Starting phenix.real_space_refine
on Fri Dec  8 17:00:54 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/12_2023/6k42_9912_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/12_2023/6k42_9912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/12_2023/6k42_9912.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/12_2023/6k42_9912.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/12_2023/6k42_9912_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/12_2023/6k42_9912_updated.pdb"
  }
  resolution = 4.1
  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=   0.010
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: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5630      2.51       5
     N    1510      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   32": "NH1" <-> "NH2"
    Residue "B TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG  116": "NH1" <-> "NH2"
    Residue "R ARG  128": "NH1" <-> "NH2"
    Residue "R ARG  359": "NH1" <-> "NH2"
    Residue "R PHE  369": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8816
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1759
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2616
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2201
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 12, 'TRANS': 257}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 1801
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 233, 1793
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
      Conformer: "B"
        Number of residues, atoms: 233, 1793
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          bond proxies already assigned to first conformer: 1828
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'CZX': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LYS H 236 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS H 236 " occ=0.00
  Time building chain proxies: 5.99, per 1000 atoms: 0.68
  Number of scatterers: 8816
  At special positions: 0
  Unit cell: (112.08, 110.679, 128.892, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1618      8.00
     N    1510      7.00
     C    5630      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " distance=2.03

  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: 3.34
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      20 helices and 14 sheets defined
      29.8% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 32
      removed outlier: 4.114A  pdb=" N   GLU A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A  19 " --> pdb=" O   ARG A  15 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU A  23 " --> pdb=" O   ILE A  19 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 through 215'
    Processing helix  chain 'A' and resid 242 through 254
      removed outlier: 3.871A  pdb=" N   LYS A 248 " --> pdb=" O   HIS A 244 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 3.823A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 271 through 275'
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.527A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASP A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 350
    Processing helix  chain 'B' and resid 4 through 18
      removed outlier: 3.770A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 21
      removed outlier: 4.101A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'G' and resid 56 through 58
      No H-bonds generated for 'chain 'G' and resid 56 through 58'
    Processing helix  chain 'R' and resid 13 through 38
      removed outlier: 3.878A  pdb=" N   ASN R  30 " --> pdb=" O   THR R  26 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ALA R  31 " --> pdb=" O   ILE R  27 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU R  32 " --> pdb=" O   PHE R  28 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 73
      removed outlier: 3.729A  pdb=" N   LEU R  64 " --> pdb=" O   LEU R  60 " (cutoff:3.500A)
      Proline residue:  R  67  - end of helix
    Processing helix  chain 'R' and resid 84 through 115
      removed outlier: 3.733A  pdb=" N   CYS R  96 " --> pdb=" O   ASP R  92 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER R  99 " --> pdb=" O   PHE R  95 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL R 114 " --> pdb=" O   ARG R 110 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 121
      No H-bonds generated for 'chain 'R' and resid 118 through 121'
    Processing helix  chain 'R' and resid 126 through 145
    Processing helix  chain 'R' and resid 170 through 180
      removed outlier: 3.858A  pdb=" N   LEU R 174 " --> pdb=" O   ALA R 170 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA R 175 " --> pdb=" O   TRP R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 182 through 203
      removed outlier: 3.704A  pdb=" N   ASN R 203 " --> pdb=" O   ALA R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 360 through 396
      removed outlier: 3.632A  pdb=" N   THR R 364 " --> pdb=" O   ARG R 360 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG R 365 " --> pdb=" O   ALA R 361 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS R 367 " --> pdb=" O   LEU R 363 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE R 377 " --> pdb=" O   LEU R 373 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   PHE R 380 " --> pdb=" O   VAL R 376 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL R 381 " --> pdb=" O   ILE R 377 " (cutoff:3.500A)
      Proline residue:  R 386  - end of helix
      removed outlier: 3.877A  pdb=" N   GLY R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   ALA R 395 " --> pdb=" O   TYR R 391 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 407 through 428
