Starting phenix.real_space_refine
on Fri Feb 16 03:28:30 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfq_27411/02_2024/8dfq_27411.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfq_27411/02_2024/8dfq_27411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfq_27411/02_2024/8dfq_27411.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfq_27411/02_2024/8dfq_27411.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfq_27411/02_2024/8dfq_27411.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfq_27411/02_2024/8dfq_27411.pdb"
  }
  resolution = 3.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    4947      2.51       5
     N    1310      2.21       5
     O    1427      1.98       5
     H    6514      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 14233
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 5414
          Classifications: {'peptide': 438}
          Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 418}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 564
          Unresolved non-hydrogen angles: 697
          Unresolved non-hydrogen dihedrals: 457
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 14, 'ASP:plan': 20, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 352
    Chain: "B"
      Number of atoms: 5269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 5269
          Classifications: {'peptide': 436}
          Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 415}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 580
          Unresolved non-hydrogen angles: 724
          Unresolved non-hydrogen dihedrals: 458
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 23, 'PHE:plan': 4, 'GLU:plan': 27, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 336
    Chain: "C"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 1707
          Classifications: {'peptide': 119}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 59
    Chain: "D"
      Number of atoms: 1745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 1745
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 62
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.91, per 1000 atoms: 0.49
  Number of scatterers: 14233
  At special positions: 0
  Unit cell: (77.9185, 133.17, 184.171, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     O    1427      8.00
     N    1310      7.00
     C    4947      6.00
     H    6514      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  58 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 136 " - pdb=" SG  CYS A 186 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 290 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 428 " - pdb=" SG  CYS A 491 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B  58 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 136 " - pdb=" SG  CYS B 186 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 233 " - pdb=" SG  CYS B 290 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 428 " - pdb=" SG  CYS B 491 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C   4 " - pdb=" SG  CYS C  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D   4 " - pdb=" SG  CYS D  89 " distance=2.01

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A1001 " - " ASN A 293 "
      " NAG E   1 " - " ASN A 300 "
      " NAG F   1 " - " ASN B 293 "
      " NAG G   1 " - " ASN B 300 "
  Time building additional restraints: 10.52
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 25 sheets defined
      17.6% alpha, 43.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'A' and resid 152 through 154
      No H-bonds generated for 'chain 'A' and resid 152 through 154'
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 152 through 154
      No H-bonds generated for 'chain 'B' and resid 152 through 154'
    Processing helix  chain 'B' and resid 176 through 180
      removed outlier: 3.579A  pdb=" N   HIS B 180 " --> pdb=" O   ARG B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 285
    Processing helix  chain 'C' and resid 9 through 13
      removed outlier: 3.963A  pdb=" N   VAL C  12 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 21
      removed outlier: 3.538A  pdb=" N   ASN C  21 " --> pdb=" O   LYS C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 63
      removed outlier: 3.996A  pdb=" N   SER C  46 " --> pdb=" O   HIS C  42 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   GLU C  47 " --> pdb=" O   CYS C  43 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   VAL C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS C  62 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   PHE C  63 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 92
    Processing helix  chain 'C' and resid 111 through 126
      removed outlier: 3.960A  pdb=" N   PHE C 126 " --> pdb=" O   SER C 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 8
    Processing helix  chain 'D' and resid 9 through 12
      removed outlier: 3.939A  pdb=" N   VAL D  12 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 9 through 12'
    Processing helix  chain 'D' and resid 13 through 21
      removed outlier: 4.340A  pdb=" N   LYS D  17 " --> pdb=" O   LYS D  13 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA D  20 " --> pdb=" O   THR D  16 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN D  21 " --> pdb=" O   LYS D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 61
      removed outlier: 4.289A  pdb=" N   TRP D  44 " --> pdb=" O   PRO D  40 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   SER D  46 " --> pdb=" O   HIS D  42 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   GLU D  47 " --> pdb=" O   CYS D  43 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL D  50 " --> pdb=" O   SER D  46 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER D  53 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASP D  61 " --> pdb=" O   THR D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 94
      removed outlier: 3.626A  pdb=" N   ILE D  75 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASN D  81 " --> pdb=" O   ASP D  77 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASP D  85 " --> pdb=" O   ASN D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 127
