Starting phenix.real_space_refine
on Fri Mar 15 23:19:57 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t94_25751/03_2024/7t94_25751_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t94_25751/03_2024/7t94_25751.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t94_25751/03_2024/7t94_25751.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t94_25751/03_2024/7t94_25751.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t94_25751/03_2024/7t94_25751_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t94_25751/03_2024/7t94_25751_updated.pdb"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4680 atoms to isotropic.
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      58      5.16       5
     Cl      1      4.86       5
     C    5344      2.51       5
     N    1412      2.21       5
     O    1573      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  121": "NH1" <-> "NH2"
    Residue "A GLU  172": "OE1" <-> "OE2"
    Residue "A PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  188": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  211": "NH1" <-> "NH2"
    Residue "A TYR  426": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  198": "NH1" <-> "NH2"
    Residue "B ARG  209": "NH1" <-> "NH2"
    Residue "B ARG  243": "NH1" <-> "NH2"
    Residue "B GLU  246": "OE1" <-> "OE2"
    Residue "B GLU  277": "OE1" <-> "OE2"
    Residue "B GLU  309": "OE1" <-> "OE2"
    Residue "B ARG  313": "NH1" <-> "NH2"
    Residue "B ARG  349": "NH1" <-> "NH2"
    Residue "C ARG   48": "NH1" <-> "NH2"
    Residue "C TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  134": "NH1" <-> "NH2"
    Residue "C PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  202": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 8388
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 1946
          Classifications: {'peptide': 265}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 10, 'TRANS': 254}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 174
          Unresolved non-hydrogen angles: 219
          Unresolved non-hydrogen dihedrals: 149
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 84
    Chain: "B"
      Number of atoms: 1711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1711
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 2541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2541
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 47
    Chain: "D"
      Number of atoms: 403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 403
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "E"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1747
          Classifications: {'peptide': 236}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 52
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 40
          Unusual residues: {'2CU': 1, 'ACH': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 5.20, per 1000 atoms: 0.62
  Number of scatterers: 8388
  At special positions: 0
  Unit cell: (90.95, 120.7, 124.1, 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)
     Cl      1     17.00
     S      58     16.00
     O    1573      8.00
     N    1412      7.00
     C    5344      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 176 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04

  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
  Time building additional restraints: 3.49
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      32.7% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 51
      removed outlier: 3.849A  pdb=" N   GLY A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   SER A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A  48 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS A  49 " --> pdb=" O   MET A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 86
      removed outlier: 3.966A  pdb=" N   MET A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 126
      removed outlier: 3.504A  pdb=" N   VAL A 105 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR A 126 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 134
      No H-bonds generated for 'chain 'A' and resid 131 through 134'
    Processing helix  chain 'A' and resid 137 through 166
      removed outlier: 3.621A  pdb=" N   SER A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      Proline residue:  A 157  - end of helix
      removed outlier: 4.478A  pdb=" N   GLN A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   PHE A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 211
      removed outlier: 3.528A  pdb=" N   ALA A 191 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      Proline residue:  A 198  - end of helix
    Processing helix  chain 'A' and resid 381 through 411
      removed outlier: 3.508A  pdb=" N   VAL A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   THR A 388 " --> pdb=" O   LYS A 384 " (cutoff:3.500A)
