Starting phenix.real_space_refine
on Fri Dec  8 05:43:46 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/12_2023/6mi7_9125_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/12_2023/6mi7_9125.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/12_2023/6mi7_9125.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/12_2023/6mi7_9125.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/12_2023/6mi7_9125_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/12_2023/6mi7_9125_updated.pdb"
  }
  resolution = 4.2
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      43      5.16       5
     C    4713      2.51       5
     N    1240      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "F ARG    5": "NH1" <-> "NH2"
    Residue "F ARG    9": "NH1" <-> "NH2"
    Residue "F ARG   33": "NH1" <-> "NH2"
    Residue "F ARG  263": "NH1" <-> "NH2"
    Residue "G ARG  133": "NH1" <-> "NH2"
    Residue "G PHE  295": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   75": "NH1" <-> "NH2"
    Residue "A ARG   77": "NH1" <-> "NH2"
    Residue "A ARG   78": "NH1" <-> "NH2"
    Residue "A ARG  114": "NH1" <-> "NH2"
    Residue "A ARG  117": "NH1" <-> "NH2"
    Residue "A ARG  131": "NH1" <-> "NH2"
    Residue "A ARG  143": "NH1" <-> "NH2"
    Residue "A ARG  150": "NH1" <-> "NH2"
    Residue "A PHE  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG    6": "NH1" <-> "NH2"
  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: 7285
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1695
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 9, 'TRANS': 207}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1778
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 12, 'TRANS': 217}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1787
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 8, 'TRANS': 221}
    Chain: "B"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1787
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 8, 'TRANS': 221}
    Chain: "C"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 187
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "F"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.34, per 1000 atoms: 0.60
  Number of scatterers: 7285
  At special positions: 0
  Unit cell: (81.18, 102.09, 109.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      43     16.00
     P       1     15.00
     O    1288      8.00
     N    1240      7.00
     C    4713      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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: 3.07
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      43.7% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'F' and resid 3 through 8
      removed outlier: 3.553A  pdb=" N   LEU F   7 " --> pdb=" O   ILE F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 11 through 23
      removed outlier: 3.709A  pdb=" N   LEU F  16 " --> pdb=" O   LEU F  12 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ALA F  17 " --> pdb=" O   LYS F  13 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE F  21 " --> pdb=" O   ALA F  17 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 51
      No H-bonds generated for 'chain 'F' and resid 48 through 51'
    Processing helix  chain 'F' and resid 56 through 58
      No H-bonds generated for 'chain 'F' and resid 56 through 58'
    Processing helix  chain 'F' and resid 64 through 81
      removed outlier: 3.569A  pdb=" N   PHE F  69 " --> pdb=" O   PRO F  65 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU F  79 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 85 through 88
      No H-bonds generated for 'chain 'F' and resid 85 through 88'
    Processing helix  chain 'F' and resid 95 through 118
      removed outlier: 3.747A  pdb=" N   LYS F 100 " --> pdb=" O   VAL F  97 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   MET F 103 " --> pdb=" O   LYS F 100 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU F 105 " --> pdb=" O   ALA F 102 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   PHE F 108 " --> pdb=" O   LEU F 105 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   ILE F 111 " --> pdb=" O   PHE F 108 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA F 113 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ASN F 116 " --> pdb=" O   ALA F 113 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET F 118 " --> pdb=" O   VAL F 115 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 122 through 125
      No H-bonds generated for 'chain 'F' and resid 122 through 125'
    Processing helix  chain 'F' and resid 270 through 273
      No H-bonds generated for 'chain 'F' and resid 270 through 273'
    Processing helix  chain 'F' and resid 276 through 283
