Starting phenix.real_space_refine
on Thu Sep 18 07:24:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uzw_26920/09_2025/7uzw_26920.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uzw_26920/09_2025/7uzw_26920.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2025/7uzw_26920.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2025/7uzw_26920.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2025/7uzw_26920.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2025/7uzw_26920.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.030
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      31      5.49       5
     S      32      5.16       5
     C    9199      2.51       5
     N    2538      2.21       5
     O    2954      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14754
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1620
          Classifications: {'peptide': 204}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 199}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1531
          Classifications: {'peptide': 193}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 188}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1620
          Classifications: {'peptide': 204}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 199}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1620
          Classifications: {'peptide': 204}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 199}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1458
          Classifications: {'peptide': 184}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 180}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 2355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2355
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 3886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3886
          Classifications: {'peptide': 478}
          Link IDs: {'PTRANS': 5, 'TRANS': 472}
          Chain breaks: 6
    Chain: "G"
      Number of atoms: 664
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 664
          Classifications: {'RNA': 31}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 11, 'rna3p': 19}
  Time building chain proxies: 3.81, per 1000 atoms: 0.26
  Number of scatterers: 14754
  At special positions: 0
  Unit cell: (92.4, 119.9, 203.5, 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      32     16.00
     P      31     15.00
     O    2954      8.00
     N    2538      7.00
     C    9199      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS F 410 " - pdb=" SG  CYS F 426 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 694.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3250

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 21 sheets defined
      39.8% alpha, 21.1% beta
      0 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 63
      removed outlier: 3.844A  pdb=" N   ILE A  51 " --> pdb=" O   PRO A  47 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A  63 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 72
      removed outlier: 3.610A  pdb=" N   HIS A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 84
    Processing helix  chain 'A' and resid 104 through 115
    Processing helix  chain 'A' and resid 161 through 178
    Processing helix  chain 'B' and resid 47 through 63
      removed outlier: 3.629A  pdb=" N   ILE B  51 " --> pdb=" O   PRO B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'B' and resid 104 through 115
    Processing helix  chain 'B' and resid 158 through 160
      No H-bonds generated for 'chain 'B' and resid 158 through 160'
    Processing helix  chain 'B' and resid 161 through 178
    Processing helix  chain 'C' and resid 47 through 63
      removed outlier: 3.899A  pdb=" N   ILE C  51 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE C  63 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 72
      removed outlier: 3.996A  pdb=" N   HIS C  72 " --> pdb=" O   LYS C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 84
    Processing helix  chain 'C' and resid 104 through 115
    Processing helix  chain 'C' and resid 161 through 178
    Processing helix  chain 'C' and resid 184 through 188
      removed outlier: 3.630A  pdb=" N   ARG C 187 " --> pdb=" O   GLY C 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 63
      removed outlier: 3.689A  pdb=" N   ILE D  51 " --> pdb=" O   PRO D  47 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   PHE D  63 " --> pdb=" O   LEU D  59 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 73
    Processing helix  chain 'D' and resid 76 through 84
    Processing helix  chain 'D' and resid 104 through 114
    Processing helix  chain 'D' and resid 161 through 178
    Processing helix  chain 'E' and resid 47 through 63
      removed outlier: 3.753A  pdb=" N   ILE E  51 " --> pdb=" O   PRO E  47 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 73
    Processing helix  chain 'E' and resid 76 through 83
    Processing helix  chain 'E' and resid 104 through 115
    Processing helix  chain 'E' and resid 161 through 178
    Processing helix  chain 'H' and resid 31 through 47
    Processing helix  chain 'H' and resid 50 through 55
      removed outlier: 3.959A  pdb=" N   ASN H  55 " --> pdb=" O   ASP H  51 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 89 through 93
    Processing helix  chain 'H' and resid 100 through 106
    Processing helix  chain 'H' and resid 110 through 121
    Processing helix  chain 'H' and resid 168 through 183
      removed outlier: 3.504A  pdb=" N   LEU H 172 " --> pdb=" O   SER H 168 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 190 through 194
    Processing helix  chain 'H' and resid 205 through 213
    Processing helix  chain 'H' and resid 228 through 236
      removed outlier: 4.446A  pdb=" N   GLU H 233 " --> pdb=" O   LYS H 229 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   SER H 234 " --> pdb=" O   GLU H 230 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 13
      removed outlier: 3.872A  pdb=" N   LEU F  13 " --> pdb=" O   TYR F   9 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 23
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 4.175A  pdb=" N   SER F  29 " --> pdb=" O   HIS F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 32 through 42
    Processing helix  chain 'F' and resid 49 through 58
      removed outlier: 3.935A  pdb=" N   TYR F  58 " --> pdb=" O   ASP F  54 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 60 through 66
      removed outlier: 3.857A  pdb=" N   LEU F  64 " --> pdb=" O   HIS F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 87
    Processing helix  chain 'F' and resid 154 through 170
    Processing helix  chain 'F' and resid 177 through 190
    Processing helix  chain 'F' and resid 205 through 227
      removed outlier: 3.614A  pdb=" N   HIS F 209 " --> pdb=" O   SER F 205 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN F 227 " --> pdb=" O   TYR F 223 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 231 through 237
    Processing helix  chain 'F' and resid 245 through 249
      removed outlier: 3.525A  pdb=" N   GLN F 248 " --> pdb=" O   SER F 245 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 261 through 267
    Processing helix  chain 'F' and resid 279 through 300