      Proline residue:  A 402  - end of helix
      removed outlier: 3.669A  pdb=" N   LEU A 408 " --> pdb=" O   ASN A 404 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ILE A 409 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 439
      removed outlier: 3.676A  pdb=" N   TRP A 422 " --> pdb=" O   ASN A 419 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   TYR A 426 " --> pdb=" O   THR A 423 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A 428 " --> pdb=" O   GLY A 425 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR A 430 " --> pdb=" O   TRP A 427 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN A 436 " --> pdb=" O   SER A 433 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
    Processing helix  chain 'A' and resid 445 through 449
      removed outlier: 3.840A  pdb=" N   LYS A 449 " --> pdb=" O   ALA A 445 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 445 through 449'
    Processing helix  chain 'B' and resid 11 through 31
    Processing helix  chain 'B' and resid 46 through 54
      removed outlier: 3.503A  pdb=" N   MET B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 212
      No H-bonds generated for 'chain 'B' and resid 209 through 212'
    Processing helix  chain 'B' and resid 214 through 216
      No H-bonds generated for 'chain 'B' and resid 214 through 216'
    Processing helix  chain 'B' and resid 243 through 255
    Processing helix  chain 'B' and resid 272 through 281
      removed outlier: 3.869A  pdb=" N   LYS B 280 " --> pdb=" O   GLY B 276 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LYS B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 311
      removed outlier: 4.323A  pdb=" N   LYS B 311 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 350
      removed outlier: 3.788A  pdb=" N   ALA B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 24
    Processing helix  chain 'C' and resid 30 through 33
      No H-bonds generated for 'chain 'C' and resid 30 through 33'
    Processing helix  chain 'D' and resid 8 through 22
    Processing helix  chain 'D' and resid 30 through 47
      removed outlier: 3.822A  pdb=" N   ALA D  45 " --> pdb=" O   CYS D  41 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   LYS D  46 " --> pdb=" O   GLU D  42 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   GLU D  47 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 31
      No H-bonds generated for 'chain 'E' and resid 29 through 31'
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 88 through 90
      No H-bonds generated for 'chain 'E' and resid 88 through 90'
    Processing helix  chain 'E' and resid 221 through 223
      No H-bonds generated for 'chain 'E' and resid 221 through 223'
    Processing sheet with id=  A, first strand: chain 'B' and resid 319 through 323
      removed outlier: 6.878A  pdb=" N   ILE B 265 " --> pdb=" O   TYR B 320 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   HIS B 322 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU B 267 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA B 221 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE B 190 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL B 186 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.879A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.937A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ARG C 137 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.774A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'C' and resid 190 through 192
      removed outlier: 3.859A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.527A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   CYS C 250 " --> pdb=" O   TYR C 264 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 276 through 278
      removed outlier: 3.970A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.643A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.526A  pdb=" N   THR E  78 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'E' and resid 115 through 117
      removed outlier: 3.609A  pdb=" N   TRP E  36 " --> pdb=" O   ALA E  49 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  45 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   LEU E  45 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'E' and resid 146 through 149
      removed outlier: 6.458A  pdb=" N   LYS E 244 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   VAL E 149 " --> pdb=" O   LYS E 244 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'E' and resid 155 through 160
      removed outlier: 3.692A  pdb=" N   ALA E 211 " --> pdb=" O   SER E 208 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'E' and resid 225 through 231
      removed outlier: 3.821A  pdb=" N   ILE E 189 " --> pdb=" O   TRP E 176 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    352 hydrogen bonds defined for protein.