      removed outlier: 3.984A  pdb=" N   ASN R 418 " --> pdb=" O   ILE R 414 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   SER R 419 " --> pdb=" O   GLY R 415 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   SER R 420 " --> pdb=" O   TYR R 416 " (cutoff:3.500A)
      Proline residue:  R 423  - end of helix
      removed outlier: 3.745A  pdb=" N   TYR R 426 " --> pdb=" O   ASN R 422 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR R 427 " --> pdb=" O   PRO R 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE R 428 " --> pdb=" O   VAL R 424 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 431 through 441
    Processing sheet with id=  A, first strand: chain 'A' and resid 36 through 39
      removed outlier: 6.261A  pdb=" N   ALA A 220 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   LEU A  39 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ILE A 222 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   SER A 263 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   PHE A 223 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE A 265 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   VAL A 225 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 5.596A  pdb=" N   PHE A 267 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   TYR A 320 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   LEU A 268 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   HIS A 322 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  A
    Processing sheet with id=  B, first strand: chain 'A' and resid 186 through 190
    Processing sheet with id=  C, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.840A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 61 through 63
      removed outlier: 3.527A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.168A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.114A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 190 through 192
    Processing sheet with id=  H, first strand: chain 'B' and resid 262 through 265
      removed outlier: 3.680A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 294 through 297
    Processing sheet with id=  J, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=  K, first strand: chain 'H' and resid 93 through 99
      removed outlier: 3.754A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'H' and resid 128 through 130
      removed outlier: 3.642A  pdb=" N   ARG H 148 " --> pdb=" O   THR H 129 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'H' and resid 213 through 219
      removed outlier: 5.557A  pdb=" N   LEU H 166 " --> pdb=" O   LEU H 175 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   LEU H 175 " --> pdb=" O   LEU H 166 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'H' and resid 191 through 196

    296 hydrogen bonds defined for protein.
    864 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: 2.17

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2622
        1.34 -     1.46: 1721
        1.46 -     1.58: 4582
        1.58 -     1.70: 1
        1.70 -     1.82: 79
  Bond restraints: 9005
  Sorted by residual:
  bond pdb=" C09 CZX R 501 "
       pdb=" C12 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.385  1.529 -0.144 2.00e-02 2.50e+03 5.17e+01
  bond pdb=" C11 CZX R 501 "
       pdb=" C12 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.386  1.528 -0.142 2.00e-02 2.50e+03 5.07e+01
  bond pdb=" C08 CZX R 501 "
       pdb=" C11 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.392  1.528 -0.136 2.00e-02 2.50e+03 4.62e+01
  bond pdb=" C04 CZX R 501 "
       pdb=" C09 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.393  1.526 -0.133 2.00e-02 2.50e+03 4.41e+01
  bond pdb=" C04 CZX R 501 "
       pdb=" C05 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.403  1.530 -0.127 2.00e-02 2.50e+03 4.01e+01
  ... (remaining 9000 not shown)

  Histogram of bond angle deviations from ideal:
       99.41 -   106.33: 194
      106.33 -   113.26: 4781
      113.26 -   120.18: 3325
      120.18 -   127.11: 3792
      127.11 -   134.03: 99
  Bond angle restraints: 12191
  Sorted by residual:
  angle pdb=" N   ILE R 396 "
        pdb=" CA  ILE R 396 "
        pdb=" C   ILE R 396 "
      ideal   model   delta    sigma   weight residual
     110.82  101.31    9.51 9.70e-01 1.06e+00 9.61e+01
  angle pdb=" C   ASN H 157 "
        pdb=" N   GLY H 158 "
        pdb=" CA  GLY H 158 "
      ideal   model   delta    sigma   weight residual
     121.70  131.39   -9.69 1.80e+00 3.09e-01 2.90e+01
  angle pdb=" C   TYR R  79 "
        pdb=" N   PHE R  80 "
        pdb=" CA  PHE R  80 "
      ideal   model   delta    sigma   weight residual
     121.54  130.87   -9.33 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C   PHE R  80 "
        pdb=" N   ARG R  81 "
        pdb=" CA  ARG R  81 "
      ideal   model   delta    sigma   weight residual
     121.54  130.81   -9.27 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" CA  ALA R 395 "
        pdb=" C   ALA R 395 "
        pdb=" N   ILE R 396 "
      ideal   model   delta    sigma   weight residual
     118.81  113.25    5.56 1.15e+00 7.56e-01 2.34e+01
  ... (remaining 12186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.97: 5108
       14.97 -    29.95: 173
       29.95 -    44.92: 56
       44.92 -    59.89: 8
       59.89 -    74.86: 3
  Dihedral angle restraints: 5348
    sinusoidal: 2102
      harmonic: 3246
  Sorted by residual:
  dihedral pdb=" CA  PRO R 146 "
           pdb=" C   PRO R 146 "
           pdb=" N   PRO R 147 "
           pdb=" CA  PRO R 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.62   24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ILE A  19 "
           pdb=" C   ILE A  19 "
           pdb=" N   ASP A  20 "
           pdb=" CA  ASP A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.10   33.90     1      1.00e+01 1.00e-02 1.63e+01