    Processing helix  chain 'F' and resid 303 through 305
      No H-bonds generated for 'chain 'F' and resid 303 through 305'
    Processing helix  chain 'F' and resid 322 through 344
    Processing helix  chain 'F' and resid 358 through 363
      removed outlier: 3.784A  pdb=" N   LEU F 362 " --> pdb=" O   SER F 358 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   MET F 363 " --> pdb=" O   GLY F 359 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 358 through 363'
    Processing helix  chain 'F' and resid 367 through 386
      removed outlier: 4.263A  pdb=" N   THR F 371 " --> pdb=" O   GLY F 367 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 397
    Processing helix  chain 'F' and resid 423 through 437
    Processing helix  chain 'F' and resid 462 through 472
    Processing helix  chain 'F' and resid 535 through 542
      removed outlier: 3.680A  pdb=" N   THR F 539 " --> pdb=" O   ASN F 535 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 550 through 567
      removed outlier: 3.634A  pdb=" N   THR F 554 " --> pdb=" O   SER F 550 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 567 through 574
    Processing helix  chain 'F' and resid 595 through 612
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.148A  pdb=" N   VAL A 151 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA A 101 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   ASP A 149 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   PHE A 103 " --> pdb=" O   GLU A 147 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   GLU A 147 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   SER A   3 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LYS A   4 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   THR A  10 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   ASP A 196 " --> pdb=" O   THR A  10 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   GLU A  12 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   PHE A 194 " --> pdb=" O   GLU A  12 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   VAL A  14 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   ILE A 192 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 127
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 3.539A  pdb=" N   PHE B 102 " --> pdb=" O   ASP B 149 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98
      removed outlier: 4.454A  pdb=" N   SER B   3 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   LYS B   4 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   THR B 201 " --> pdb=" O   LYS B   4 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LYS B   6 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   ILE B 199 " --> pdb=" O   LYS B   6 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   SER B   8 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   THR B 197 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127
    Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46
      removed outlier: 3.750A  pdb=" N   PHE C 102 " --> pdb=" O   ASP C 149 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP C 149 " --> pdb=" O   PHE C 102 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46
      removed outlier: 3.750A  pdb=" N   PHE C 102 " --> pdb=" O   ASP C 149 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP C 149 " --> pdb=" O   PHE C 102 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   SER C   3 " --> pdb=" O   VAL C 156 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LYS C   4 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   THR C  10 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   ASP C 196 " --> pdb=" O   THR C  10 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLU C  12 " --> pdb=" O   PHE C 194 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   PHE C 194 " --> pdb=" O   GLU C  12 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127
    Processing sheet with id=AA9, first strand: chain 'D' and resid 96 through 103
      removed outlier: 5.190A  pdb=" N   VAL D 151 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ALA D 101 " --> pdb=" O   ASP D 149 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ASP D 149 " --> pdb=" O   ALA D 101 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   PHE D 103 " --> pdb=" O   GLU D 147 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   GLU D 147 " --> pdb=" O   PHE D 103 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   SER D   3 " --> pdb=" O   VAL D 156 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   LYS D   4 " --> pdb=" O   THR D 201 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   THR D 201 " --> pdb=" O   LYS D   4 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   LYS D   6 " --> pdb=" O   ILE D 199 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE D 199 " --> pdb=" O   LYS D   6 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   SER D   8 " --> pdb=" O   THR D 197 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   THR D 197 " --> pdb=" O   SER D   8 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 119 through 127
    Processing sheet with id=AB2, first strand: chain 'E' and resid 96 through 98
      removed outlier: 4.203A  pdb=" N   SER E   3 " --> pdb=" O   VAL E 156 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   SER E   8 " --> pdb=" O   THR E 197 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   THR E 197 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103
      removed outlier: 3.990A  pdb=" N   PHE E 102 " --> pdb=" O   ASP E 149 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   SER E   3 " --> pdb=" O   VAL E 156 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   LYS E   4 " --> pdb=" O   VAL E 202 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59
      removed outlier: 3.893A  pdb=" N   ILE H  58 " --> pdb=" O   LYS H 166 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS H 166 " --> pdb=" O   ILE H  58 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR H  71 " --> pdb=" O   PRO H  64 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 59
      removed outlier: 3.893A  pdb=" N   ILE H  58 " --> pdb=" O   LYS H 166 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS H 166 " --> pdb=" O   ILE H  58 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 131
    Processing sheet with id=AB7, first strand: chain 'H' and resid 220 through 221
    Processing sheet with id=AB8, first strand: chain 'H' and resid 239 through 240
    Processing sheet with id=AB9, first strand: chain 'H' and resid 243 through 246
      removed outlier: 3.591A  pdb=" N   SER H 267 " --> pdb=" O   THR H 244 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 283 through 284
    Processing sheet with id=AC2, first strand: chain 'F' and resid 307 through 311
      removed outlier: 5.899A  pdb=" N   LEU F 307 " --> pdb=" O   LEU F 318 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   LEU F 318 " --> pdb=" O   LEU F 307 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 450 through 452
      removed outlier: 3.958A  pdb=" N   LYS F 456 " --> pdb=" O   MET F 452 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ILE F 478 " --> pdb=" O   THR F 492 " (cutoff:3.500A)

    636 hydrogen bonds defined for protein.