    912 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: 2.12

  Time building geometry restraints manager: 3.76 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1359
        1.30 -     1.43: 2376
        1.43 -     1.56: 4744
        1.56 -     1.70: 2
        1.70 -     1.83: 83
  Bond restraints: 8564
  Sorted by residual:
  bond pdb=" C01 2CU A 502 "
       pdb=" N02 2CU A 502 "
    ideal  model  delta    sigma   weight residual
    1.445  1.258  0.187 2.00e-02 2.50e+03 8.72e+01
  bond pdb=" C08 2CU A 502 "
       pdb=" N05 2CU A 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.474 -0.128 2.00e-02 2.50e+03 4.11e+01
  bond pdb=" C24 2CU A 502 "
       pdb=" N26 2CU A 502 "
    ideal  model  delta    sigma   weight residual
    1.353  1.466 -0.113 2.00e-02 2.50e+03 3.22e+01
  bond pdb=" C18 2CU A 502 "
       pdb=" N19 2CU A 502 "
    ideal  model  delta    sigma   weight residual
    1.356  1.465 -0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C12 2CU A 502 "
       pdb=" O11 2CU A 502 "
    ideal  model  delta    sigma   weight residual
    1.323  1.414 -0.091 2.00e-02 2.50e+03 2.06e+01
  ... (remaining 8559 not shown)

  Histogram of bond angle deviations from ideal:
       59.90 -    74.77: 3
       74.77 -    89.64: 0
       89.64 -   104.52: 121
      104.52 -   119.39: 7052
      119.39 -   134.26: 4485
  Bond angle restraints: 11661
  Sorted by residual:
  angle pdb=" C   GLU B   8 "
        pdb=" N   ASP B   9 "
        pdb=" CA  ASP B   9 "
      ideal   model   delta    sigma   weight residual
     121.70  134.16  -12.46 1.80e+00 3.09e-01 4.79e+01
  angle pdb=" N   PRO A 418 "
        pdb=" CA  PRO A 418 "
        pdb=" C   PRO A 418 "
      ideal   model   delta    sigma   weight residual
     111.14  100.44   10.70 1.56e+00 4.11e-01 4.70e+01
  angle pdb=" N   LEU A  43 "
        pdb=" CA  LEU A  43 "
        pdb=" C   LEU A  43 "
      ideal   model   delta    sigma   weight residual
     113.19  105.25    7.94 1.19e+00 7.06e-01 4.45e+01
  angle pdb=" N   ASN A  41 "
        pdb=" CA  ASN A  41 "
        pdb=" C   ASN A  41 "
      ideal   model   delta    sigma   weight residual
     111.82  104.32    7.50 1.16e+00 7.43e-01 4.19e+01
  angle pdb=" CA  PHE A 180 "
        pdb=" CB  PHE A 180 "
        pdb=" CG  PHE A 180 "
      ideal   model   delta    sigma   weight residual
     113.80  119.82   -6.02 1.00e+00 1.00e+00 3.62e+01
  ... (remaining 11656 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.32: 4498
       14.32 -    28.64: 385
       28.64 -    42.96: 107
       42.96 -    57.28: 16
       57.28 -    71.60: 5
  Dihedral angle restraints: 5011
    sinusoidal: 1790
      harmonic: 3221
  Sorted by residual:
  dihedral pdb=" C   THR A 420 "
           pdb=" N   THR A 420 "
           pdb=" CA  THR A 420 "
           pdb=" CB  THR A 420 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -110.13  -11.87     0      2.50e+00 1.60e-01 2.25e+01
  dihedral pdb=" N   THR A 420 "
           pdb=" C   THR A 420 "
           pdb=" CA  THR A 420 "
           pdb=" CB  THR A 420 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  112.43   10.97     0      2.50e+00 1.60e-01 1.93e+01
  dihedral pdb=" C   THR A 187 "
           pdb=" N   THR A 187 "
           pdb=" CA  THR A 187 "
           pdb=" CB  THR A 187 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -111.15  -10.85     0      2.50e+00 1.60e-01 1.88e+01
  ... (remaining 5008 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1076
       0.060 -    0.120: 225
       0.120 -    0.181: 37
       0.181 -    0.241: 7
       0.241 -    0.301: 11
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CA  ASN B 330 "
            pdb=" N   ASN B 330 "
            pdb=" C   ASN B 330 "
            pdb=" CB  ASN B 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  THR A 423 "
            pdb=" N   THR A 423 "
            pdb=" C   THR A 423 "
            pdb=" CB  THR A 423 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.83   -0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" CA  ASP E  74 "
            pdb=" N   ASP E  74 "
            pdb=" C   ASP E  74 "
            pdb=" CB  ASP E  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+00