  ... (remaining 5345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1139
       0.061 -    0.123: 198
       0.123 -    0.184: 32
       0.184 -    0.246: 2
       0.246 -    0.307: 2
  Chirality restraints: 1373
  Sorted by residual:
  chirality pdb=" CA  ILE R 396 "
            pdb=" N   ILE R 396 "
            pdb=" C   ILE R 396 "
            pdb=" CB  ILE R 396 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" C03 CZX R 501 "
            pdb=" C04 CZX R 501 "
            pdb=" C06 CZX R 501 "
            pdb=" C07 CZX R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.76    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  CYS R 397 "
            pdb=" N   CYS R 397 "
            pdb=" C   CYS R 397 "
            pdb=" CB  CYS R 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 1370 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 146 "    0.063 5.00e-02 4.00e+02   9.39e-02 1.41e+01
        pdb=" N   PRO R 147 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO R 147 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO R 147 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 340 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   THR A 340 "    0.042 2.00e-02 2.50e+03
        pdb=" O   THR A 340 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASP A 341 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 395 "    0.011 2.00e-02 2.50e+03   2.40e-02 5.78e+00
        pdb=" C   ALA R 395 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ALA R 395 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE R 396 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2389
        2.81 -     3.33: 7268
        3.33 -     3.86: 13820
        3.86 -     4.38: 15445
        4.38 -     4.90: 27047
  Nonbonded interactions: 65969
  Sorted by model distance:
  nonbonded pdb=" OG  SER R  69 "
            pdb=" OH  TYR R  88 "
     model   vdw
     2.288 2.440
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.302 2.440
  nonbonded pdb=" O   PRO R 423 "
            pdb=" OG1 THR R 427 "
     model   vdw
     2.323 2.440
  nonbonded pdb=" O   LEU B  30 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.343 2.440
  nonbonded pdb=" O   CYS R 397 "
            pdb=" N   CYS R 401 "
     model   vdw
     2.345 2.520
  ... (remaining 65964 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=0.00 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:             0.940
  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:             0.010
  Extract box with map and model:          3.260
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     28.000
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
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      :  0.005   0.144   9005  Z= 0.319
  Angle     :  0.823   9.687  12191  Z= 0.478
  Chirality :  0.049   0.307   1373
  Planarity :  0.007   0.094   1537
  Dihedral  :  9.237  74.864   3241
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.78 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -4.37 (0.19), residues: 1095
  helix: -2.64 (0.19), residues: 340
  sheet: -2.22 (0.30), residues: 242
  loop : -3.42 (0.21), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B 211 
   HIS   0.010   0.001   HIS R 102 
   PHE   0.031   0.002   PHE R 369 
   TYR   0.017   0.002   TYR R  79 
   ARG   0.005   0.000   ARG B  68 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 431
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 431
  average time/residue: 0.2477
  time to fit residues: 138.6417
Evaluate side-chains
  287 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 286
  time to evaluate  : 0.951 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0827
  time to fit residues: 1.5937
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0570
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0870
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 244 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
A 346 ASN
B  16 ASN
B  75 GLN
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
B 295 ASN
B 311 HIS
R  30 ASN
R 121 ASN
** R 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 418 ASN
H 155 HIS
H 159 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9005  Z= 0.197
  Angle     :  0.595   7.101  12191  Z= 0.316
  Chirality :  0.042   0.253   1373
  Planarity :  0.005   0.079   1537
  Dihedral  :  4.572  17.770   1225
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.99 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.22), residues: 1095
  helix: -0.63 (0.26), residues: 330
  sheet: -1.86 (0.30), residues: 244
  loop : -2.96 (0.22), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP R  84 
   HIS   0.008   0.001   HIS H 155 
   PHE   0.031   0.002   PHE R 369 
   TYR   0.017   0.002   TYR H 216 
   ARG   0.012   0.001   ARG G  27 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.2032
  time to fit residues: 90.4724
Evaluate side-chains
  256 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.954 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3594
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 108 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 362 GLN
R 409 GLN
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 155 HIS
** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.4967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9005  Z= 0.224
  Angle     :  0.635   7.397  12191  Z= 0.337
  Chirality :  0.043   0.165   1373
  Planarity :  0.005   0.072   1537
  Dihedral  :  4.695  19.710   1225
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  2.62 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.23), residues: 1095
  helix:  0.08 (0.27), residues: 335