    1833 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 2.54

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 4805
        1.34 -     1.47: 3719
        1.47 -     1.60: 6459
        1.60 -     1.73: 33
        1.73 -     1.85: 57
  Bond restraints: 15073
  Sorted by residual:
  bond pdb=" C1'   U G  24 "
       pdb=" N1    U G  24 "
    ideal  model  delta    sigma   weight residual
    1.480  1.563 -0.083 1.50e-02 4.44e+03 3.04e+01
  bond pdb=" N   LEU A 130 "
       pdb=" CA  LEU A 130 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.043 1.29e-02 6.01e+03 1.11e+01
  bond pdb=" N   SER B  33 "
       pdb=" CA  SER B  33 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.035 1.41e-02 5.03e+03 5.99e+00
  bond pdb=" N   ARG D 137 "
       pdb=" CA  ARG D 137 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.029 1.25e-02 6.40e+03 5.38e+00
  bond pdb=" CB  CYS F 214 "
       pdb=" SG  CYS F 214 "
    ideal  model  delta    sigma   weight residual
    1.808  1.738  0.070 3.30e-02 9.18e+02 4.54e+00
  ... (remaining 15068 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 19916
        2.09 -     4.18: 445
        4.18 -     6.28: 47
        6.28 -     8.37: 7
        8.37 -    10.46: 4
  Bond angle restraints: 20419
  Sorted by residual:
  angle pdb=" O4'   G G  15 "
        pdb=" C1'   G G  15 "
        pdb=" N9    G G  15 "
      ideal   model   delta    sigma   weight residual
     108.20  116.11   -7.91 1.50e+00 4.44e-01 2.78e+01
  angle pdb=" N   ARG F 279 "
        pdb=" CA  ARG F 279 "
        pdb=" C   ARG F 279 "
      ideal   model   delta    sigma   weight residual
     114.56  108.85    5.71 1.27e+00 6.20e-01 2.02e+01
  angle pdb=" C3'   G G  15 "
        pdb=" O3'   G G  15 "
        pdb=" P     C G  16 "
      ideal   model   delta    sigma   weight residual
     120.20  126.41   -6.21 1.50e+00 4.44e-01 1.71e+01
  angle pdb=" CB  MET F 468 "
        pdb=" CG  MET F 468 "
        pdb=" SD  MET F 468 "
      ideal   model   delta    sigma   weight residual
     112.70  123.16  -10.46 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" N   SER F 440 "
        pdb=" CA  SER F 440 "
        pdb=" C   SER F 440 "
      ideal   model   delta    sigma   weight residual
     110.61  114.87   -4.26 1.25e+00 6.40e-01 1.16e+01
  ... (remaining 20414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.05: 8853
       35.05 -    70.09: 192
       70.09 -   105.14: 10
      105.14 -   140.19: 2
      140.19 -   175.23: 3
  Dihedral angle restraints: 9060
    sinusoidal: 4003
      harmonic: 5057
  Sorted by residual:
  dihedral pdb=" O4'   C G  10 "
           pdb=" C1'   C G  10 "
           pdb=" N1    C G  10 "
           pdb=" C2    C G  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -3.18 -156.82     1      1.50e+01 4.44e-03 8.19e+01
  dihedral pdb=" O4'   C G   2 "
           pdb=" C1'   C G   2 "
           pdb=" N1    C G   2 "
           pdb=" C2    C G   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   43.41 -171.41     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" O4'   C G   8 "
           pdb=" C1'   C G   8 "
           pdb=" N1    C G   8 "
           pdb=" C2    C G   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -41.40 -118.60     1      1.50e+01 4.44e-03 6.31e+01
  ... (remaining 9057 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1826
       0.060 -    0.120: 371
       0.120 -    0.181: 61
       0.181 -    0.241: 7
       0.241 -    0.301: 2
  Chirality restraints: 2267
  Sorted by residual:
  chirality pdb=" C1'   G G  15 "
            pdb=" O4'   G G  15 "
            pdb=" C2'   G G  15 "
            pdb=" N9    G G  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.14    0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  SER B  33 "
            pdb=" N   SER B  33 "
            pdb=" C   SER B  33 "
            pdb=" CB  SER B  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  ARG D 137 "
            pdb=" N   ARG D 137 "
            pdb=" C   ARG D 137 "
            pdb=" CB  ARG D 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 2264 not shown)

  Planarity restraints: 2531
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G G  15 "    0.043 2.00e-02 2.50e+03   2.14e-02 1.38e+01
        pdb=" N9    G G  15 "   -0.059 2.00e-02 2.50e+03
        pdb=" C8    G G  15 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G G  15 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    G G  15 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    G G  15 "    0.008 2.00e-02 2.50e+03
        pdb=" O6    G G  15 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    G G  15 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G G  15 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2    G G  15 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G G  15 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    G G  15 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 135 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO C 136 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 136 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 136 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  46 "    0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO E  47 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E  47 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E  47 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2528 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 99
        2.54 -     3.13: 11025
        3.13 -     3.72: 20974
        3.72 -     4.31: 29287
        4.31 -     4.90: 49855
  Nonbonded interactions: 111240
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B  57 "
            pdb=" O2    C G   8 "
     model   vdw
     1.945 3.120
  nonbonded pdb=" O   ILE A  19 "
            pdb=" O2'   G G  15 "
     model   vdw
     1.982 3.040
  nonbonded pdb=" OG1 THR B 126 "
            pdb=" OD1 ASN B 135 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" OH  TYR H 148 "