  ... (remaining 1353 not shown)

  Planarity restraints: 1469
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  74 "    0.024 2.00e-02 2.50e+03   4.78e-02 2.29e+01
        pdb=" C   VAL A  74 "   -0.083 2.00e-02 2.50e+03
        pdb=" O   VAL A  74 "    0.031 2.00e-02 2.50e+03
        pdb=" N   PHE A  75 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  51 "    0.016 2.00e-02 2.50e+03   3.22e-02 1.03e+01
        pdb=" C   LYS B  51 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   LYS B  51 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLN B  52 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  40 "    0.014 2.00e-02 2.50e+03   2.89e-02 8.37e+00
        pdb=" C   GLY A  40 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A  40 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN A  41 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1466 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 117
        2.65 -     3.21: 7759
        3.21 -     3.77: 12083
        3.77 -     4.34: 16668
        4.34 -     4.90: 28000
  Nonbonded interactions: 64627
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  74 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.081 2.440
  nonbonded pdb=" OG  SER C 161 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.139 2.440
  nonbonded pdb=" OG  SER C 331 "
            pdb=" OD1 ASP C 333 "
     model   vdw
     2.177 2.440
  nonbonded pdb=" OG  SER C 245 "
            pdb=" OD1 ASP C 247 "
     model   vdw
     2.237 2.440
  nonbonded pdb=" O   TRP A 148 "
            pdb=" OG  SER A 151 "
     model   vdw
     2.257 2.440
  ... (remaining 64622 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          6.860
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     25.970
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  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:2.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
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   0.187   8564  Z= 0.460
  Angle     :  0.928  12.464  11661  Z= 0.580
  Chirality :  0.057   0.301   1356
  Planarity :  0.005   0.048   1469
  Dihedral  : 12.228  71.603   2926
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.46 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.68 (0.26), residues: 1093
  helix:  0.74 (0.29), residues: 342
  sheet: -0.24 (0.31), residues: 284
  loop : -1.45 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  82 
 HIS   0.007   0.002   HIS B 189 
 PHE   0.036   0.002   PHE A 180 
 TYR   0.018   0.002   TYR A 426 
 ARG   0.020   0.001   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.6999 (t80) cc_final: 0.6635 (t80)
REVERT: A  122 TYR cc_start: 0.7092 (t80) cc_final: 0.6846 (t80)
REVERT: B   24 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7840 (ttmt)
REVERT: C   61 MET cc_start: 0.7402 (tmm) cc_final: 0.7171 (tmm)
REVERT: C  290 ASP cc_start: 0.7995 (m-30) cc_final: 0.7666 (m-30)
REVERT: D   24 ASN cc_start: 0.7975 (t0) cc_final: 0.7581 (t0)
REVERT: E   67 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7662 (mtm180)
REVERT: E   87 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6767 (ttm110)
REVERT: E  178 LEU cc_start: 0.8036 (tp) cc_final: 0.7779 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2285
  time to fit residues: 62.3560
Evaluate side-chains
  186 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.0370
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.6662

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
B 270 ASN
B 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8564  Z= 0.227
  Angle     :  0.601  13.423  11661  Z= 0.325
  Chirality :  0.045   0.210   1356
  Planarity :  0.005   0.058   1469
  Dihedral  :  5.066  42.238   1204
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.98 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.30 (0.26), residues: 1093
  helix:  1.06 (0.29), residues: 345
  sheet:  0.11 (0.31), residues: 291
  loop : -1.38 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  82 
 HIS   0.005   0.001   HIS B 196 
 PHE   0.019   0.001   PHE A 396 
 TYR   0.015   0.001   TYR C 105 