      removed outlier: 4.091A  pdb=" N   PHE D 126 " --> pdb=" O   SER D 122 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   LYS D 127 " --> pdb=" O   ILE D 123 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40
      removed outlier: 3.580A  pdb=" N   LEU A  57 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49
      removed outlier: 6.298A  pdb=" N   LEU A  46 " --> pdb=" O   PHE A 110 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   ARG A 112 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL A  48 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS A  94 " --> pdb=" O   GLU A  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127
      removed outlier: 7.013A  pdb=" N   GLY A 126 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134
    Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 150
      removed outlier: 4.601A  pdb=" N   TYR A 146 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   SER A 187 " --> pdb=" O   TYR A 146 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   LEU A 148 " --> pdb=" O   HIS A 185 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   HIS A 185 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 5.253A  pdb=" N   GLY A 150 " --> pdb=" O   CYS A 183 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   CYS A 183 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 150
      removed outlier: 4.601A  pdb=" N   TYR A 146 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   SER A 187 " --> pdb=" O   TYR A 146 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   LEU A 148 " --> pdb=" O   HIS A 185 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   HIS A 185 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 5.253A  pdb=" N   GLY A 150 " --> pdb=" O   CYS A 183 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   CYS A 183 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 182 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 216
      removed outlier: 3.741A  pdb=" N   VAL A 213 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 224
      removed outlier: 6.763A  pdb=" N   TYR A 221 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   VAL A 308 " --> pdb=" O   TYR A 221 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU A 223 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 317
    Processing sheet with id=AB1, first strand: chain 'A' and resid 322 through 326
      removed outlier: 6.593A  pdb=" N   VAL A 323 " --> pdb=" O   TYR A 408 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ASN A 410 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL A 325 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   LYS A 412 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 322 through 326
      removed outlier: 6.593A  pdb=" N   VAL A 323 " --> pdb=" O   TYR A 408 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ASN A 410 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL A 325 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   LYS A 412 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   LYS A 412 " --> pdb=" O   PHE A 433 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   PHE A 433 " --> pdb=" O   LYS A 412 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 437 through 441
      removed outlier: 20.417A  pdb=" N   LYS A 499 " --> pdb=" O   LYS B 499 " (cutoff:3.500A)
      removed outlier: 17.459A  pdb=" N   SER B 501 " --> pdb=" O   LYS A 499 " (cutoff:3.500A)
      removed outlier: 13.296A  pdb=" N   SER A 501 " --> pdb=" O   SER B 501 " (cutoff:3.500A)
      removed outlier: 11.540A  pdb=" N   TYR B 503 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   TYR A 503 " --> pdb=" O   TYR B 503 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   ASN B 505 " --> pdb=" O   TYR A 503 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ASN A 505 " --> pdb=" O   ASN B 505 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 38 through 40
      removed outlier: 3.581A  pdb=" N   LEU B  57 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 49
      removed outlier: 6.328A  pdb=" N   LEU B  46 " --> pdb=" O   PHE B 110 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   ARG B 112 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL B  48 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 126 through 127
      removed outlier: 6.915A  pdb=" N   GLY B 126 " --> pdb=" O   ARG B 205 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 132 through 134
    Processing sheet with id=AB8, first strand: chain 'B' and resid 144 through 150
      removed outlier: 5.556A  pdb=" N   ASN B 145 " --> pdb=" O   ASP B 189 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASP B 189 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 144 through 150
      removed outlier: 5.556A  pdb=" N   ASN B 145 " --> pdb=" O   ASP B 189 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASP B 189 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 213 through 216
    Processing sheet with id=AC2, first strand: chain 'B' and resid 221 through 224
      removed outlier: 6.605A  pdb=" N   TYR B 221 " --> pdb=" O   GLU B 306 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL B 308 " --> pdb=" O   TYR B 221 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   LEU B 223 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 317
    Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 326
      removed outlier: 6.158A  pdb=" N   VAL B 323 " --> pdb=" O   TYR B 408 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ASN B 410 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   VAL B 325 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 414 through 420
      removed outlier: 4.089A  pdb=" N   LEU B 426 " --> pdb=" O   ILE B 478 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 28 through 31
    Processing sheet with id=AC7, first strand: chain 'D' and resid 28 through 31

    396 hydrogen bonds defined for protein.