            pdb=" O2'   A G   7 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" O   SER F  11 "
            pdb=" ND1 HIS F  14 "
     model   vdw
     2.137 3.120
  ... (remaining 111235 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 63 or resid 76 through 120 or resid 141 through  \ 
214))
  selection = (chain 'B' and (resid 2 through 23 or resid 33 through 120 or resid 141 through  \ 
214))
  selection = (chain 'C' and (resid 2 through 63 or resid 76 through 120 or resid 141 through  \ 
214))
  selection = (chain 'D' and (resid 2 through 63 or resid 76 through 120 or resid 141 through  \ 
214))
  selection = (chain 'E' and (resid 2 through 63 or resid 76 through 214))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.220
  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:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.140
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
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   0.083  15074  Z= 0.293
  Angle     :  0.767  10.461  20421  Z= 0.434
  Chirality :  0.050   0.301   2267
  Planarity :  0.004   0.054   2531
  Dihedral  : 14.769 175.232   5807
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.75 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.39 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.19), residues: 1718
  helix:  0.56 (0.21), residues: 632
  sheet:  0.13 (0.28), residues: 343
  loop : -1.98 (0.20), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D 187 
 TYR   0.021   0.002   TYR C 206 
 PHE   0.025   0.002   PHE C 166 
 TRP   0.009   0.001   TRP F 339 
 HIS   0.018   0.001   HIS D  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 (15073)
  covalent geometry    : angle       0.76608 (20419)
  SS BOND              : bond        0.00504 (    1)
  SS BOND              : angle       3.27684 (    2)
  hydrogen bonds       : bond        0.13583 (  623)
  hydrogen bonds       : angle       6.07084 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 275
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 276
  average time/residue: 0.1704
  time to fit residues: 64.5541
Evaluate side-chains
  119 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  40 GLN
E  69 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 110 HIS
** H  17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  45 GLN
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 HIS
F 183 GLN
F 295 GLN
F 493 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.059718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.044638 restraints weight = 78818.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.046044 restraints weight = 43138.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.046994 restraints weight = 29549.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.047642 restraints weight = 23106.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.048070 restraints weight = 19525.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  15074  Z= 0.162
  Angle     :  0.660  10.369  20421  Z= 0.355
  Chirality :  0.045   0.209   2267
  Planarity :  0.004   0.049   2531
  Dihedral  : 14.099 179.535   2344
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.51 %
    Favored  : 89.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.20), residues: 1718
  helix:  1.16 (0.20), residues: 647
  sheet:  0.51 (0.29), residues: 334
  loop : -1.76 (0.20), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 187 
 TYR   0.013   0.001   TYR F  21 
 PHE   0.017   0.001   PHE E 148 
 TRP   0.021   0.002   TRP H  52 
 HIS   0.018   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (15073)
  covalent geometry    : angle       0.65981 (20419)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       2.31399 (    2)
  hydrogen bonds       : bond        0.04447 (  623)
  hydrogen bonds       : angle       5.00307 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  147 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8162 (mm-30)
REVERT: H  129 GLN cc_start: 0.7687 (mp10) cc_final: 0.7482 (mp10)
REVERT: F    8 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.9343 (mtm)
REVERT: F  184 TRP cc_start: 0.9028 (t60) cc_final: 0.8780 (t60)
REVERT: F  290 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8991 (tp30)
REVERT: F  331 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8612 (tm-30)
REVERT: F  565 PHE cc_start: 0.9176 (m-80) cc_final: 0.8579 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 154
  average time/residue: 0.1493
  time to fit residues: 33.1649
Evaluate side-chains
  118 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   90 ASN
Chi-restraints excluded: chain E residue  193 GLN
Chi-restraints excluded: chain E residue  202 VAL
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue    8 MET
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 126 optimal weight:    0.9990
   chunk 145 optimal weight:    1.9990
   chunk 170 optimal weight:    9.9990
   chunk 112 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 113 GLN
C  40 GLN
D 138 GLN
E 110 HIS
** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  38 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 = 0.3468 r_free = 0.3468 target = 0.057593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.042734 restraints weight = 80932.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.044129 restraints weight = 44108.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.045077 restraints weight = 30179.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.045690 restraints weight = 23376.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.045946 restraints weight = 19783.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15074  Z= 0.204
  Angle     :  0.624   9.520  20421  Z= 0.336
  Chirality :  0.044   0.293   2267
  Planarity :  0.004   0.039   2531
  Dihedral  : 14.063 175.252   2344
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.25 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.20), residues: 1718
