Starting phenix.real_space_refine
on Tue Dec 31 09:51:48 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q6v_18199/12_2024/8q6v_18199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q6v_18199/12_2024/8q6v_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_18199/12_2024/8q6v_18199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q6v_18199/12_2024/8q6v_18199.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q6v_18199/12_2024/8q6v_18199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q6v_18199/12_2024/8q6v_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-5532/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: 7.73, per 1000 atoms: 0.50
  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: 4.16
  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: 1.32
  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: 5.96

  Time building geometry restraints manager: 4.93 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:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.270
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     35.670
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.570
-------------------------------------------------------------------------------
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= 0.773
  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 

*********************** 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  : 1.328 
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: 0.4871
  time to fit residues: 101.9536
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  : 1.497 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
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= 0.207
  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 

*********************** 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  : 1.367 
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: B  349 ASP cc_start: 0.8616 (p0) cc_final: 0.8208 (p0)
REVERT: B  640 MET cc_start: 0.8605 (ttm) cc_final: 0.8394 (ttp)
REVERT: B  912 THR cc_start: 0.8641 (m) cc_final: 0.8326 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 100
  average time/residue: 0.4284
  time to fit residues: 59.7279
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 77 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8110  Z= 0.164
  Angle     :  0.555   5.518  11033  Z= 0.291
  Chirality :  0.041   0.147   1221
  Planarity :  0.004   0.040   1429
  Dihedral  :  5.663  65.425   1104
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  8.72 %
    Favored  : 90.91 %
  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:  0.50 (0.27), residues: 1003
  helix:  1.28 (0.26), residues: 388
  sheet: -0.54 (0.40), residues: 129
  loop : -0.10 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 291 
 HIS   0.002   0.001   HIS B 206 
 PHE   0.021   0.001   PHE A 131 
 TYR   0.017   0.001   TYR A 285 
 ARG   0.003   0.000   ARG B 318 

*********************** 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
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 1.331 
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  278 TYR cc_start: 0.8850 (m-80) cc_final: 0.8648 (m-10)
REVERT: B  349 ASP cc_start: 0.8663 (p0) cc_final: 0.8228 (p0)
REVERT: B  912 THR cc_start: 0.8628 (m) cc_final: 0.8400 (t)
  outliers start: 3
  outliers final: 2
  residues processed: 86
  average time/residue: 0.4207
  time to fit residues: 50.7363
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  : 1.311 
-------------------------------------------------------------------------------
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 69 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 98 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0030
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.7394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8110  Z= 0.151
  Angle     :  0.517   5.273  11033  Z= 0.269
  Chirality :  0.040   0.142   1221
  Planarity :  0.004   0.034   1429
  Dihedral  :  5.177  58.519   1104
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  9.59 %
    Favored  : 89.79 %
  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:  0.82 (0.27), residues: 1003
  helix:  1.72 (0.27), residues: 389
  sheet: -0.45 (0.41), residues: 127
  loop : -0.06 (0.30), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 291 
 HIS   0.001   0.000   HIS B 396 
 PHE   0.019   0.001   PHE A 131 
 TYR   0.015   0.001   TYR B 717 
 ARG   0.007   0.000   ARG A 127 

*********************** 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
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.345 
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: B  349 ASP cc_start: 0.8606 (p0) cc_final: 0.8178 (p0)
REVERT: B  912 THR cc_start: 0.8666 (m) cc_final: 0.8362 (t)
  outliers start: 5
  outliers final: 4
  residues processed: 77
  average time/residue: 0.3999
  time to fit residues: 44.1336
Evaluate side-chains
  73 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  638 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0170
   overall best weight:    3.4026