    993 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: 5.66

  Time building geometry restraints manager: 10.89 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 6512
        1.04 -     1.25: 1146
        1.25 -     1.45: 2280
        1.45 -     1.65: 4425
        1.65 -     1.86: 44
  Bond restraints: 14407
  Sorted by residual:
  bond pdb=" C7  NAG F   1 "
       pdb=" N2  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.346  1.466 -0.120 2.00e-02 2.50e+03 3.60e+01
  bond pdb=" C7  NAG G   2 "
       pdb=" N2  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.465 -0.119 2.00e-02 2.50e+03 3.52e+01
  bond pdb=" C7  NAG E   1 "
       pdb=" N2  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.346  1.464 -0.118 2.00e-02 2.50e+03 3.48e+01
  bond pdb=" C7  NAG A1001 "
       pdb=" N2  NAG A1001 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.43e+01
  bond pdb=" C7  NAG E   2 "
       pdb=" N2  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.462 -0.116 2.00e-02 2.50e+03 3.37e+01
  ... (remaining 14402 not shown)

  Histogram of bond angle deviations from ideal:
       98.91 -   105.97: 246
      105.97 -   113.03: 15749
      113.03 -   120.09: 4408
      120.09 -   127.15: 5220
      127.15 -   134.21: 95
  Bond angle restraints: 25718
  Sorted by residual:
  angle pdb=" C3  NAG G   1 "
        pdb=" C2  NAG G   1 "
        pdb=" N2  NAG G   1 "
      ideal   model   delta    sigma   weight residual
     110.74  126.54  -15.80 3.00e+00 1.11e-01 2.77e+01
  angle pdb=" CA  TRP B 246 "
        pdb=" CB  TRP B 246 "
        pdb=" CG  TRP B 246 "
      ideal   model   delta    sigma   weight residual
     113.60  121.35   -7.75 1.90e+00 2.77e-01 1.67e+01
  angle pdb=" CA  CYS B 428 "
        pdb=" CB  CYS B 428 "
        pdb=" SG  CYS B 428 "
      ideal   model   delta    sigma   weight residual
     114.40  123.13   -8.73 2.30e+00 1.89e-01 1.44e+01
  angle pdb=" CA  TRP A 246 "
        pdb=" CB  TRP A 246 "
        pdb=" CG  TRP A 246 "
      ideal   model   delta    sigma   weight residual
     113.60  120.60   -7.00 1.90e+00 2.77e-01 1.36e+01
  angle pdb=" C1  NAG G   1 "
        pdb=" C2  NAG G   1 "
        pdb=" C3  NAG G   1 "
      ideal   model   delta    sigma   weight residual
     109.80   98.91   10.89 3.00e+00 1.11e-01 1.32e+01
  ... (remaining 25713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.37: 6488
       16.37 -    32.74: 502
       32.74 -    49.11: 121
       49.11 -    65.48: 139
       65.48 -    81.85: 33
  Dihedral angle restraints: 7283
    sinusoidal: 3476
      harmonic: 3807
  Sorted by residual:
  dihedral pdb=" CB  CYS B 151 "
           pdb=" SG  CYS B 151 "
           pdb=" SG  CYS B 183 "
           pdb=" CB  CYS B 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.42   80.42     1      1.00e+01 1.00e-02 8.00e+01
  dihedral pdb=" CA  GLU B 198 "
           pdb=" C   GLU B 198 "
           pdb=" N   LYS B 199 "
           pdb=" CA  LYS B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.55  -29.45     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  CYS B 183 "
           pdb=" C   CYS B 183 "
           pdb=" N   LEU B 184 "
           pdb=" CA  LEU B 184 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.85  -29.15     0      5.00e+00 4.00e-02 3.40e+01
  ... (remaining 7280 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1270
       0.118 -    0.235: 78
       0.235 -    0.353: 1
       0.353 -    0.470: 1
       0.470 -    0.588: 1
  Chirality restraints: 1351
  Sorted by residual:
  chirality pdb=" C2  NAG G   1 "
            pdb=" C1  NAG G   1 "
            pdb=" C3  NAG G   1 "
            pdb=" N2  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -1.90   -0.59 2.00e-01 2.50e+01 8.63e+00
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN B 300 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  ILE A 172 "
            pdb=" N   ILE A 172 "
            pdb=" C   ILE A 172 "
            pdb=" CB  ILE A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1348 not shown)

  Planarity restraints: 2435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 129 "    0.001 2.00e-02 2.50e+03   7.71e-02 1.78e+02
        pdb=" CG  PHE D 129 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 129 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 129 "   -0.048 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 129 "    0.099 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 129 "   -0.123 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 129 "    0.085 2.00e-02 2.50e+03
        pdb=" HD1 PHE D 129 "    0.043 2.00e-02 2.50e+03
        pdb=" HD2 PHE D 129 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE1 PHE D 129 "   -0.039 2.00e-02 2.50e+03
        pdb=" HE2 PHE D 129 "    0.138 2.00e-02 2.50e+03
        pdb=" HZ  PHE D 129 "   -0.101 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 271 "    0.264 9.50e-02 1.11e+02   9.84e-02 5.18e+01
        pdb=" NE  ARG B 271 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 271 "    0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 271 "    0.049 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 271 "   -0.073 2.00e-02 2.50e+03
        pdb="HH11 ARG B 271 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG B 271 "   -0.060 2.00e-02 2.50e+03
        pdb="HH21 ARG B 271 "   -0.004 2.00e-02 2.50e+03
        pdb="HH22 ARG B 271 "    0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 248 "    0.030 9.50e-02 1.11e+02   3.26e-02 2.17e+01