      removed outlier: 3.999A  pdb=" N   ALA F 280 " --> pdb=" O   VAL F 276 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   LEU F 281 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 295 through 298
      No H-bonds generated for 'chain 'F' and resid 295 through 298'
    Processing helix  chain 'F' and resid 300 through 318
      removed outlier: 3.896A  pdb=" N   LEU F 305 " --> pdb=" O   PRO F 301 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN F 313 " --> pdb=" O   PHE F 309 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   THR F 314 " --> pdb=" O   PHE F 310 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   LYS F 317 " --> pdb=" O   GLN F 313 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 330 through 344
      removed outlier: 3.723A  pdb=" N   THR F 333 " --> pdb=" O   TRP F 330 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE F 337 " --> pdb=" O   VAL F 334 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   TYR F 338 " --> pdb=" O   ASN F 335 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU F 341 " --> pdb=" O   TYR F 338 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL F 344 " --> pdb=" O   LEU F 341 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 34
      removed outlier: 3.869A  pdb=" N   GLY G  12 " --> pdb=" O   ASP G   8 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LYS G  13 " --> pdb=" O   ARG G   9 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   MET G  20 " --> pdb=" O   PHE G  16 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU G  23 " --> pdb=" O   ILE G  19 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU G  26 " --> pdb=" O   THR G  22 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE G  33 " --> pdb=" O   LEU G  29 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS G  34 " --> pdb=" O   SER G  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 58
      No H-bonds generated for 'chain 'G' and resid 55 through 58'
    Processing helix  chain 'G' and resid 60 through 64
      removed outlier: 3.811A  pdb=" N   VAL G  64 " --> pdb=" O   VAL G  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 60 through 64'
    Processing helix  chain 'G' and resid 78 through 81
      No H-bonds generated for 'chain 'G' and resid 78 through 81'
    Processing helix  chain 'G' and resid 89 through 95
      removed outlier: 3.883A  pdb=" N   ALA G  94 " --> pdb=" O   VAL G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 99 through 108
      removed outlier: 3.720A  pdb=" N   VAL G 106 " --> pdb=" O   VAL G 102 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   MET G 107 " --> pdb=" O   ALA G 103 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 111 through 122
      removed outlier: 3.898A  pdb=" N   LEU G 115 " --> pdb=" O   ILE G 111 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU G 116 " --> pdb=" O   PRO G 112 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE G 120 " --> pdb=" O   LEU G 116 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY G 121 " --> pdb=" O   THR G 117 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLU G 122 " --> pdb=" O   MET G 118 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 125 through 130
    Processing helix  chain 'G' and resid 132 through 135
      No H-bonds generated for 'chain 'G' and resid 132 through 135'
    Processing helix  chain 'G' and resid 270 through 279
      removed outlier: 3.657A  pdb=" N   LYS G 278 " --> pdb=" O   ASN G 274 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 283 through 292
      removed outlier: 3.565A  pdb=" N   LEU G 290 " --> pdb=" O   ALA G 286 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 307 through 323
      removed outlier: 4.420A  pdb=" N   GLY G 316 " --> pdb=" O   GLY G 312 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL G 318 " --> pdb=" O   SER G 314 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   PHE G 319 " --> pdb=" O   PHE G 315 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   TYR G 320 " --> pdb=" O   GLY G 316 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL G 321 " --> pdb=" O   PHE G 317 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 326 through 332
      removed outlier: 3.651A  pdb=" N   THR G 330 " --> pdb=" O   PHE G 326 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 344 through 355
      removed outlier: 3.851A  pdb=" N   PHE G 348 " --> pdb=" O   PRO G 344 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   PHE G 349 " --> pdb=" O   SER G 345 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE G 351 " --> pdb=" O   SER G 347 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   SER G 352 " --> pdb=" O   PHE G 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 50
      removed outlier: 3.635A  pdb=" N   MET A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 78