 ARG   0.007   0.001   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A   83 TYR cc_start: 0.7368 (t80) cc_final: 0.5970 (t80)
REVERT: B   24 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7880 (ttmt)
REVERT: B   35 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7669 (mtpp)
REVERT: B  190 PHE cc_start: 0.7652 (p90) cc_final: 0.7429 (p90)
REVERT: B  211 LYS cc_start: 0.7535 (mmtp) cc_final: 0.7253 (mmtp)
REVERT: C   61 MET cc_start: 0.7499 (tmm) cc_final: 0.7092 (tmm)
REVERT: C  246 ASP cc_start: 0.6962 (t0) cc_final: 0.6545 (t0)
REVERT: C  258 ASP cc_start: 0.6966 (t70) cc_final: 0.6637 (t70)
REVERT: C  265 SER cc_start: 0.8313 (p) cc_final: 0.8105 (p)
REVERT: C  289 TYR cc_start: 0.8393 (m-80) cc_final: 0.8025 (m-80)
REVERT: C  290 ASP cc_start: 0.7963 (m-30) cc_final: 0.7686 (m-30)
REVERT: E   67 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7643 (mtm180)
REVERT: E   87 ARG cc_start: 0.7049 (ttm110) cc_final: 0.6420 (ttm110)
  outliers start: 13
  outliers final: 7
  residues processed: 193
  average time/residue: 0.2218
  time to fit residues: 57.1222
Evaluate side-chains
  183 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 176
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  141 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 87 optimal weight:    0.1980
   chunk 97 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  52 GLN
B 331 ASN
C  32 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8564  Z= 0.218
  Angle     :  0.570  13.426  11661  Z= 0.309
  Chirality :  0.044   0.213   1356
  Planarity :  0.004   0.058   1469
  Dihedral  :  4.837  42.554   1204
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 12.88 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.22 (0.26), residues: 1093
  helix:  1.06 (0.29), residues: 347
  sheet:  0.29 (0.31), residues: 285
  loop : -1.38 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B 196 
 PHE   0.017   0.001   PHE A 396 
 TYR   0.014   0.001   TYR C 105 
 ARG   0.007   0.000   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.7351 (t80) cc_final: 0.6085 (t80)
REVERT: A  431 ILE cc_start: 0.7453 (mt) cc_final: 0.7238 (mp)
REVERT: B   24 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7872 (ttmt)
REVERT: B   35 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7668 (mtpp)
REVERT: B  211 LYS cc_start: 0.7624 (mmtp) cc_final: 0.7345 (mmtp)
REVERT: B  354 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6535 (m-80)
REVERT: C   61 MET cc_start: 0.7536 (tmm) cc_final: 0.7295 (tmm)
REVERT: C  246 ASP cc_start: 0.7059 (t0) cc_final: 0.6641 (t0)
REVERT: C  289 TYR cc_start: 0.8409 (m-80) cc_final: 0.8068 (m-80)
REVERT: C  290 ASP cc_start: 0.7980 (m-30) cc_final: 0.7667 (m-30)
REVERT: D   24 ASN cc_start: 0.8024 (t0) cc_final: 0.7760 (t0)
REVERT: E   67 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7732 (mtm180)
REVERT: E   87 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6555 (ttm110)
  outliers start: 20
  outliers final: 13
  residues processed: 195
  average time/residue: 0.2070
  time to fit residues: 54.3486
Evaluate side-chains
  191 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 177
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 330 ASN
C  32 GLN
C  88 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8564  Z= 0.322
  Angle     :  0.615  13.649  11661  Z= 0.332
  Chirality :  0.046   0.208   1356
  Planarity :  0.005   0.057   1469
  Dihedral  :  5.086  42.165   1204
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.31 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.29 (0.26), residues: 1093
  helix:  0.99 (0.29), residues: 350
  sheet:  0.31 (0.31), residues: 285
  loop : -1.46 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  82 
 HIS   0.006   0.001   HIS B 196 
 PHE   0.018   0.002   PHE A 396 
 TYR   0.015   0.002   TYR E 190 
 ARG   0.009   0.001   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A  127 LYS cc_start: 0.7731 (mttt) cc_final: 0.7516 (mttt)
REVERT: B   35 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7699 (mtpp)
REVERT: B  211 LYS cc_start: 0.7690 (mmtp) cc_final: 0.7360 (mmtp)
REVERT: B  354 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6791 (m-80)