        pdb=" NE  ARG B 248 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 248 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 248 "    0.043 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 248 "   -0.046 2.00e-02 2.50e+03
        pdb="HH11 ARG B 248 "    0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG B 248 "   -0.048 2.00e-02 2.50e+03
        pdb="HH21 ARG B 248 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG B 248 "    0.047 2.00e-02 2.50e+03
  ... (remaining 2432 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 1611
        2.28 -     2.86: 28945
        2.86 -     3.44: 31290
        3.44 -     4.02: 42408
        4.02 -     4.60: 63187
  Nonbonded interactions: 167441
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 219 "
            pdb=" HG1 THR B 303 "
     model   vdw
     1.696 1.850
  nonbonded pdb=" O   ALA A 219 "
            pdb=" HG1 THR A 303 "
     model   vdw
     1.729 1.850
  nonbonded pdb=" H   GLU B 344 "
            pdb=" O   SER B 395 "
     model   vdw
     1.770 1.850
  nonbonded pdb=" O   LYS B 116 "
            pdb=" HG1 THR B 139 "
     model   vdw
     1.783 1.850
  nonbonded pdb=" O   GLY B  62 "
            pdb=" H   LYS B 100 "
     model   vdw
     1.788 1.850
  ... (remaining 167436 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 36 through 46 or (resid 47 through 50 and (name N or name  \ 
CA or name C or name O or name CB or name H or name HA )) or resid 51 through 55 \ 
 or (resid 56 through 57 and (name N or name CA or name C or name O or name CB o \ 
r name H or name HA )) or resid 58 through 66 or (resid 67 and (name N or name C \ 
A or name C or name O or name CB or name H or name HA )) or resid 68 through 69  \ 
or (resid 70 and (name N or name CA or name C or name O or name CB or name H or  \ 
name HA )) or resid 71 through 79 or (resid 80 through 81 and (name N or name CA \ 
 or name C or name O or name CB or name H or name HA )) or resid 82 through 91 o \ 
r (resid 92 and (name N or name CA or name C or name O or name CB or name H or n \ 
ame HA )) or resid 93 through 106 or (resid 107 and (name N or name CA or name C \ 
 or name O or name CB or name H or name HA )) or resid 108 through 130 or (resid \ 
 131 and (name N or name CA or name C or name O or name CB or name H or name HA  \ 
)) or resid 132 through 142 or (resid 143 through 145 and (name N or name CA or  \ 
name C or name O or name CB or name H or name HA )) or resid 146 through 172 or  \ 
(resid 173 and (name N or name CA or name C or name O or name CB or name H or na \ 
me HA )) or resid 174 through 184 or (resid 185 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ 
 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 
2)) or resid 186 through 221 or (resid 222 through 225 and (name N or name CA or \ 
 name C or name O or name CB or name H or name HA )) or resid 226 through 235 or \ 
 (resid 236 through 237 and (name N or name CA or name C or name O or name CB or \ 
 name H or name HA )) or resid 238 through 244 or (resid 245 and (name N or name \ 
 CA or name C or name O or name CB or name H or name HA )) or resid 246 or (resi \ 
d 247 and (name N or name CA or name C or name O or name CB or name H or name HA \ 
 )) or resid 248 through 252 or (resid 253 through 258 and (name N or name CA or \ 
 name C or name O or name CB or name H or name HA )) or resid 259 through 313 or \ 
 (resid 314 and (name N or name CA or name C or name O or name CB or name H or n \ 
ame HA )) or resid 315 or (resid 316 and (name N or name CA or name C or name O  \ 
or name CB or name H or name HA )) or resid 317 through 321 or (resid 322 throug \ 
h 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ 
 )) or resid 326 through 331 or (resid 332 and (name N or name CA or name C or n \ 
ame O or name CB or name H or name HA )) or resid 333 through 346 or (resid 347  \ 
and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ 
 resid 348 through 351 or (resid 352 through 353 and (name N or name CA or name  \ 
C or name O or name CB or name H or name HA )) or resid 354 through 355 or (resi \ 
d 356 through 358 and (name N or name CA or name C or name O or name CB or name  \ 
H or name HA )) or resid 359 through 398 or (resid 399 and (name N or name CA or \ 
 name C or name O or name CB or name H or name HA )) or resid 400 through 414 or \ 
 (resid 415 through 416 and (name N or name CA or name C or name O or name CB or \ 
 name H or name HA )) or resid 417 through 437 or (resid 438 through 441 and (na \ 
me N or name CA or name C or name O or name CB or name H or name HA )) or (resid \ 
 471 through 473 and (name N or name CA or name C or name O or name CB or name H \ 
 or name HA )) or resid 474 through 478 or (resid 479 and (name N or name CA or  \ 
name C or name O or name CB or name H or name HA )) or resid 486 through 496 or  \ 
(resid 497 and (name N or name CA or name C or name O or name CB or name H or na \ 
me HA )) or resid 498 through 507))
  selection = (chain 'B' and (resid 36 through 63 or (resid 64 through 65 and (name N or name  \ 
CA or name C or name O or name CB or name H or name HA )) or resid 66 through 74 \ 
 or (resid 75 through 81 and (name N or name CA or name C or name O or name CB o \ 
r name H or name HA )) or resid 82 through 93 or (resid 94 and (name N or name C \ 
A or name C or name O or name CB or name H or name HA )) or resid 95 through 111 \ 