  helix:  1.26 (0.20), residues: 648
  sheet:  0.65 (0.29), residues: 338
  loop : -1.74 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  93 
 TYR   0.019   0.001   TYR A 180 
 PHE   0.021   0.002   PHE E 148 
 TRP   0.015   0.001   TRP H  52 
 HIS   0.014   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (15073)
  covalent geometry    : angle       0.62393 (20419)
  SS BOND              : bond        0.00361 (    1)
  SS BOND              : angle       1.90256 (    2)
  hydrogen bonds       : bond        0.04374 (  623)
  hydrogen bonds       : angle       4.83947 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 95
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 TYR cc_start: 0.8812 (p90) cc_final: 0.8607 (p90)
REVERT: B  193 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7321 (tm-30)
REVERT: D  164 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8198 (p0)
REVERT: E  147 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8156 (mm-30)
REVERT: E  193 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7831 (tp40)
REVERT: H   13 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7710 (pttt)
REVERT: H  129 GLN cc_start: 0.8102 (mp10) cc_final: 0.7808 (mp10)
REVERT: F    1 MET cc_start: 0.7848 (mmt) cc_final: 0.7457 (mmt)
REVERT: F  290 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9014 (tp30)
  outliers start: 37
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1477
  time to fit residues: 27.0809
Evaluate side-chains
  108 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   90 ASN
Chi-restraints excluded: chain E residue  144 ARG
Chi-restraints excluded: chain E residue  193 GLN
Chi-restraints excluded: chain E residue  202 VAL
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  297 LEU
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 82 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.057735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.042805 restraints weight = 81032.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.044254 restraints weight = 44378.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.045197 restraints weight = 30352.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.045820 restraints weight = 23617.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.046210 restraints weight = 20010.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15074  Z= 0.151
  Angle     :  0.567  11.545  20421  Z= 0.303
  Chirality :  0.042   0.190   2267
  Planarity :  0.003   0.036   2531
  Dihedral  : 13.813 176.856   2344
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 11.41 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.20), residues: 1718
  helix:  1.53 (0.20), residues: 648
  sheet:  0.89 (0.29), residues: 324
  loop : -1.67 (0.20), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  93 
 TYR   0.016   0.001   TYR F 463 
 PHE   0.025   0.001   PHE E 148 
 TRP   0.022   0.002   TRP F 184 
 HIS   0.007   0.001   HIS D  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (15073)
  covalent geometry    : angle       0.56662 (20419)
  SS BOND              : bond        0.00330 (    1)
  SS BOND              : angle       1.58157 (    2)
  hydrogen bonds       : bond        0.03771 (  623)
  hydrogen bonds       : angle       4.65121 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 ASP cc_start: 0.8052 (t0) cc_final: 0.7813 (t0)
REVERT: B  193 GLN cc_start: 0.7464 (tm-30) cc_final: 0.7139 (tm-30)
REVERT: D  164 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8285 (p0)
REVERT: H   13 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7734 (pttt)
REVERT: F    1 MET cc_start: 0.7953 (mmt) cc_final: 0.7508 (mmt)
REVERT: F  257 MET cc_start: 0.8256 (mpp) cc_final: 0.7901 (mpp)
REVERT: F  290 GLU cc_start: 0.9378 (mm-30) cc_final: 0.8964 (tp30)
  outliers start: 36
  outliers final: 22
  residues processed: 124
  average time/residue: 0.1337
  time to fit residues: 24.8844
Evaluate side-chains
  108 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 PHE
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   90 ASN
Chi-restraints excluded: chain E residue  144 ARG
Chi-restraints excluded: chain E residue  193 GLN
Chi-restraints excluded: chain E residue  202 VAL
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain H residue  163 PHE
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 149 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 169 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 68 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 136 optimal weight:    8.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
E  72 HIS
H 214 GLN
** F  38 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 = 0.3471 r_free = 0.3471 target = 0.057605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.042722 restraints weight = 81493.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.044178 restraints weight = 44582.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.045121 restraints weight = 30516.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.045753 restraints weight = 23781.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.046017 restraints weight = 20135.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15074  Z= 0.136
  Angle     :  0.563   8.601  20421  Z= 0.300
  Chirality :  0.042   0.187   2267
  Planarity :  0.003   0.048   2531
  Dihedral  : 13.661 176.867   2344
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.28 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.20), residues: 1718
  helix:  1.67 (0.21), residues: 648
  sheet:  0.97 (0.29), residues: 324
  loop : -1.61 (0.20), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E  37 
 TYR   0.012   0.001   TYR A 180 
 PHE   0.020   0.001   PHE E 152 
 TRP   0.026   0.002   TRP F 184 
 HIS   0.006   0.001   HIS D  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (15073)
  covalent geometry    : angle       0.56320 (20419)
  SS BOND              : bond        0.00292 (    1)
  SS BOND              : angle       1.41909 (    2)