      removed outlier: 5.850A  pdb=" N   ALA A  76 " --> pdb=" O   HIS A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 101 through 104
      No H-bonds generated for 'chain 'A' and resid 101 through 104'
    Processing helix  chain 'A' and resid 113 through 122
      removed outlier: 4.082A  pdb=" N   ALA A 118 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 152
      removed outlier: 4.068A  pdb=" N   ARG A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   ARG A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ALA A 151 " --> pdb=" O   GLU A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 185
      removed outlier: 3.716A  pdb=" N   ARG A 178 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 200
      No H-bonds generated for 'chain 'A' and resid 197 through 200'
    Processing helix  chain 'B' and resid 42 through 49
    Processing helix  chain 'B' and resid 72 through 75
      No H-bonds generated for 'chain 'B' and resid 72 through 75'
    Processing helix  chain 'B' and resid 95 through 102
      removed outlier: 3.587A  pdb=" N   MET B 100 " --> pdb=" O   TYR B  96 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 101 " --> pdb=" O   ASP B  97 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL B 102 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 124
      removed outlier: 4.171A  pdb=" N   ALA B 118 " --> pdb=" O   ARG B 114 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ASN B 119 " --> pdb=" O   GLU B 115 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLU B 123 " --> pdb=" O   ASN B 119 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 153
      removed outlier: 3.773A  pdb=" N   ILE B 148 " --> pdb=" O   ARG B 144 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ALA B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA B 151 " --> pdb=" O   GLU B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 183
      removed outlier: 3.981A  pdb=" N   ILE B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASP B 175 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG B 178 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE B 179 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 202
      removed outlier: 3.589A  pdb=" N   LEU B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   ALA B 202 " --> pdb=" O   ARG B 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 197 through 202'
    Processing helix  chain 'B' and resid 221 through 223
      No H-bonds generated for 'chain 'B' and resid 221 through 223'
    Processing helix  chain 'C' and resid 5 through 22
      removed outlier: 3.876A  pdb=" N   ILE C   9 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ILE C  10 " --> pdb=" O   ARG C   6 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL C  11 " --> pdb=" O   TRP C   7 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   SER C  13 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   MET C  19 " --> pdb=" O   ALA C  15 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLY C  21 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE C  22 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 24 through 27
      removed outlier: 3.551A  pdb=" N   LEU A  24 " --> pdb=" O   ALA A   6 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A  26 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU A   4 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 31 through 33
      removed outlier: 6.512A  pdb=" N   VAL A 190 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'A' and resid 34 through 36
      removed outlier: 7.191A  pdb=" N   TYR A 208 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA A 217 " --> pdb=" O   ILE A 209 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER A 211 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   LEU A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 80 through 82
      removed outlier: 6.927A  pdb=" N   PHE A 158 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  D
    Processing sheet with id=  E, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.565A  pdb=" N   ILE B  61 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 31 through 33
      removed outlier: 6.563A  pdb=" N   VAL B 190 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU B 191 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   THR B 193 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP B 162 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.590A  pdb=" N   LYS B  11 " --> pdb=" O   VAL B  19 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL B  19 " --> pdb=" O   LYS B  11 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   TYR B  13 " --> pdb=" O   ARG B  17 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ARG B  17 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  G