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

Flipped N/Q/H residues before XYZ refinement:
A  64 GLN
B 804 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   8110  Z= 0.329
  Angle     :  0.571   4.757  11033  Z= 0.305
  Chirality :  0.040   0.152   1221
  Planarity :  0.004   0.043   1429
  Dihedral  :  5.243  57.066   1104
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.34 %
    Favored  : 89.29 %
  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:  0.45 (0.27), residues: 1003
  helix:  1.48 (0.26), residues: 390
  sheet: -0.66 (0.42), residues: 126
  loop : -0.34 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 291 
 HIS   0.005   0.001   HIS B 396 
 PHE   0.021   0.001   PHE A 131 
 TYR   0.021   0.002   TYR A 285 
 ARG   0.005   0.001   ARG A 354 

*********************** 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
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 1.265 
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: B  349 ASP cc_start: 0.8745 (p0) cc_final: 0.8366 (p0)
REVERT: B  640 MET cc_start: 0.8759 (ttt) cc_final: 0.8483 (ttp)
REVERT: B  912 THR cc_start: 0.8743 (m) cc_final: 0.8523 (t)
  outliers start: 11
  outliers final: 8
  residues processed: 75
  average time/residue: 0.3800
  time to fit residues: 41.3640
Evaluate side-chains
  75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  178 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  638 VAL
Chi-restraints excluded: chain B residue  771 VAL
Chi-restraints excluded: chain B residue  780 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8110  Z= 0.251
  Angle     :  0.532   4.784  11033  Z= 0.280
  Chirality :  0.040   0.145   1221
  Planarity :  0.004   0.035   1429
  Dihedral  :  5.088  55.122   1104
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.21 %
    Favored  : 88.54 %
  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:  0.53 (0.27), residues: 1003
  helix:  1.63 (0.26), residues: 392
  sheet: -0.75 (0.42), residues: 126
  loop : -0.35 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 291 
 HIS   0.004   0.001   HIS A 338 
 PHE   0.018   0.001   PHE A 131 
 TYR   0.018   0.001   TYR A 285 
 ARG   0.003   0.000   ARG B 213 

*********************** 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
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 1.163 
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: B  349 ASP cc_start: 0.8727 (p0) cc_final: 0.8351 (p0)
REVERT: B  640 MET cc_start: 0.8750 (ttt) cc_final: 0.8493 (ttp)
REVERT: B  912 THR cc_start: 0.8722 (m) cc_final: 0.8500 (t)
  outliers start: 10
  outliers final: 9
  residues processed: 75
  average time/residue: 0.4089
  time to fit residues: 43.7058
Evaluate side-chains
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
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  229 ILE
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  638 VAL
Chi-restraints excluded: chain B residue  814 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.4494

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= 0.152
  Angle     :  0.503   5.136  11033  Z= 0.258
  Chirality :  0.040   0.141   1221
  Planarity :  0.004   0.035   1429
  Dihedral  :  4.792  48.608   1104
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.71 %
    Favored  : 88.54 %
  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:  0.88 (0.27), residues: 1003
  helix:  1.99 (0.27), residues: 392
  sheet: -0.69 (0.43), residues: 127
  loop : -0.17 (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 B 383 
 PHE   0.017   0.001   PHE A 131 
 TYR   0.013   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 354 

*********************** 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
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 1.695 
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: B  349 ASP cc_start: 0.8622 (p0) cc_final: 0.8229 (p0)
REVERT: B  912 THR cc_start: 0.8678 (m) cc_final: 0.8439 (t)
  outliers start: 6
  outliers final: 6
  residues processed: 76
  average time/residue: 0.3967
  time to fit residues: 44.2910
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  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
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
Chi-restraints excluded: chain B residue  780 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8110  Z= 0.209
  Angle     :  0.511   4.891  11033  Z= 0.265
  Chirality :  0.040   0.143   1221
  Planarity :  0.004   0.043   1429
  Dihedral  :  4.716  44.696   1104
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.21 %
    Favored  : 87.80 %
  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:  0.76 (0.27), residues: 1003
  helix:  1.94 (0.27), residues: 393
  sheet: -0.78 (0.43), residues: 127
  loop : -0.28 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.014   0.001   PHE A 348 
 TYR   0.015   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 354 