  hydrogen bonds       : bond        0.03629 (  623)
  hydrogen bonds       : angle       4.58990 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 89
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  193 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7255 (tm-30)
REVERT: D  164 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8382 (p0)
REVERT: E   35 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7631 (p)
REVERT: E   37 ARG cc_start: 0.9123 (mtt90) cc_final: 0.8830 (mtt90)
REVERT: E  147 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8202 (mt-10)
REVERT: H   13 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7736 (pttt)
REVERT: F    1 MET cc_start: 0.8059 (mmt) cc_final: 0.7670 (mmt)
REVERT: F  264 ASP cc_start: 0.8899 (t0) cc_final: 0.8684 (t0)
REVERT: F  290 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8963 (tp30)
  outliers start: 30
  outliers final: 20
  residues processed: 112
  average time/residue: 0.1298
  time to fit residues: 22.0046
Evaluate side-chains
  107 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  144 ARG
Chi-restraints excluded: chain E residue  193 GLN
Chi-restraints excluded: chain E residue  202 VAL
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain H residue  163 PHE
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 165 optimal weight:    6.9990
   chunk 163 optimal weight:    6.9990
   chunk 142 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 82 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 139 optimal weight:    0.2980
   chunk 22 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
C 174 HIS
E 189 ASN
H 174 HIS
** F  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.054068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.039624 restraints weight = 84845.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.040947 restraints weight = 46810.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.041809 restraints weight = 32393.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.042373 restraints weight = 25448.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.042719 restraints weight = 21727.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
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      :  0.007   0.070  15074  Z= 0.336
  Angle     :  0.728   9.939  20421  Z= 0.387
  Chirality :  0.046   0.223   2267
  Planarity :  0.004   0.037   2531
  Dihedral  : 13.717 171.824   2344
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.25 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.19), residues: 1718
  helix:  1.01 (0.20), residues: 647
  sheet:  0.65 (0.28), residues: 329
  loop : -1.77 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 141 
 TYR   0.031   0.002   TYR A 180 
 PHE   0.019   0.002   PHE F  28 
 TRP   0.032   0.002   TRP F 184 
 HIS   0.010   0.001   HIS D  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00723 (15073)
  covalent geometry    : angle       0.72737 (20419)
  SS BOND              : bond        0.00658 (    1)
  SS BOND              : angle       1.78389 (    2)
  hydrogen bonds       : bond        0.04869 (  623)
  hydrogen bonds       : angle       5.06833 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 ASP cc_start: 0.8607 (t0) cc_final: 0.8374 (t0)
REVERT: B   55 MET cc_start: 0.8812 (mtp) cc_final: 0.8604 (mmt)
REVERT: C   67 MET cc_start: 0.8461 (tmm) cc_final: 0.7890 (tmm)
REVERT: D   67 MET cc_start: 0.8220 (pmm) cc_final: 0.7648 (pmm)
REVERT: D  164 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8214 (p0)
REVERT: E   37 ARG cc_start: 0.9071 (mtt90) cc_final: 0.8824 (mtm-85)
REVERT: E  147 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8248 (mt-10)
REVERT: H   13 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8101 (pttt)
REVERT: H   50 THR cc_start: 0.9578 (OUTLIER) cc_final: 0.9318 (t)
REVERT: H  129 GLN cc_start: 0.8062 (mp10) cc_final: 0.7756 (mp10)
REVERT: F  264 ASP cc_start: 0.8869 (t0) cc_final: 0.8663 (t0)
REVERT: F  290 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9080 (tp30)
  outliers start: 32
  outliers final: 19
  residues processed: 109
  average time/residue: 0.1280
  time to fit residues: 21.3601
Evaluate side-chains
  94 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   90 ASN
Chi-restraints excluded: chain E residue  193 GLN
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  202 VAL
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain H residue  163 PHE
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0030
   chunk 62 optimal weight:    6.9990
   chunk 124 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 149 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 145 optimal weight:    0.7980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 161 GLN
** E  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.056178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.041539 restraints weight = 81490.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.042949 restraints weight = 44400.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.043875 restraints weight = 30374.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.044487 restraints weight = 23619.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.044865 restraints weight = 20007.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.5264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15074  Z= 0.121
  Angle     :  0.561   9.305  20421  Z= 0.300
  Chirality :  0.042   0.166   2267
  Planarity :  0.003   0.033   2531
  Dihedral  : 13.509 177.537   2344
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.83 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.20), residues: 1718
  helix:  1.58 (0.21), residues: 648
  sheet:  0.81 (0.29), residues: 316
  loop : -1.61 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  37 
 TYR   0.015   0.001   TYR A 180 
 PHE   0.025   0.001   PHE E 152 
 TRP   0.032   0.002   TRP F 184 
 HIS   0.008   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (15073)
