirality :  0.040   0.140   1221
  Planarity :  0.003   0.035   1429
  Dihedral  :  4.525  43.874   1104
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 12.33 %
    Favored  : 87.05 %
  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:  0.87 (0.28), residues: 1003
  helix:  2.11 (0.27), residues: 392
  sheet: -0.91 (0.41), residues: 131
  loop : -0.22 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 382 
 HIS   0.002   0.000   HIS A 352 
 PHE   0.013   0.001   PHE A 348 
 TYR   0.012   0.001   TYR A 285 
 ARG   0.004   0.000   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  343)
  hydrogen bonds       : angle       4.47623 (  939)
  covalent geometry    : bond        0.00229 ( 8110)
  covalent geometry    : angle       0.50145 (11033)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue THR  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue LYS  303 is missing expected H atoms. Skipping.
Residue LEU  322 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue ILE  331 is missing expected H atoms. Skipping.
Residue LEU  368 is missing expected H atoms. Skipping.
Residue LEU  386 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue VAL    3 is missing expected H atoms. Skipping.
Residue LEU   22 is missing expected H atoms. Skipping.
Residue SER   39 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue LYS   67 is missing expected H atoms. Skipping.
Residue LYS  109 is missing expected H atoms. Skipping.
Residue ILE  126 is missing expected H atoms. Skipping.
Residue LYS  249 is missing expected H atoms. Skipping.
Residue LYS  363 is missing expected H atoms. Skipping.
Residue VAL  597 is missing expected H atoms. Skipping.
Residue LYS  598 is missing expected H atoms. Skipping.
Residue LYS  625 is missing expected H atoms. Skipping.
Residue MET  725 is missing expected H atoms. Skipping.
Residue LYS  728 is missing expected H atoms. Skipping.
Residue LYS  729 is missing expected H atoms. Skipping.
Residue MET  730 is missing expected H atoms. Skipping.
Residue LEU  756 is missing expected H atoms. Skipping.
Residue LEU  757 is missing expected H atoms. Skipping.
Residue LYS  786 is missing expected H atoms. Skipping.
Residue LYS  791 is missing expected H atoms. Skipping.
Residue LYS  801 is missing expected H atoms. Skipping.
Residue LEU  822 is missing expected H atoms. Skipping.
Residue LYS  825 is missing expected H atoms. Skipping.
Residue ILE  826 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue THR  840 is missing expected H atoms. Skipping.
Residue TYR  875 is missing expected H atoms. Skipping.
Residue SER  879 is missing expected H atoms. Skipping.
Residue MET  881 is missing expected H atoms. Skipping.
Residue TYR  882 is missing expected H atoms. Skipping.
Residue ILE  903 is missing expected H atoms. Skipping.
Evaluate side-chains
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.9391 (tt0) cc_final: 0.8388 (tp-100)
REVERT: A  278 TYR cc_start: 0.8553 (m-80) cc_final: 0.8329 (m-80)
REVERT: B   76 MET cc_start: 0.8864 (mtp) cc_final: 0.8518 (mtt)
REVERT: B  110 MET cc_start: 0.8492 (mtm) cc_final: 0.8274 (mtm)
REVERT: B  687 MET cc_start: 0.9699 (mmm) cc_final: 0.9356 (mmm)
REVERT: B  780 ASN cc_start: 0.9382 (m-40) cc_final: 0.9056 (t0)
REVERT: B  912 THR cc_start: 0.9410 (m) cc_final: 0.9015 (t)
  outliers start: 5
  outliers final: 4
  residues processed: 76
  average time/residue: 0.4862
  time to fit residues: 52.9920
Evaluate side-chains
  75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  638 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0970
   chunk 64 optimal weight:    0.9980
   chunk 72 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 99 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    1.3982

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.070909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.055630 restraints weight = 80638.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 5.06
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.4832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8110  Z= 0.112
  Angle     :  0.506   5.379  11033  Z= 0.258
  Chirality :  0.039   0.138   1221
  Planarity :  0.004   0.057   1429
  Dihedral  :  4.442  39.378   1104
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 12.58 %
    Favored  : 86.92 %
  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:  0.93 (0.28), residues: 1003
  helix:  2.22 (0.27), residues: 392
  sheet: -0.99 (0.42), residues: 123
  loop : -0.23 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 382 
 HIS   0.002   0.000   HIS A 338 
 PHE   0.011   0.001   PHE A 131 
 TYR   0.012   0.001   TYR A 285 
 ARG   0.014   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  343)
  hydrogen bonds       : angle       4.45344 (  939)
  covalent geometry    : bond        0.00257 ( 8110)
  covalent geometry    : angle       0.50571 (11033)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4903.60 seconds
wall clock time: 85 minutes 23.64 seconds (5123.64 seconds total)