Starting phenix.real_space_refine
on Thu Feb 13 07:32:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m1i_30048/02_2025/6m1i_30048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m1i_30048/02_2025/6m1i_30048.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m1i_30048/02_2025/6m1i_30048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m1i_30048/02_2025/6m1i_30048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m1i_30048/02_2025/6m1i_30048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m1i_30048/02_2025/6m1i_30048.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5682      2.51       5
     N    1537      2.21       5
     O    1639      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8916
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2841
          Classifications: {'peptide': 353}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 13, 'TRANS': 339}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 62
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 221
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "C"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "D"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 2595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2595
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1862
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.24, per 1000 atoms: 0.59
  Number of scatterers: 8916
  At special positions: 0
  Unit cell: (84.007, 105.827, 153.831, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1639      8.00
     N    1537      7.00
     C    5682      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  34 " - pdb=" SG  CYS A  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 226 " - pdb=" SG  CYS A 296 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  99 " - pdb=" SG  CYS C 107 " distance=2.02

  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: 2.24
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 11 sheets defined
      39.1% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 41
      removed outlier: 4.274A  pdb=" N   GLN A  31 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 82
    Processing helix  chain 'A' and resid 87 through 111
      removed outlier: 3.504A  pdb=" N   MET A 111 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 111'
    Processing helix  chain 'A' and resid 129 through 135
      removed outlier: 3.573A  pdb=" N   CYS A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 170
      removed outlier: 4.044A  pdb=" N   TYR A 157 " --> pdb=" O   VAL A 153 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   VAL A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU A 163 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   SER A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU A 170 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 176
      removed outlier: 3.675A  pdb=" N   ILE A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   LEU A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   CYS A 176 " --> pdb=" O   MET A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 170 through 176'
    Processing helix  chain 'A' and resid 185 through 209
      removed outlier: 3.580A  pdb=" N   MET A 190 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ASN A 191 " --> pdb=" O   PHE A 187 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   MET A 197 " --> pdb=" O   PHE A 193 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ARG A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 219
      removed outlier: 3.536A  pdb=" N   HIS A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 239
      removed outlier: 4.279A  pdb=" N   MET A 230 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 254
      removed outlier: 3.622A  pdb=" N   GLY A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 286
      removed outlier: 3.756A  pdb=" N   TYR A 265 " --> pdb=" O   PRO A 261 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE A 266 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   TYR A 267 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TRP A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE A 271 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ILE A 272 " --> pdb=" O   TRP A 268 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TRP A 274 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ALA A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      Proline residue:  A 277  - end of helix
      removed outlier: 3.712A  pdb=" N   PHE A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   THR A 282 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.667A  pdb=" N   VAL A 308 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 329
      removed outlier: 4.101A  pdb=" N   SER A 316 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ASN A 320 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL A 322 " --> pdb=" O   MET A 318 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A 323 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 327 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 336
    Processing helix  chain 'A' and resid 347 through 351