  covalent geometry    : angle       0.56052 (20419)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       1.62056 (    2)
  hydrogen bonds       : bond        0.03661 (  623)
  hydrogen bonds       : angle       4.64033 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  164 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8446 (p0)
REVERT: E  147 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8207 (mt-10)
REVERT: H   13 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7582 (pttt)
REVERT: F  252 PHE cc_start: 0.8905 (p90) cc_final: 0.8611 (p90)
REVERT: F  264 ASP cc_start: 0.8889 (t0) cc_final: 0.8682 (t0)
REVERT: F  290 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9088 (tp30)
  outliers start: 24
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1269
  time to fit residues: 20.6979
Evaluate side-chains
  92 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  202 VAL
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain H residue  163 PHE
Chi-restraints excluded: chain H residue  211 LEU
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 162 optimal weight:    4.9990
   chunk 140 optimal weight:    0.0980
   chunk 143 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0170
   chunk 163 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0020
   chunk 138 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.3426

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

Flipped N/Q/H residues before XYZ refinement:
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 HIS
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  17 HIS
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.057167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.042542 restraints weight = 80670.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.043925 restraints weight = 43952.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.044859 restraints weight = 30092.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.045469 restraints weight = 23399.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.045852 restraints weight = 19809.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.5425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  15074  Z= 0.105
  Angle     :  0.589  13.655  20421  Z= 0.301
  Chirality :  0.041   0.241   2267
  Planarity :  0.003   0.031   2531
  Dihedral  : 13.390 178.196   2344
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.80 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.20), residues: 1718
  helix:  1.79 (0.21), residues: 647
  sheet:  0.87 (0.28), residues: 323
  loop : -1.60 (0.20), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  37 
 TYR   0.012   0.001   TYR F 284 
 PHE   0.014   0.001   PHE E 152 
 TRP   0.031   0.002   TRP F 184 
 HIS   0.008   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (15073)
  covalent geometry    : angle       0.58876 (20419)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       1.31016 (    2)
  hydrogen bonds       : bond        0.03345 (  623)
  hydrogen bonds       : angle       4.53270 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8391 (ttp80)
REVERT: D  164 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8507 (p0)
REVERT: E  147 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8184 (mt-10)
REVERT: H   13 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7612 (pttt)
REVERT: H  254 ASN cc_start: 0.8543 (t0) cc_final: 0.8182 (m110)
REVERT: F    8 MET cc_start: 0.9520 (mtm) cc_final: 0.8797 (mtm)
REVERT: F   41 LEU cc_start: 0.8808 (tt) cc_final: 0.8232 (mt)
REVERT: F  264 ASP cc_start: 0.8876 (t0) cc_final: 0.8663 (t0)
REVERT: F  290 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9038 (tp30)
REVERT: F  452 MET cc_start: 0.8049 (tpp) cc_final: 0.7627 (tpp)
  outliers start: 23
  outliers final: 15
  residues processed: 104
  average time/residue: 0.1316
  time to fit residues: 20.5399
Evaluate side-chains
  95 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain H residue  163 PHE
Chi-restraints excluded: chain H residue  211 LEU
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 175 optimal weight:    5.9990
   chunk 115 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 170 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 171 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  72 HIS
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.054841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.040437 restraints weight = 84092.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.041790 restraints weight = 45918.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.042665 restraints weight = 31554.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.043256 restraints weight = 24634.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.043495 restraints weight = 20897.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.5592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  15074  Z= 0.240
  Angle     :  0.674  17.349  20421  Z= 0.350
  Chirality :  0.043   0.178   2267
  Planarity :  0.004   0.063   2531
  Dihedral  : 13.436 174.093   2344
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.05 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.20), residues: 1718
  helix:  1.53 (0.20), residues: 649
  sheet:  0.73 (0.28), residues: 331
  loop : -1.61 (0.21), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  37 
 TYR   0.020   0.001   TYR F 284 
 PHE   0.017   0.002   PHE A 166 
 TRP   0.031   0.002   TRP F 184 
 HIS   0.011   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (15073)
  covalent geometry    : angle       0.67425 (20419)
  SS BOND              : bond        0.00513 (    1)
  SS BOND              : angle       1.46611 (    2)
  hydrogen bonds       : bond        0.04126 (  623)
  hydrogen bonds       : angle       4.75209 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8790 (ttp80)
REVERT: E  147 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8176 (mt-10)