 or (resid 112 through 113 and (name N or name CA or name C or name O or name CB \ 
 or name H or name HA )) or resid 114 through 116 or (resid 117 and (name N or n \ 
ame CA or name C or name O or name CB or name H or name HA )) or resid 118 throu \ 
gh 139 or (resid 140 and (name N or name CA or name C or name O or name CB or na \ 
me H or name HA )) or resid 141 through 148 or (resid 149 and (name N or name CA \ 
 or name C or name O or name CB or name H or name HA )) or resid 150 through 189 \ 
 or (resid 190 through 191 and (name N or name CA or name C or name O or name CB \ 
 or name H or name HA )) or resid 192 through 194 or (resid 195 and (name N or n \ 
ame CA or name C or name O or name CB or name H or name HA )) or resid 196 throu \ 
gh 198 or (resid 199 and (name N or name CA or name C or name O or name CB or na \ 
me H or name HA )) or resid 200 through 323 or (resid 324 through 325 and (name  \ 
N or name CA or name C or name O or name CB or name H or name HA )) or resid 326 \ 
 through 344 or (resid 345 through 347 and (name N or name CA or name C or name  \ 
O or name CB or name H or name HA )) or resid 348 through 379 or (resid 380 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 381 or (resid 382 through 383 and (name N or name CA or name C or name O or n \ 
ame CB or name H or name HA )) or resid 384 through 409 or (resid 410 through 41 \ 
2 and (name N or name CA or name C or name O or name CB or name H or name HA ))  \ 
or resid 413 through 425 or (resid 426 through 427 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 428 or (resid 429 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 430 through 493 or (resid 494 through 497 and (name N or name CA or name C or \ 
 name O or name CB or name H or name HA )) or resid 498 through 507))
}
ncs_group {
  reference = (chain 'C' and (resid 3 through 5 or (resid 6 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 7 through 57 or (resid 58 a \ 
nd (name N or name CA or name C or name O or name CB or name H or name HA )) or  \ 
resid 59 through 77 or (resid 78 and (name N or name CA or name C or name O or n \ 
ame CB or name H or name HA )) or resid 79 through 130))
  selection = (chain 'D' and (resid 3 through 7 or (resid 8 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 9 through 20 or (resid 21 a \ 
nd (name N or name CA or name C or name O or name CB or name H or name HA )) or  \ 
resid 22 through 35 or (resid 36 through 39 and (name N or name CA or name C or  \ 
name O or name CB or name H or name HA )) or resid 40 through 95 or resid 105 th \ 
rough 130))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.740
  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:             0.260
  Extract box with map and model:          24.170
  Check model and map are aligned:         0.200
  Set scattering table:                    0.120
  Process input model:                     47.510
  Find NCS groups from input model:        0.750
  Set up NCS constraints:                  0.090
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   81.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
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      :  0.007   0.120   7893  Z= 0.477
  Angle     :  1.121  15.798  10860  Z= 0.633
  Chirality :  0.061   0.588   1351
  Planarity :  0.008   0.085   1378
  Dihedral  : 13.047  81.846   2553
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 0.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.11 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    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: -1.00 (0.23), residues: 1094
  helix: -0.57 (0.39), residues: 126
  sheet:  0.35 (0.23), residues: 440
  loop : -1.59 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.007   TRP B  66 
 HIS   0.009   0.003   HIS A 180 
 PHE   0.108   0.006   PHE D 129 
 TYR   0.028   0.007   TYR B 350 
 ARG   0.020   0.004   ARG B 271 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  31 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 MET cc_start: 0.8213 (ttp) cc_final: 0.8002 (ttm)
REVERT: B  170 ILE cc_start: 0.7807 (mt) cc_final: 0.7432 (tt)
REVERT: B  289 MET cc_start: 0.8034 (ttp) cc_final: 0.7738 (ttt)
REVERT: D   36 MET cc_start: 0.9322 (ppp) cc_final: 0.8689 (ppp)
REVERT: D   85 ASP cc_start: 0.9212 (m-30) cc_final: 0.8948 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 31
  average time/residue: 0.5114
  time to fit residues: 21.6374
Evaluate side-chains
  22 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.0870
   chunk 82 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 98 optimal weight:    0.4980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
B 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7893  Z= 0.217
  Angle     :  0.688   8.878  10860  Z= 0.369
  Chirality :  0.046   0.162   1351
  Planarity :  0.005   0.045   1378
  Dihedral  :  9.306  59.167   1317
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  3.63 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.24), residues: 1094
  helix:  0.53 (0.41), residues: 134
  sheet:  0.37 (0.24), residues: 434
  loop : -0.98 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  66 
 HIS   0.003   0.001   HIS A 180 
 PHE   0.016   0.002   PHE B 312 
 TYR   0.018   0.002   TYR A 146 
 ARG   0.004   0.001   ARG A 205 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  30 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 MET cc_start: 0.7015 (tpp) cc_final: 0.6647 (tpp)