    Processing helix  chain 'A' and resid 351 through 356
    Processing helix  chain 'A' and resid 358 through 363
      removed outlier: 3.586A  pdb=" N   GLY A 363 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.606A  pdb=" N   VAL A 368 " --> pdb=" O   HIS A 365 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE A 369 " --> pdb=" O   TYR A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 378
      removed outlier: 3.615A  pdb=" N   LYS A 378 " --> pdb=" O   GLU A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
      removed outlier: 3.685A  pdb=" N   PHE A 384 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 400
      removed outlier: 3.821A  pdb=" N   ALA A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL A 398 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 419
      removed outlier: 3.584A  pdb=" N   LYS A 412 " --> pdb=" O   GLN A 408 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ARG A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS A 414 " --> pdb=" O   GLU A 410 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG A 416 " --> pdb=" O   LYS A 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 24
      removed outlier: 3.670A  pdb=" N   SER B  11 " --> pdb=" O   THR B   7 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   MET B  17 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA B  18 " --> pdb=" O   ARG B  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.865A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 65
      removed outlier: 3.594A  pdb=" N   LYS C  65 " --> pdb=" O   GLY C  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 62 through 65'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.575A  pdb=" N   ASP C  90 " --> pdb=" O   LYS C  87 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 87 through 91'
    Processing helix  chain 'D' and resid 7 through 22
      removed outlier: 3.504A  pdb=" N   VAL D  16 " --> pdb=" O   ALA D  12 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET D  21 " --> pdb=" O   GLU D  17 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU D  22 " --> pdb=" O   GLN D  18 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.773A  pdb=" N   ASP D  36 " --> pdb=" O   LYS D  32 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LEU D  37 " --> pdb=" O   ALA D  33 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA D  43 " --> pdb=" O   ALA D  39 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 26
      removed outlier: 3.526A  pdb=" N   ARG E  22 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 34
      removed outlier: 3.657A  pdb=" N   ILE E  33 " --> pdb=" O   THR E  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 13 through 38
      removed outlier: 3.786A  pdb=" N   ALA F  18 " --> pdb=" O   ASN F  14 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASN F  23 " --> pdb=" O   GLN F  19 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN F  29 " --> pdb=" O   LYS F  25 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   GLN F  35 " --> pdb=" O   GLN F  31 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL F  36 " --> pdb=" O   LYS F  32 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 59
      removed outlier: 3.550A  pdb=" N   ASN F  54 " --> pdb=" O   GLU F  50 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE F  56 " --> pdb=" O   GLY F  52 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   VAL F  57 " --> pdb=" O   LYS F  53 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LYS F  58 " --> pdb=" O   ASN F  54 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 265 through 278
      removed outlier: 3.689A  pdb=" N   SER F 275 " --> pdb=" O   LYS F 271 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 294 through 299
      removed outlier: 3.601A  pdb=" N   GLU F 299 " --> pdb=" O   ASP F 295 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 331 through 350
      removed outlier: 3.749A  pdb=" N   ARG F 347 " --> pdb=" O   ASP F 343 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE F 348 " --> pdb=" O   GLU F 344 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 370 through 390
      removed outlier: 4.015A  pdb=" N   ASP F 381 " --> pdb=" O   ASN F 377 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE F 383 " --> pdb=" O   CYS F 379 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 76
      removed outlier: 4.428A  pdb=" N   VAL A  75 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   VAL A 114 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 8
      removed outlier: 3.552A  pdb=" N   SER C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 60
      removed outlier: 3.521A  pdb=" N   SER C  59 " --> pdb=" O   ASP C  50 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL C 124 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 46 through 51