REVERT: C   61 MET cc_start: 0.7607 (tmm) cc_final: 0.7406 (tmm)
REVERT: C   79 LEU cc_start: 0.8079 (tt) cc_final: 0.7859 (tt)
REVERT: C  289 TYR cc_start: 0.8449 (m-80) cc_final: 0.8095 (m-80)
REVERT: C  290 ASP cc_start: 0.8001 (m-30) cc_final: 0.7711 (m-30)
REVERT: D   24 ASN cc_start: 0.8051 (t0) cc_final: 0.7799 (t0)
REVERT: E   67 ARG cc_start: 0.8199 (mtm110) cc_final: 0.7765 (mtm180)
REVERT: E   87 ARG cc_start: 0.7087 (ttm110) cc_final: 0.6475 (ttm110)
  outliers start: 32
  outliers final: 25
  residues processed: 211
  average time/residue: 0.2070
  time to fit residues: 59.8647
Evaluate side-chains
  217 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 191
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  217 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0980
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 93 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN
B  52 GLN
B 295 ASN
B 330 ASN
B 331 ASN
C  32 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8564  Z= 0.188
  Angle     :  0.558  12.979  11661  Z= 0.300
  Chirality :  0.043   0.198   1356
  Planarity :  0.004   0.055   1469
  Dihedral  :  4.753  41.917   1204
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.24 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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 (0.26), residues: 1093
  helix:  1.14 (0.29), residues: 349
  sheet:  0.41 (0.32), residues: 284
  loop : -1.43 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  82 
 HIS   0.004   0.001   HIS B 196 
 PHE   0.013   0.001   PHE A  61 
 TYR   0.013   0.001   TYR C 105 
 ARG   0.006   0.000   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 LEU cc_start: 0.8294 (mt) cc_final: 0.8028 (mp)
REVERT: B   35 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7670 (mtpp)
REVERT: B  211 LYS cc_start: 0.7643 (mmtp) cc_final: 0.7332 (mmtp)
REVERT: B  354 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6698 (m-80)
REVERT: C   61 MET cc_start: 0.7581 (tmm) cc_final: 0.7331 (ppp)
REVERT: C   79 LEU cc_start: 0.8024 (tt) cc_final: 0.7805 (tt)
REVERT: C  289 TYR cc_start: 0.8431 (m-80) cc_final: 0.8050 (m-80)
REVERT: C  290 ASP cc_start: 0.7978 (m-30) cc_final: 0.7655 (m-30)
REVERT: D   24 ASN cc_start: 0.8056 (t0) cc_final: 0.7794 (t0)
REVERT: E   67 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7934 (mtm180)
  outliers start: 32
  outliers final: 20
  residues processed: 202
  average time/residue: 0.2152
  time to fit residues: 58.3564
Evaluate side-chains
  210 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 330 ASN
C  32 GLN
C 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8564  Z= 0.269
  Angle     :  0.591  13.329  11661  Z= 0.317
  Chirality :  0.044   0.211   1356
  Planarity :  0.004   0.060   1469
  Dihedral  :  4.873  41.629   1204
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 16.71 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.23 (0.26), residues: 1093
  helix:  1.08 (0.29), residues: 349
  sheet:  0.35 (0.32), residues: 285
  loop : -1.47 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  82 
 HIS   0.006   0.001   HIS B 196 
 PHE   0.014   0.001   PHE A 396 
 TYR   0.014   0.002   TYR E 190 
 ARG   0.011   0.000   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 195
  time to evaluate  : 0.948 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7712 (mtpp)
REVERT: B  211 LYS cc_start: 0.7657 (mmtp) cc_final: 0.7343 (mmtp)
REVERT: B  354 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6744 (m-80)
REVERT: C   52 ARG cc_start: 0.8459 (ptp90) cc_final: 0.8223 (ptp-170)
REVERT: C   61 MET cc_start: 0.7632 (tmm) cc_final: 0.7364 (ppp)
REVERT: C  117 LEU cc_start: 0.8408 (mt) cc_final: 0.8182 (mt)
REVERT: C  289 TYR cc_start: 0.8450 (m-80) cc_final: 0.8146 (m-80)
REVERT: C  290 ASP cc_start: 0.7992 (m-30) cc_final: 0.7692 (m-30)
REVERT: D   24 ASN cc_start: 0.8068 (t0) cc_final: 0.7810 (t0)
REVERT: E   67 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7737 (mtm180)
REVERT: E   87 ARG cc_start: 0.7099 (ttm110) cc_final: 0.6476 (ttm110)
  outliers start: 34
  outliers final: 29
  residues processed: 215