  sheet: -1.62 (0.33), residues: 235
  loop : -2.56 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.002   TRP H 111 
   HIS   0.008   0.002   HIS H 155 
   PHE   0.028   0.002   PHE R 369 
   TYR   0.021   0.002   TYR H 216 
   ARG   0.006   0.001   ARG B  68 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 329
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 330
  average time/residue: 0.2304
  time to fit residues: 101.6785
Evaluate side-chains
  266 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 265
  time to evaluate  : 1.005 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1199
  time to fit residues: 1.6102
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0870
   chunk 11 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0370
   chunk 106 optimal weight:    0.0030
   chunk 52 optimal weight:    0.0670
   chunk 95 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 304 GLN
A 346 ASN
B  75 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
R 102 HIS
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 362 GLN
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS
** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.5429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9005  Z= 0.152
  Angle     :  0.589   7.354  12191  Z= 0.306
  Chirality :  0.043   0.283   1373
  Planarity :  0.004   0.065   1537
  Dihedral  :  4.371  17.016   1225
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  1.47 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.90 (0.24), residues: 1095
  helix:  0.47 (0.28), residues: 333
  sheet: -1.52 (0.33), residues: 230
  loop : -2.32 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP R  84 
   HIS   0.024   0.002   HIS R 102 
   PHE   0.027   0.002   PHE R 369 
   TYR   0.017   0.002   TYR H 103 
   ARG   0.005   0.000   ARG H 168 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 343
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 344
  average time/residue: 0.2175
  time to fit residues: 101.2711
Evaluate side-chains
  269 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 268
  time to evaluate  : 0.984 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1153
  time to fit residues: 1.7048
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.0870
   chunk 60 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0570
   chunk 90 optimal weight:    2.9990
   chunk 73 optimal weight:    0.3980
   chunk 0 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
B  75 GLN
B  88 ASN
B 156 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS
H 157 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.5808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9005  Z= 0.169
  Angle     :  0.578   7.351  12191  Z= 0.302
  Chirality :  0.042   0.268   1373
  Planarity :  0.004   0.068   1537
  Dihedral  :  4.323  19.357   1225
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  1.57 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.73 (0.24), residues: 1095
  helix:  0.63 (0.28), residues: 338
  sheet: -1.36 (0.33), residues: 240
  loop : -2.30 (0.24), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  99 
   HIS   0.005   0.001   HIS R 102 
   PHE   0.027   0.002   PHE R 369 
   TYR   0.020   0.001   TYR H  95 
   ARG   0.009   0.000   ARG H  38 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 315
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 316
  average time/residue: 0.2257
  time to fit residues: 95.6442
Evaluate side-chains
  265 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 264
  time to evaluate  : 1.050 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1093
  time to fit residues: 1.5870
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 95 optimal weight:    5.9990
   chunk 21 optimal weight:    0.2980
   chunk 62 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
B 239 ASN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.6255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9005  Z= 0.198
  Angle     :  0.603   7.408  12191  Z= 0.314
  Chirality :  0.043   0.260   1373
  Planarity :  0.004   0.068   1537
  Dihedral  :  4.344  18.362   1225
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.36 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.59 (0.24), residues: 1095
  helix:  0.84 (0.28), residues: 331
  sheet: -1.20 (0.34), residues: 237
  loop : -2.30 (0.24), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP H 111 
   HIS   0.003   0.001   HIS R 102 
   PHE   0.027   0.002   PHE R 369 
   TYR   0.027   0.002   TYR H  95 
   ARG   0.005   0.000   ARG B   8 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 308
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 308
  average time/residue: 0.2169
  time to fit residues: 90.6877
Evaluate side-chains
  261 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 260
  time to evaluate  : 0.993 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1206
  time to fit residues: 1.5201
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0980
   chunk 106 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 239 ASN
B 293 ASN
G  11 GLN
R  30 ASN
R 121 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS
H 159 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.6651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9005  Z= 0.186
  Angle     :  0.599   7.308  12191  Z= 0.314
  Chirality :  0.043   0.299   1373
  Planarity :  0.004   0.067   1537
  Dihedral  :  4.368  17.551   1225
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.47 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.61 (0.25), residues: 1095
  helix:  0.84 (0.28), residues: 338
  sheet: -1.29 (0.33), residues: 244
  loop : -2.31 (0.24), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B  82 