      removed outlier: 6.672A  pdb=" N   ILE E 338 " --> pdb=" O   ARG E  48 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   THR E  50 " --> pdb=" O   LEU E 336 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   LEU E 336 " --> pdb=" O   THR E  50 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ALA E 328 " --> pdb=" O   LEU E 318 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LEU E 318 " --> pdb=" O   ALA E 328 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   GLY E 330 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 58 through 62
      removed outlier: 3.560A  pdb=" N   ALA E  60 " --> pdb=" O   ALA E  73 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LYS E  78 " --> pdb=" O   SER E  74 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   HIS E  91 " --> pdb=" O   ILE E  81 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ASP E  83 " --> pdb=" O   LYS E  89 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   LYS E  89 " --> pdb=" O   ASP E  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 105
      removed outlier: 3.697A  pdb=" N   ARG E 137 " --> pdb=" O   ILE E 123 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ASN E 125 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL E 135 " --> pdb=" O   ASN E 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 146 through 151
      removed outlier: 3.979A  pdb=" N   ILE E 157 " --> pdb=" O   TRP E 169 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   CYS E 166 " --> pdb=" O   THR E 179 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   THR E 179 " --> pdb=" O   CYS E 166 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU E 168 " --> pdb=" O   THR E 177 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN E 175 " --> pdb=" O   ASP E 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 187 through 192
      removed outlier: 6.855A  pdb=" N   GLY E 202 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   LEU E 190 " --> pdb=" O   VAL E 200 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL E 200 " --> pdb=" O   LEU E 190 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   PHE E 199 " --> pdb=" O   TRP E 211 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA E 203 " --> pdb=" O   SER E 207 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   SER E 207 " --> pdb=" O   ALA E 203 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ALA E 208 " --> pdb=" O   THR E 221 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   THR E 221 " --> pdb=" O   ALA E 208 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LEU E 210 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 229 through 234
      removed outlier: 3.820A  pdb=" N   MET E 262 " --> pdb=" O   LEU E 252 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASP E 254 " --> pdb=" O   GLU E 260 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   GLU E 260 " --> pdb=" O   ASP E 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 275 through 278
      removed outlier: 3.806A  pdb=" N   SER E 275 " --> pdb=" O   GLY E 288 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ASP E 298 " --> pdb=" O   ARG E 304 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ARG E 304 " --> pdb=" O   ASP E 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 207 through 214
      removed outlier: 4.370A  pdb=" N   VAL F 224 " --> pdb=" O   LEU F  45 " (cutoff:3.500A)
      removed outlier: 9.564A  pdb=" N   ALA F 243 " --> pdb=" O   THR F  40 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   ARG F  42 " --> pdb=" O   ALA F 243 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE F 245 " --> pdb=" O   ARG F  42 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU F  44 " --> pdb=" O   ILE F 245 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   ILE F 244 " --> pdb=" O   ILE F 288 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   PHE F 290 " --> pdb=" O   ILE F 244 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   PHE F 246 " --> pdb=" O   PHE F 290 " (cutoff:3.500A)

    333 hydrogen bonds defined for protein.
    951 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2643
        1.33 -     1.45: 2009
        1.45 -     1.58: 4382
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 9114
  Sorted by residual:
  bond pdb=" N   PHE A 402 "
       pdb=" CA  PHE A 402 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.032 1.20e-02 6.94e+03 7.29e+00
  bond pdb=" N   TYR A 400 "
       pdb=" CA  TYR A 400 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.29e-02 6.01e+03 6.16e+00
  bond pdb=" N   GLU A 247 "
       pdb=" CA  GLU A 247 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.17e+00
  bond pdb=" N   ARG A 379 "
       pdb=" CA  ARG A 379 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.15e-02 7.56e+03 4.20e+00
  bond pdb=" N   ARG A 263 "
       pdb=" CA  ARG A 263 "
    ideal  model  delta    sigma   weight residual
    1.456  1.482 -0.026 1.33e-02 5.65e+03 3.81e+00
  ... (remaining 9109 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 11983
        2.41 -     4.82: 314
        4.82 -     7.23: 34
        7.23 -     9.64: 12
        9.64 -    12.05: 2
  Bond angle restraints: 12345
  Sorted by residual:
  angle pdb=" N   ARG A 263 "
        pdb=" CA  ARG A 263 "
        pdb=" C   ARG A 263 "
      ideal   model   delta    sigma   weight residual