  average time/residue: 0.2056
  time to fit residues: 59.1245
Evaluate side-chains
  221 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 191
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  196 HIS
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0770
   chunk 63 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 330 ASN
C  32 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8564  Z= 0.221
  Angle     :  0.576  13.065  11661  Z= 0.308
  Chirality :  0.043   0.196   1356
  Planarity :  0.004   0.060   1469
  Dihedral  :  4.761  41.486   1204
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.10 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.21 (0.26), residues: 1093
  helix:  1.11 (0.29), residues: 349
  sheet:  0.25 (0.31), residues: 294
  loop : -1.41 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B 196 
 PHE   0.012   0.001   PHE C 234 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.008   0.000   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A   83 TYR cc_start: 0.7296 (t80) cc_final: 0.6087 (t80)
REVERT: B   35 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7693 (mtpp)
REVERT: B  211 LYS cc_start: 0.7636 (mmtp) cc_final: 0.7374 (mmtp)
REVERT: B  354 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6568 (m-80)
REVERT: C   52 ARG cc_start: 0.8430 (ptp90) cc_final: 0.8213 (ptp-170)
REVERT: C   61 MET cc_start: 0.7616 (tmm) cc_final: 0.7347 (ppp)
REVERT: C  289 TYR cc_start: 0.8443 (m-80) cc_final: 0.7999 (m-80)
REVERT: C  290 ASP cc_start: 0.7959 (m-30) cc_final: 0.7660 (m-30)
REVERT: C  327 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8144 (t)
REVERT: D   24 ASN cc_start: 0.8067 (t0) cc_final: 0.7807 (t0)
REVERT: E   67 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7768 (mtm180)
REVERT: E   87 ARG cc_start: 0.7107 (ttm110) cc_final: 0.6478 (ttm110)
  outliers start: 34
  outliers final: 27
  residues processed: 217
  average time/residue: 0.2117
  time to fit residues: 61.4400
Evaluate side-chains
  216 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  196 HIS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 62 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 330 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8564  Z= 0.225
  Angle     :  0.580  13.079  11661  Z= 0.310
  Chirality :  0.043   0.200   1356
  Planarity :  0.004   0.062   1469
  Dihedral  :  4.703  41.224   1204
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 18.33 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.22 (0.26), residues: 1093
  helix:  1.11 (0.30), residues: 349
  sheet:  0.26 (0.31), residues: 294
  loop : -1.43 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B 196 
 PHE   0.012   0.001   PHE C 234 
 TYR   0.012   0.001   TYR C 105 
 ARG   0.008   0.000   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 187
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: B  211 LYS cc_start: 0.7642 (mmtp) cc_final: 0.7363 (mmtp)
REVERT: B  354 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6584 (m-80)
REVERT: C   61 MET cc_start: 0.7639 (tmm) cc_final: 0.7342 (ppp)
REVERT: C  289 TYR cc_start: 0.8440 (m-80) cc_final: 0.8139 (m-80)
REVERT: C  290 ASP cc_start: 0.7958 (m-30) cc_final: 0.7646 (m-30)
REVERT: C  327 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8145 (t)
REVERT: D   24 ASN cc_start: 0.8070 (t0) cc_final: 0.7837 (t0)
REVERT: E   67 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7849 (mtm180)
REVERT: E   87 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6624 (ttm110)
REVERT: E  117 LEU cc_start: 0.8297 (tp) cc_final: 0.8050 (tt)
  outliers start: 36
  outliers final: 31
  residues processed: 208
  average time/residue: 0.2028
  time to fit residues: 57.1928
Evaluate side-chains
  221 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  196 HIS
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 91 optimal weight:    0.3980
   chunk 96 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 330 ASN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8564  Z= 0.254
  Angle     :  0.600  13.154  11661  Z= 0.318
  Chirality :  0.044   0.198   1356
  Planarity :  0.005   0.063   1469
  Dihedral  :  4.778  41.236   1204