    165 hydrogen bonds defined for protein.
    420 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: 1.59

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2100
        1.33 -     1.45: 1009
        1.45 -     1.57: 4213
        1.57 -     1.69: 2
        1.69 -     1.81: 82
  Bond restraints: 7406
  Sorted by residual:
  bond pdb=" C11 PGT F 401 "
       pdb=" O3  PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.452 -0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" C31 PGT F 401 "
       pdb=" O2  PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.331  1.450 -0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" C   LEU F 300 "
       pdb=" N   PRO F 301 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.65e+00
  bond pdb=" O3P PGT F 401 "
       pdb=" P   PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.640  1.603  0.037 2.00e-02 2.50e+03 3.50e+00
  bond pdb=" O4P PGT F 401 "
       pdb=" P   PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.641  1.606  0.035 2.00e-02 2.50e+03 3.06e+00
  ... (remaining 7401 not shown)

  Histogram of bond angle deviations from ideal:
       99.45 -   106.35: 217
      106.35 -   113.26: 4070
      113.26 -   120.17: 2817
      120.17 -   127.08: 2842
      127.08 -   133.98: 77
  Bond angle restraints: 10023
  Sorted by residual:
  angle pdb=" N   VAL B 230 "
        pdb=" CA  VAL B 230 "
        pdb=" C   VAL B 230 "
      ideal   model   delta    sigma   weight residual
     113.71  106.45    7.26 9.50e-01 1.11e+00 5.84e+01
  angle pdb=" N   ILE A 171 "
        pdb=" CA  ILE A 171 "
        pdb=" C   ILE A 171 "
      ideal   model   delta    sigma   weight residual
     111.91  105.59    6.32 8.90e-01 1.26e+00 5.04e+01
  angle pdb=" N   ILE B 216 "
        pdb=" CA  ILE B 216 "
        pdb=" C   ILE B 216 "
      ideal   model   delta    sigma   weight residual
     112.43  107.05    5.38 9.20e-01 1.18e+00 3.42e+01
  angle pdb=" N   VAL A 230 "
        pdb=" CA  VAL A 230 "
        pdb=" C   VAL A 230 "
      ideal   model   delta    sigma   weight residual
     112.80  106.98    5.82 1.15e+00 7.56e-01 2.56e+01
  angle pdb=" C   LEU F 266 "
        pdb=" N   ASN F 267 "
        pdb=" CA  ASN F 267 "
      ideal   model   delta    sigma   weight residual
     121.54  130.54   -9.00 1.91e+00 2.74e-01 2.22e+01
  ... (remaining 10018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.94: 4316
       25.94 -    51.88: 164
       51.88 -    77.82: 11
       77.82 -   103.76: 0
      103.76 -   129.70: 1
  Dihedral angle restraints: 4492
    sinusoidal: 1817
      harmonic: 2675
  Sorted by residual:
  dihedral pdb=" CA  ASN F 290 "
           pdb=" C   ASN F 290 "
           pdb=" N   PRO F 291 "
           pdb=" CA  PRO F 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.24  -32.76     0      5.00e+00 4.00e-02 4.29e+01
  dihedral pdb=" CA  PHE B  90 "
           pdb=" C   PHE B  90 "
           pdb=" N   ARG B  91 "
           pdb=" CA  ARG B  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.88  -26.12     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  PHE G 280 "
           pdb=" C   PHE G 280 "
           pdb=" N   GLN G 281 "
           pdb=" CA  GLN G 281 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.07   25.93     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 4489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1074
       0.090 -    0.179: 116
       0.179 -    0.269: 11
       0.269 -    0.358: 3
       0.358 -    0.448: 1
  Chirality restraints: 1205
  Sorted by residual:
  chirality pdb=" CB  ILE A 105 "
            pdb=" CA  ILE A 105 "
            pdb=" CG1 ILE A 105 "
            pdb=" CG2 ILE A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.45 2.00e-01 2.50e+01 5.01e+00
  chirality pdb=" CB  ILE A  62 "
            pdb=" CA  ILE A  62 "
            pdb=" CG1 ILE A  62 "
            pdb=" CG2 ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" CB  VAL G 258 "
            pdb=" CA  VAL G 258 "
            pdb=" CG1 VAL G 258 "
            pdb=" CG2 VAL G 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.95e+00
  ... (remaining 1202 not shown)