*********************** 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
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 1.912 
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: B  349 ASP cc_start: 0.8613 (p0) cc_final: 0.8211 (p0)
REVERT: B  912 THR cc_start: 0.8708 (m) cc_final: 0.8479 (t)
  outliers start: 8
  outliers final: 7
  residues processed: 76
  average time/residue: 0.3803
  time to fit residues: 42.1429
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  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
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  814 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0060
   chunk 82 optimal weight:    0.8980
   chunk 86 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.1600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4714

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= 0.152
  Angle     :  0.496   5.608  11033  Z= 0.253
  Chirality :  0.040   0.140   1221
  Planarity :  0.003   0.035   1429
  Dihedral  :  4.475  36.324   1104
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 11.83 %
    Favored  : 87.67 %
  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:  0.95 (0.28), residues: 1003
  helix:  2.13 (0.27), residues: 393
  sheet: -0.73 (0.43), residues: 127
  loop : -0.18 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 382 
 HIS   0.002   0.000   HIS A 352 
 PHE   0.009   0.001   PHE A 131 
 TYR   0.011   0.001   TYR A 285 
 ARG   0.006   0.000   ARG A 354 

*********************** 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
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 1.414 
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  278 TYR cc_start: 0.8719 (m-80) cc_final: 0.8515 (m-10)
REVERT: B  349 ASP cc_start: 0.8561 (p0) cc_final: 0.8147 (p0)
REVERT: B  912 THR cc_start: 0.8680 (m) cc_final: 0.8453 (t)
  outliers start: 4
  outliers final: 4
  residues processed: 74
  average time/residue: 0.3862
  time to fit residues: 41.4495
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  : 1.255 
-------------------------------------------------------------------------------
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 101 optimal weight:    4.9990
   chunk 93 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.4784

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= 0.178
  Angle     :  0.500   5.335  11033  Z= 0.256
  Chirality :  0.039   0.140   1221
  Planarity :  0.004   0.035   1429
  Dihedral  :  4.403  31.715   1104
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 11.96 %
    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:  0.91 (0.27), residues: 1003
  helix:  2.10 (0.27), residues: 393
  sheet: -0.79 (0.42), residues: 129
  loop : -0.21 (0.30), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 382 
 HIS   0.002   0.000   HIS B 383 
 PHE   0.013   0.001   PHE A 348 
 TYR   0.012   0.001   TYR A 285 
 ARG   0.004   0.000   ARG A 354 

********************** 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
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 1.231 
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  278 TYR cc_start: 0.8738 (m-80) cc_final: 0.8471 (m-10)
REVERT: B  349 ASP cc_start: 0.8574 (p0) cc_final: 0.8146 (p0)
REVERT: B  912 THR cc_start: 0.8692 (m) cc_final: 0.8472 (t)
  outliers start: 4
  outliers final: 4
  residues processed: 73
  average time/residue: 0.3665
  time to fit residues: 38.6990
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  : 1.268 
-------------------------------------------------------------------------------
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 22 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.070490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.055160 restraints weight = 81437.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 5.07
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.4828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8110  Z= 0.251
  Angle     :  0.526   5.413  11033  Z= 0.273
  Chirality :  0.040   0.144   1221
  Planarity :  0.004   0.037   1429
  Dihedral  :  4.479  28.503   1104
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  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:  0.71 (0.27), residues: 1003
  helix:  1.99 (0.27), residues: 394
  sheet: -0.90 (0.42), residues: 129
  loop : -0.37 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 382 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.010   0.001   PHE A 131 
 TYR   0.017   0.001   TYR A 285 
 ARG   0.004   0.000   ARG A 354 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3251.17 seconds
wall clock time: 59 minutes 4.27 seconds (3544.27 seconds total)