   HIS   0.004   0.001   HIS R 102 
   PHE   0.039   0.002   PHE R  21 
   TYR   0.021   0.002   TYR R 416 
   ARG   0.004   0.000   ARG R 368 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 308
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2114
  time to fit residues: 88.8759
Evaluate side-chains
  265 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 1.000 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2989
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.0870
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 72 optimal weight:    0.2980
   chunk 52 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 101 optimal weight:    5.9990
   chunk 92 optimal weight:    0.2980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.6908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9005  Z= 0.187
  Angle     :  0.620   7.622  12191  Z= 0.323
  Chirality :  0.043   0.249   1373
  Planarity :  0.004   0.055   1537
  Dihedral  :  4.423  22.077   1225
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.63 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.60 (0.25), residues: 1095
  helix:  0.86 (0.28), residues: 340
  sheet: -1.31 (0.32), residues: 258
  loop : -2.34 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.035   0.002   TRP H 111 
   HIS   0.003   0.001   HIS B  54 
   PHE   0.036   0.002   PHE R  21 
   TYR   0.020   0.002   TYR H 103 
   ARG   0.004   0.000   ARG H 168 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 1.012 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.2151
  time to fit residues: 89.7103
Evaluate side-chains
  252 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 1.037 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4022
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 30 optimal weight:    0.2980
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    0.4980
   chunk 64 optimal weight:    0.7980
   chunk 104 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0570
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
A 255 ASN
A 304 GLN
** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 293 ASN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS
H 167 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.7128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9005  Z= 0.191
  Angle     :  0.620   7.788  12191  Z= 0.325
  Chirality :  0.043   0.279   1373
  Planarity :  0.004   0.058   1537
  Dihedral  :  4.398  18.852   1225
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.73 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.49 (0.25), residues: 1095
  helix:  1.00 (0.28), residues: 333
  sheet: -1.24 (0.33), residues: 259
  loop : -2.27 (0.25), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.002   TRP H 111 
   HIS   0.005   0.001   HIS B  54 
   PHE   0.032   0.002   PHE R  21 
   TYR   0.020   0.002   TYR H 103 
   ARG   0.003   0.000   ARG H 168 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 1.564 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 294
  average time/residue: 0.2063
  time to fit residues: 83.7987
Evaluate side-chains
  259 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.049 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5766
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 109 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
A 255 ASN
B  75 GLN
B 220 GLN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS
H 167 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.7483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   9005  Z= 0.239
  Angle     :  0.694  13.455  12191  Z= 0.356
  Chirality :  0.044   0.268   1373
  Planarity :  0.004   0.057   1537
  Dihedral  :  4.638  17.547   1225
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.52 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.60 (0.25), residues: 1095
  helix:  0.75 (0.28), residues: 340
  sheet: -1.29 (0.33), residues: 260
  loop : -2.25 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.029   0.002   TRP H 111 
   HIS   0.011   0.002   HIS A 244 
   PHE   0.035   0.002   PHE R  21 
   TYR   0.021   0.002   TYR H 103 
   ARG   0.003   0.001   ARG H 168 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 303
  average time/residue: 0.2118
  time to fit residues: 87.8538
Evaluate side-chains
  259 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.987 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4270
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    0.3980
   chunk 4 optimal weight:    0.0010
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B  75 GLN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.162285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.143441 restraints weight = 31754.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.147671 restraints weight = 39296.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.149375 restraints weight = 14207.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.7811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9005  Z= 0.210
  Angle     :  0.674  12.641  12191  Z= 0.344
  Chirality :  0.044   0.259   1373
  Planarity :  0.004   0.056   1537
  Dihedral  :  4.512  16.914   1225
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.31 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.55 (0.25), residues: 1095
  helix:  0.60 (0.28), residues: 352
  sheet: -1.17 (0.34), residues: 260
  loop : -2.18 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.029   0.002   TRP H 111 
   HIS   0.005   0.001   HIS B  54 
   PHE   0.030   0.002   PHE R  21 
   TYR   0.020   0.002   TYR H 103 
   ARG   0.004   0.000   ARG H 168 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2494.68 seconds
wall clock time: 45 minutes 41.37 seconds (2741.37 seconds total)