  Planarity restraints: 1246
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 284 "   -0.045 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO F 285 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO F 285 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO F 285 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY G 327 "    0.043 5.00e-02 4.00e+02   6.50e-02 6.76e+00
        pdb=" N   PRO G 328 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO G 328 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO G 328 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G 335 "    0.043 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO G 336 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO G 336 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G 336 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1243 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 67
        2.62 -     3.19: 6103
        3.19 -     3.76: 10784
        3.76 -     4.33: 14416
        4.33 -     4.90: 22472
  Nonbonded interactions: 53842
  Sorted by model distance:
  nonbonded pdb=" O1P PGT F 401 "
            pdb=" O5  PGT F 401 "
     model   vdw
     2.053 2.440
  nonbonded pdb=" OG1 THR A 220 "
            pdb=" OE1 GLU A 223 "
     model   vdw
     2.270 2.440
  nonbonded pdb=" OH  TYR A  96 "
            pdb=" OE1 GLU A 115 "
     model   vdw
     2.342 2.440
  nonbonded pdb=" O   SER A  88 "
            pdb=" NH2 ARG A 150 "
     model   vdw
     2.352 2.520
  nonbonded pdb=" OE2 GLU F  82 "
            pdb=" NH1 ARG B  91 "
     model   vdw
     2.353 2.520
  ... (remaining 53837 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  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:          1.990
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     22.900
  Find NCS groups from input model:        0.340
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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      :  0.006   0.125   7406  Z= 0.381
  Angle     :  1.187  13.614  10023  Z= 0.592
  Chirality :  0.062   0.448   1205
  Planarity :  0.008   0.067   1246
  Dihedral  : 12.825 129.702   2760
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  9.29 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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: -5.97 (0.19), residues: 911
  helix: -4.39 (0.11), residues: 436
  sheet: -3.55 (0.43), residues: 78
  loop : -3.37 (0.25), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP G 276 
   HIS   0.009   0.001   HIS F  89 
   PHE   0.039   0.003   PHE G  67 
   TYR   0.039   0.002   TYR F  80 
   ARG   0.005   0.001   ARG B 143 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 373
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 374
  average time/residue: 0.2067
  time to fit residues: 99.9909
Evaluate side-chains
  251 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.870 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1645
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 69 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0020
   chunk 47 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    0.2980
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  85 GLN
B  73 HIS
B  85 GLN
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7406  Z= 0.173
  Angle     :  0.707  11.661  10023  Z= 0.350
  Chirality :  0.044   0.222   1205
  Planarity :  0.006   0.048   1246
  Dihedral  :  9.092 116.194   1050
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.83 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.64 (0.23), residues: 911
  helix: -3.17 (0.19), residues: 432
  sheet: -3.12 (0.49), residues: 68
  loop : -2.86 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP G 354 
   HIS   0.002   0.001   HIS B 129 
   PHE   0.036   0.002   PHE G  67 
   TYR   0.020   0.001   TYR G 257 
   ARG   0.004   0.000   ARG B  16 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 327
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 329
  average time/residue: 0.1818
  time to fit residues: 80.4151
Evaluate side-chains
  252 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.870 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2092
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 56 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 74 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 GLN
B  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7406  Z= 0.243
  Angle     :  0.708   9.457  10023  Z= 0.351
  Chirality :  0.045   0.221   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  8.647 107.025   1050
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.25), residues: 911
  helix: -2.58 (0.21), residues: 456
  sheet: -2.90 (0.49), residues: 68
  loop : -2.63 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP G 354 
   HIS   0.004   0.001   HIS F  89 
   PHE   0.029   0.002   PHE G  67 
   TYR   0.025   0.001   TYR B  82 
   ARG   0.004   0.000   ARG B 106 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1799
  time to fit residues: 70.0432
Evaluate side-chains
  244 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.857 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1542
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 83 optimal weight:    0.4980
   chunk 88 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0570
   chunk 23 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7406  Z= 0.164
  Angle     :  0.681  10.976  10023  Z= 0.329
  Chirality :  0.044   0.231   1205
  Planarity :  0.005   0.046   1246
  Dihedral  :  8.028 102.907   1050
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.26), residues: 911
  helix: -2.21 (0.22), residues: 467
  sheet: -2.43 (0.52), residues: 68
  loop : -2.46 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP G 354 
   HIS   0.002   0.000   HIS B  73 
   PHE   0.038   0.001   PHE G  67 
   TYR   0.024   0.001   TYR F  80 
   ARG   0.003   0.000   ARG B  75 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 310
  average time/residue: 0.1939
  time to fit residues: 81.0315
Evaluate side-chains
  252 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.853 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1571
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7406  Z= 0.173
  Angle     :  0.668  10.614  10023  Z= 0.323
  Chirality :  0.043   0.235   1205
  Planarity :  0.005   0.045   1246
  Dihedral  :  7.717  98.047   1050
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.16 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.26), residues: 911
  helix: -1.87 (0.23), residues: 459
  sheet: -2.09 (0.56), residues: 68
  loop : -2.39 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP F 268 
   HIS   0.003   0.000   HIS F  89 
   PHE   0.025   0.001   PHE G  67 
   TYR   0.020   0.001   TYR B  13 
   ARG   0.005   0.000   ARG B 150 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 293
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 293
  average time/residue: 0.1781
  time to fit residues: 70.0194
Evaluate side-chains
  239 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.785 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0661
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0770
   chunk 46 optimal weight:    5.9990
   chunk 85 optimal weight:    0.5980
   overall best weight:    1.5344

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

Flipped N/Q/H residues before XYZ refinement:
F 128 GLN
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.4712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7406  Z= 0.215
  Angle     :  0.693  10.538  10023  Z= 0.336
  Chirality :  0.045   0.245   1205
  Planarity :  0.005   0.045   1246
  Dihedral  :  7.687  93.499   1050
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.27), residues: 911
  helix: -1.69 (0.23), residues: 459
  sheet: -2.05 (0.56), residues: 68
  loop : -2.30 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP F 268 
   HIS   0.004   0.001   HIS F  89 
   PHE   0.026   0.002   PHE G 319 
   TYR   0.016   0.001   TYR B  82 
   ARG   0.003   0.000   ARG B 150 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.946 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.1939
  time to fit residues: 70.5073
Evaluate side-chains
  232 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.846 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2279
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 88 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0010
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.8788