REVERT: A  275 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7480 (tp)
REVERT: B  170 ILE cc_start: 0.8368 (mt) cc_final: 0.7882 (tt)
REVERT: D   36 MET cc_start: 0.9175 (ppp) cc_final: 0.8224 (ppp)
  outliers start: 4
  outliers final: 3
  residues processed: 29
  average time/residue: 0.2348
  time to fit residues: 12.4309
Evaluate side-chains
  28 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 CYS
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain B residue  428 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 107 optimal weight:    0.4980
   chunk 88 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7893  Z= 0.224
  Angle     :  0.607  10.126  10860  Z= 0.321
  Chirality :  0.045   0.287   1351
  Planarity :  0.004   0.037   1378
  Dihedral  :  8.006  59.153   1317
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.59 %
    Favored  : 94.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    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: -0.24 (0.25), residues: 1094
  helix:  1.33 (0.45), residues: 134
  sheet:  0.29 (0.23), residues: 452
  loop : -0.95 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 345 
 PHE   0.016   0.001   PHE B  63 
 TYR   0.013   0.001   TYR A 146 
 ARG   0.002   0.000   ARG B 112 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  26 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   36 MET cc_start: 0.9029 (ppp) cc_final: 0.8123 (ppp)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.2288
  time to fit residues: 10.4885
Evaluate side-chains
  24 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain B residue  428 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0070
   chunk 10 optimal weight:    0.0980
   chunk 47 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 105 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.5398

-------------------------------------------------------------------------------
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: 0.7994
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7893  Z= 0.171
  Angle     :  0.544   6.339  10860  Z= 0.287
  Chirality :  0.045   0.253   1351
  Planarity :  0.004   0.035   1378
  Dihedral  :  7.433  59.738   1317
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.44 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.25), residues: 1094
  helix:  1.75 (0.46), residues: 134
  sheet:  0.22 (0.23), residues: 459
  loop : -0.83 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 440 
 HIS   0.003   0.001   HIS A 185 
 PHE   0.009   0.001   PHE C 116 
 TYR   0.010   0.001   TYR A 269 
 ARG   0.002   0.000   ARG A 205 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  25 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8157 (t0)
REVERT: D   36 MET cc_start: 0.9006 (ppp) cc_final: 0.8058 (ppp)
  outliers start: 2
  outliers final: 1
  residues processed: 25
  average time/residue: 0.2319
  time to fit residues: 10.5763
Evaluate side-chains
  24 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain B residue  428 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0570
   chunk 72 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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: 0.8005
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7893  Z= 0.170
  Angle     :  0.525   6.384  10860  Z= 0.276
  Chirality :  0.044   0.266   1351
  Planarity :  0.004   0.034   1378
  Dihedral  :  6.945  59.073   1317
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  5.29 %
    Favored  : 93.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    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:  0.02 (0.25), residues: 1094
  helix:  2.05 (0.47), residues: 134
  sheet:  0.29 (0.23), residues: 460
  loop : -0.78 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.009   0.001   PHE B  63 
 TYR   0.010   0.001   TYR A 146 
 ARG   0.001   0.000   ARG D   7 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  29 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7670 (tp)
REVERT: A  293 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (t0)
REVERT: D   36 MET cc_start: 0.9005 (ppp) cc_final: 0.8042 (ppp)
  outliers start: 7
  outliers final: 4
  residues processed: 28
  average time/residue: 0.2120
  time to fit residues: 11.1241
Evaluate side-chains
  28 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue  428 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 105 optimal weight:    0.5980
   chunk 87 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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: 0.8015
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7893  Z= 0.172
  Angle     :  0.524   7.572  10860  Z= 0.275
  Chirality :  0.044   0.259   1351
  Planarity :  0.004   0.034   1378
  Dihedral  :  6.797  58.038   1317
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  4.83 %
    Favored  : 94.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    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:  0.02 (0.25), residues: 1094
  helix:  2.09 (0.47), residues: 134
  sheet:  0.21 (0.23), residues: 469
  loop : -0.71 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.008   0.001   TYR A 146 
 ARG   0.001   0.000   ARG D   7 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  29 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 MET cc_start: 0.8252 (mmm) cc_final: 0.7841 (tpp)
REVERT: A  275 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7644 (tp)