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 18.79 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.21 (0.26), residues: 1093
  helix:  1.10 (0.30), residues: 346
  sheet:  0.29 (0.31), residues: 294
  loop : -1.41 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B 196 
 PHE   0.013   0.001   PHE C 234 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.014   0.001   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 0.944 
Fit side-chains
REVERT: B  211 LYS cc_start: 0.7664 (mmtp) cc_final: 0.7383 (mmtp)
REVERT: B  354 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6607 (m-80)
REVERT: C   61 MET cc_start: 0.7644 (tmm) cc_final: 0.7342 (ppp)
REVERT: C  289 TYR cc_start: 0.8448 (m-80) cc_final: 0.8138 (m-80)
REVERT: C  290 ASP cc_start: 0.7963 (m-30) cc_final: 0.7649 (m-30)
REVERT: C  327 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8151 (t)
REVERT: D   24 ASN cc_start: 0.8095 (t0) cc_final: 0.7862 (t0)
REVERT: E  117 LEU cc_start: 0.8278 (tp) cc_final: 0.8039 (tt)
  outliers start: 35
  outliers final: 31
  residues processed: 207
  average time/residue: 0.1866
  time to fit residues: 53.9409
Evaluate side-chains
  219 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  196 HIS
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.2980
   chunk 62 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0470
   chunk 107 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 85 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 330 ASN
C 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8564  Z= 0.179
  Angle     :  0.573  12.835  11661  Z= 0.305
  Chirality :  0.043   0.198   1356
  Planarity :  0.004   0.063   1469
  Dihedral  :  4.594  40.954   1204
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.68 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.08 (0.26), residues: 1093
  helix:  1.21 (0.30), residues: 347
  sheet:  0.37 (0.32), residues: 292
  loop : -1.35 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B 196 
 PHE   0.012   0.001   PHE A  61 
 TYR   0.013   0.001   TYR C 105 
 ARG   0.014   0.000   ARG C 134 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 173
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
REVERT: B  211 LYS cc_start: 0.7650 (mmtp) cc_final: 0.7348 (mmtp)
REVERT: B  354 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6523 (m-80)
REVERT: C   61 MET cc_start: 0.7621 (tmm) cc_final: 0.7309 (ppp)
REVERT: C  289 TYR cc_start: 0.8420 (m-80) cc_final: 0.7936 (m-80)
REVERT: C  290 ASP cc_start: 0.7936 (m-30) cc_final: 0.7629 (m-30)
REVERT: D   24 ASN cc_start: 0.8091 (t0) cc_final: 0.7863 (t0)
REVERT: E  117 LEU cc_start: 0.8290 (tp) cc_final: 0.8052 (tt)
  outliers start: 34
  outliers final: 31
  residues processed: 194
  average time/residue: 0.1855
  time to fit residues: 50.0030
Evaluate side-chains
  205 residues out of total 948 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  196 HIS
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  220 GLN
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  147 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0670
   chunk 79 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 316 ASN
B 330 ASN
C 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.114411 restraints weight = 13273.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.00
r_work: 0.3416 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8564  Z= 0.214
  Angle     :  0.586  12.963  11661  Z= 0.312
  Chirality :  0.043   0.199   1356
  Planarity :  0.005   0.062   1469
  Dihedral  :  4.642  40.841   1204
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 19.26 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.09 %
    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: -0.04 (0.26), residues: 1093
  helix:  1.27 (0.30), residues: 347
  sheet:  0.41 (0.32), residues: 290
  loop : -1.34 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B 196 
 PHE   0.011   0.001   PHE A 396 
 TYR   0.014   0.001   TYR C 105 
 ARG   0.015   0.001   ARG C 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2441.86 seconds
wall clock time: 44 minutes 31.17 seconds (2671.17 seconds total)