REVERT: H   13 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7624 (pttt)
REVERT: H   50 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9250 (t)
REVERT: F    8 MET cc_start: 0.9522 (mtm) cc_final: 0.8749 (mtm)
REVERT: F  252 PHE cc_start: 0.9013 (p90) cc_final: 0.8726 (p90)
REVERT: F  290 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9044 (tp30)
REVERT: F  452 MET cc_start: 0.8321 (tpp) cc_final: 0.7862 (tpp)
  outliers start: 23
  outliers final: 17
  residues processed: 98
  average time/residue: 0.1414
  time to fit residues: 20.6021
Evaluate side-chains
  94 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain E residue   90 ASN
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain H residue  163 PHE
Chi-restraints excluded: chain H residue  211 LEU
Chi-restraints excluded: chain H residue  273 VAL
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 119 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 135 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 127 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0050
   chunk 74 optimal weight:    3.9990
   chunk 145 optimal weight:    0.9990
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.055621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.041159 restraints weight = 82940.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.042521 restraints weight = 45111.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.043421 restraints weight = 30907.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.043990 restraints weight = 24078.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.044410 restraints weight = 20505.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.5700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15074  Z= 0.158
  Angle     :  0.621  16.165  20421  Z= 0.323
  Chirality :  0.042   0.177   2267
  Planarity :  0.003   0.033   2531
  Dihedral  : 13.422 176.113   2344
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.12 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.20), residues: 1718
  helix:  1.61 (0.20), residues: 648
  sheet:  0.74 (0.28), residues: 318
  loop : -1.56 (0.21), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 144 
 TYR   0.057   0.001   TYR F 284 
 PHE   0.017   0.001   PHE H 121 
 TRP   0.032   0.002   TRP F 184 
 HIS   0.010   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (15073)
  covalent geometry    : angle       0.62097 (20419)
  SS BOND              : bond        0.00360 (    1)
  SS BOND              : angle       1.45404 (    2)
  hydrogen bonds       : bond        0.03730 (  623)
  hydrogen bonds       : angle       4.65575 ( 1833)

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

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

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3436 Ramachandran restraints generated.
    1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8810 (ttp80)
REVERT: D  164 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8430 (p0)
REVERT: E  147 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8150 (mt-10)
REVERT: H   13 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7612 (pttt)
REVERT: F    8 MET cc_start: 0.9509 (mtm) cc_final: 0.8746 (mtm)
REVERT: F  252 PHE cc_start: 0.8950 (p90) cc_final: 0.8624 (p90)
REVERT: F  290 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9043 (tp30)
REVERT: F  452 MET cc_start: 0.8308 (tpp) cc_final: 0.7873 (tpp)
  outliers start: 23
  outliers final: 19
  residues processed: 99
  average time/residue: 0.1427
  time to fit residues: 20.9915
Evaluate side-chains
  100 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain E residue   90 ASN
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain H residue  163 PHE
Chi-restraints excluded: chain H residue  211 LEU
Chi-restraints excluded: chain H residue  273 VAL
Chi-restraints excluded: chain F residue    2 ASN
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  432 ILE
Chi-restraints excluded: chain F residue  443 VAL
Chi-restraints excluded: chain F residue  478 ILE
Chi-restraints excluded: chain F residue  548 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 129 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 120 optimal weight:    4.9990
   chunk 163 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 122 optimal weight:    0.6980
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  97 GLN
** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.053782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.039508 restraints weight = 84314.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.040816 restraints weight = 46202.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.041684 restraints weight = 31731.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.042262 restraints weight = 24798.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.042614 restraints weight = 21024.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.5940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  15074  Z= 0.287
  Angle     :  0.728  14.954  20421  Z= 0.381
  Chirality :  0.045   0.173   2267
  Planarity :  0.004   0.041   2531
  Dihedral  : 13.555 172.409   2344
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.51 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.19), residues: 1718
  helix:  1.15 (0.20), residues: 649
  sheet:  0.66 (0.28), residues: 308
  loop : -1.73 (0.20), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  93 
 TYR   0.032   0.002   TYR F 284 
 PHE   0.018   0.002   PHE A 166 
 TRP   0.035   0.003   TRP F 184 
 HIS   0.012   0.001   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 (15073)
  covalent geometry    : angle       0.72737 (20419)
  SS BOND              : bond        0.00656 (    1)
  SS BOND              : angle       1.68902 (    2)
  hydrogen bonds       : bond        0.04486 (  623)
  hydrogen bonds       : angle       4.95028 ( 1833)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2873.51 seconds
wall clock time: 50 minutes 39.19 seconds (3039.19 seconds total)