REVERT: A  293 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8109 (t0)
REVERT: D   36 MET cc_start: 0.8993 (ppp) cc_final: 0.8052 (ppp)
  outliers start: 7
  outliers final: 5
  residues processed: 27
  average time/residue: 0.2601
  time to fit residues: 12.5596
Evaluate side-chains
  28 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain D residue   72 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 105 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 260 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7893  Z= 0.243
  Angle     :  0.550   8.033  10860  Z= 0.289
  Chirality :  0.044   0.273   1351
  Planarity :  0.004   0.036   1378
  Dihedral  :  6.815  54.524   1317
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  5.14 %
    Favored  : 93.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.25), residues: 1094
  helix:  1.93 (0.46), residues: 133
  sheet:  0.19 (0.23), residues: 468
  loop : -0.92 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.011   0.001   PHE A 118 
 TYR   0.010   0.001   TYR D  26 
 ARG   0.002   0.000   ARG B 181 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  32 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7676 (tp)
REVERT: D   36 MET cc_start: 0.9146 (ppp) cc_final: 0.8054 (ppp)
  outliers start: 10
  outliers final: 7
  residues processed: 30
  average time/residue: 0.2290
  time to fit residues: 12.4203
Evaluate side-chains
  29 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain D residue   72 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 71 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 100 optimal weight:    0.1980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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: 0.8041
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   7893  Z= 0.155
  Angle     :  0.511   8.258  10860  Z= 0.267
  Chirality :  0.044   0.261   1351
  Planarity :  0.004   0.033   1378
  Dihedral  :  6.529  55.649   1317
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  5.59 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    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:  0.01 (0.26), residues: 1094
  helix:  2.21 (0.47), residues: 134
  sheet:  0.12 (0.23), residues: 488
  loop : -0.68 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 185 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.008   0.001   TYR A 269 
 ARG   0.001   0.000   ARG D   7 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  27 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7633 (tp)
REVERT: D   36 MET cc_start: 0.9115 (ppp) cc_final: 0.7958 (ppp)
  outliers start: 6
  outliers final: 5
  residues processed: 26
  average time/residue: 0.2261
  time to fit residues: 10.9786
Evaluate side-chains
  27 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain D residue   72 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C  42 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7893  Z= 0.230
  Angle     :  0.537   8.802  10860  Z= 0.281
  Chirality :  0.044   0.271   1351
  Planarity :  0.004   0.033   1378
  Dihedral  :  6.558  54.100   1317
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  5.89 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    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: -0.16 (0.26), residues: 1094
  helix:  2.06 (0.46), residues: 133
  sheet:  0.03 (0.23), residues: 491
  loop : -0.83 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.010   0.001   PHE A 118 
 TYR   0.010   0.001   TYR A 269 
 ARG   0.001   0.000   ARG B 181 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  27 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7662 (tp)
REVERT: A  289 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7794 (ptm)
REVERT: D   36 MET cc_start: 0.9224 (ppp) cc_final: 0.8182 (ppp)
  outliers start: 7
  outliers final: 5
  residues processed: 26
  average time/residue: 0.2269
  time to fit residues: 10.8860
Evaluate side-chains
  27 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain D residue   72 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0670
   chunk 99 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0770
   chunk 53 optimal weight:    0.0770
   chunk 68 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.3634

-------------------------------------------------------------------------------
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: 0.8043
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7893  Z= 0.142
  Angle     :  0.500   9.092  10860  Z= 0.259
  Chirality :  0.044   0.248   1351
  Planarity :  0.004   0.031   1378
  Dihedral  :  6.220  55.555   1317
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  6.04 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    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:  0.09 (0.26), residues: 1094
  helix:  2.40 (0.47), residues: 134
  sheet:  0.14 (0.23), residues: 493
  loop : -0.63 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 185 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.007   0.001   TYR A 269 
 ARG   0.001   0.000   ARG A 205 

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue VAL   64 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue LYS   94 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue LYS  149 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue VAL  195 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue THR  380 is missing expected H atoms. Skipping.