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

Flipped N/Q/H residues before XYZ refinement:
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7406  Z= 0.177
  Angle     :  0.686  10.347  10023  Z= 0.329
  Chirality :  0.044   0.207   1205
  Planarity :  0.005   0.054   1246
  Dihedral  :  7.533  91.947   1050
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.27), residues: 911
  helix: -1.51 (0.24), residues: 456
  sheet: -1.91 (0.62), residues: 58
  loop : -2.12 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP F 268 
   HIS   0.003   0.001   HIS B  73 
   PHE   0.018   0.001   PHE A 165 
   TYR   0.015   0.001   TYR B  82 
   ARG   0.009   0.000   ARG B 150 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1679
  time to fit residues: 64.6169
Evaluate side-chains
  236 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.754 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0236
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 80 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0670
   chunk 82 optimal weight:    6.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
F 128 GLN
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.5019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7406  Z= 0.221
  Angle     :  0.709   9.391  10023  Z= 0.345
  Chirality :  0.045   0.178   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  7.589  88.723   1050
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.27), residues: 911
  helix: -1.40 (0.24), residues: 455
  sheet: -1.94 (0.59), residues: 68
  loop : -2.10 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP F 268 
   HIS   0.003   0.001   HIS B  73 
   PHE   0.017   0.002   PHE G 295 
   TYR   0.014   0.001   TYR B  82 
   ARG   0.003   0.000   ARG B 150 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.866 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.1817
  time to fit residues: 64.5999
Evaluate side-chains
  228 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.888 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1893
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0370
   chunk 74 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0170
   chunk 87 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.8102

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

Flipped N/Q/H residues before XYZ refinement:
F 128 GLN
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7406  Z= 0.236
  Angle     :  0.711   9.727  10023  Z= 0.344
  Chirality :  0.045   0.171   1205
  Planarity :  0.005   0.052   1246
  Dihedral  :  7.597  85.821   1050
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.27), residues: 911
  helix: -1.39 (0.24), residues: 459
  sheet: -1.92 (0.60), residues: 68
  loop : -2.15 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP G 123 
   HIS   0.004   0.001   HIS F  89 
   PHE   0.018   0.002   PHE G 295 
   TYR   0.018   0.001   TYR F   6 
   ARG   0.003   0.000   ARG B 106 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.897 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.1827
  time to fit residues: 66.2014
Evaluate side-chains
  229 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.847 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1850
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0070
   chunk 77 optimal weight:    0.0870
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** F  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  73 HIS
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.5309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7406  Z= 0.166
  Angle     :  0.703  10.392  10023  Z= 0.337
  Chirality :  0.043   0.157   1205
  Planarity :  0.005   0.044   1246
  Dihedral  :  7.373  85.345   1050
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.28), residues: 911
  helix: -1.28 (0.25), residues: 459
  sheet: -1.78 (0.65), residues: 58
  loop : -1.94 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP F 268 
   HIS   0.003   0.001   HIS A  73 
   PHE   0.019   0.001   PHE A 165 
   TYR   0.008   0.001   TYR F  80 
   ARG   0.003   0.000   ARG B  75 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1698
  time to fit residues: 61.1108
Evaluate side-chains
  229 residues out of total 786 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.811 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1518
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0970
   chunk 20 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0770
   chunk 30 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0000
   chunk 64 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.0344

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

Flipped N/Q/H residues before XYZ refinement:
** F  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 128 GLN
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  85 GLN
B   8 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.137697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.112472 restraints weight = 12360.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.115030 restraints weight = 8102.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.116629 restraints weight = 6068.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.5384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7406  Z= 0.185
  Angle     :  0.712  10.114  10023  Z= 0.342
  Chirality :  0.043   0.186   1205
  Planarity :  0.005   0.053   1246
  Dihedral  :  7.342  84.023   1050
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.13 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.28), residues: 911
  helix: -1.17 (0.25), residues: 455
  sheet: -1.82 (0.64), residues: 58
  loop : -1.93 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP F 268 
   HIS   0.005   0.001   HIS B  73 
   PHE   0.021   0.001   PHE G 295 
   TYR   0.018   0.001   TYR F  80 
   ARG   0.003   0.000   ARG B  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2024.70 seconds
wall clock time: 36 minutes 56.29 seconds (2216.29 seconds total)