Residue LEU  382 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue LEU  426 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue TYR  494 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue ILE   39 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue VAL   48 is missing expected H atoms. Skipping.
Residue VAL   50 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue THR   59 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Residue THR   67 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue THR   84 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue THR   90 is missing expected H atoms. Skipping.
Residue THR   92 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue LYS  100 is missing expected H atoms. Skipping.
Residue LEU  103 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue VAL  143 is missing expected H atoms. Skipping.
Residue THR  144 is missing expected H atoms. Skipping.
Residue LYS  154 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LYS  176 is missing expected H atoms. Skipping.
Residue LYS  193 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue LYS  218 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue LEU  223 is missing expected H atoms. Skipping.
Residue LYS  236 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue THR  253 is missing expected H atoms. Skipping.
Residue LYS  254 is missing expected H atoms. Skipping.
Residue LEU  255 is missing expected H atoms. Skipping.
Residue LYS  258 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue MET  318 is missing expected H atoms. Skipping.
Residue ILE  319 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue VAL  325 is missing expected H atoms. Skipping.
Residue LYS  342 is missing expected H atoms. Skipping.
Residue MET  351 is missing expected H atoms. Skipping.
Residue THR  356 is missing expected H atoms. Skipping.
Residue LYS  358 is missing expected H atoms. Skipping.
Residue LYS  364 is missing expected H atoms. Skipping.
Residue LEU  379 is missing expected H atoms. Skipping.
Residue LYS  383 is missing expected H atoms. Skipping.
Residue VAL  399 is missing expected H atoms. Skipping.
Residue LYS  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue LEU  416 is missing expected H atoms. Skipping.
Residue LEU  419 is missing expected H atoms. Skipping.
Residue VAL  420 is missing expected H atoms. Skipping.
Residue MET  425 is missing expected H atoms. Skipping.
Residue THR  437 is missing expected H atoms. Skipping.
Residue ILE  438 is missing expected H atoms. Skipping.
Residue TYR  441 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LEU  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ILE  478 is missing expected H atoms. Skipping.
Residue THR  488 is missing expected H atoms. Skipping.
Residue VAL  489 is missing expected H atoms. Skipping.
Residue LYS  492 is missing expected H atoms. Skipping.
Residue VAL  497 is missing expected H atoms. Skipping.
Residue LYS  499 is missing expected H atoms. Skipping.
Residue THR  500 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue MET   36 is missing expected H atoms. Skipping.
Residue VAL   38 is missing expected H atoms. Skipping.
Residue LEU   39 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS   24 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LYS   91 is missing expected H atoms. Skipping.
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  27 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7755 (ptm)
REVERT: D   36 MET cc_start: 0.9140 (ppp) cc_final: 0.8023 (ppp)
  outliers start: 5
  outliers final: 3
  residues processed: 26
  average time/residue: 0.2287
  time to fit residues: 10.8163
Evaluate side-chains
  25 residues out of total 1018 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain D residue   72 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.8586

-------------------------------------------------------------------------------
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 = 0.3309 r_free = 0.3309 target = 0.050133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.042360 restraints weight = 173872.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.043592 restraints weight = 78891.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.044387 restraints weight = 45697.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7893  Z= 0.235
  Angle     :  0.530   8.580  10860  Z= 0.277
  Chirality :  0.044   0.260   1351
  Planarity :  0.004   0.033   1378
  Dihedral  :  6.361  54.268   1317
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.04 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.73 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1094
  helix:  2.14 (0.46), residues: 133
  sheet:  0.08 (0.23), residues: 509
  loop : -0.86 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.011   0.001   PHE A 118 
 TYR   0.011   0.001   TYR A 269 
 ARG   0.001   0.000   ARG B 181 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2959.80 seconds
wall clock time: 55 minutes 2.86 seconds (3302.86 seconds total)