     113.28  105.28    8.00 1.22e+00 6.72e-01 4.31e+01
  angle pdb=" C   TYR A 400 "
        pdb=" N   CYS A 401 "
        pdb=" CA  CYS A 401 "
      ideal   model   delta    sigma   weight residual
     122.79  114.01    8.78 1.70e+00 3.46e-01 2.67e+01
  angle pdb=" N   ILE A 309 "
        pdb=" CA  ILE A 309 "
        pdb=" C   ILE A 309 "
      ideal   model   delta    sigma   weight residual
     111.56  107.22    4.34 8.60e-01 1.35e+00 2.55e+01
  angle pdb=" C   LYS C  76 "
        pdb=" N   ASN C  77 "
        pdb=" CA  ASN C  77 "
      ideal   model   delta    sigma   weight residual
     122.46  129.04   -6.58 1.41e+00 5.03e-01 2.18e+01
  angle pdb=" C   SER A 302 "
        pdb=" N   THR A 303 "
        pdb=" CA  THR A 303 "
      ideal   model   delta    sigma   weight residual
     121.54  130.14   -8.60 1.91e+00 2.74e-01 2.03e+01
  ... (remaining 12340 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 4728
       17.77 -    35.53: 546
       35.53 -    53.30: 82
       53.30 -    71.07: 23
       71.07 -    88.84: 6
  Dihedral angle restraints: 5385
    sinusoidal: 2116
      harmonic: 3269
  Sorted by residual:
  dihedral pdb=" CB  CYS A  54 "
           pdb=" SG  CYS A  54 "
           pdb=" SG  CYS A 118 "
           pdb=" CB  CYS A 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.22   58.22     1      1.00e+01 1.00e-02 4.54e+01
  dihedral pdb=" CA  PHE A 127 "
           pdb=" C   PHE A 127 "
           pdb=" N   PRO A 128 "
           pdb=" CA  PRO A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.56   33.44     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  THR C 114 "
           pdb=" C   THR C 114 "
           pdb=" N   TYR C 115 "
           pdb=" CA  TYR C 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.82   31.18     0      5.00e+00 4.00e-02 3.89e+01
  ... (remaining 5382 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 968
       0.058 -    0.117: 314
       0.117 -    0.175: 70
       0.175 -    0.233: 7
       0.233 -    0.292: 5
  Chirality restraints: 1364
  Sorted by residual:
  chirality pdb=" CB  VAL F 241 "
            pdb=" CA  VAL F 241 "
            pdb=" CG1 VAL F 241 "
            pdb=" CG2 VAL F 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CB  ILE A 221 "
            pdb=" CA  ILE A 221 "
            pdb=" CG1 ILE A 221 "
            pdb=" CG2 ILE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CB  THR C  91 "
            pdb=" CA  THR C  91 "
            pdb=" OG1 THR C  91 "
            pdb=" CG2 THR C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.26 2.00e-01 2.50e+01 1.69e+00
  ... (remaining 1361 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 311 "    0.056 5.00e-02 4.00e+02   8.57e-02 1.17e+01
        pdb=" N   PRO A 312 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 312 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 312 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 235 "    0.045 5.00e-02 4.00e+02   6.77e-02 7.34e+00
        pdb=" N   PRO E 236 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  87 "   -0.037 5.00e-02 4.00e+02   5.68e-02 5.15e+00
        pdb=" N   PRO C  88 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C  88 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C  88 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1376
        2.75 -     3.29: 8293
        3.29 -     3.82: 14927
        3.82 -     4.36: 17396
        4.36 -     4.90: 29175
  Nonbonded interactions: 71167
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 189 "
            pdb=" OE2 GLU A 247 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG  SER E 245 "
            pdb=" OD1 ASP E 247 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OH  TYR A 150 "
            pdb=" OG  SER B   9 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ARG C  98 "
            pdb=" OH  TYR C 115 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   THR C 111 "
            pdb=" NH2 ARG C 118 "
     model   vdw
     2.299 3.120
  ... (remaining 71162 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.620
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
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      :  0.008   0.076   9114  Z= 0.516
  Angle     :  0.968  12.046  12345  Z= 0.554
  Chirality :  0.061   0.292   1364
  Planarity :  0.007   0.086   1574
  Dihedral  : 15.399  88.836   3258
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 12.61 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.80 (0.20), residues: 1102
  helix: -4.08 (0.13), residues: 400
  sheet: -1.74 (0.34), residues: 229
  loop : -2.96 (0.23), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP F 234 
 HIS   0.013   0.002   HIS F 357 
 PHE   0.024   0.003   PHE E 241 
 TYR   0.030   0.003   TYR E 105 
 ARG   0.005   0.001   ARG F 385 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 189
  time to evaluate  : 0.946 
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: A  361 LEU cc_start: 0.8332 (tt) cc_final: 0.7946 (tp)
REVERT: B    3 ASP cc_start: 0.8810 (m-30) cc_final: 0.8562 (m-30)
REVERT: B   12 ARG cc_start: 0.8951 (ttp-170) cc_final: 0.8239 (ttp-110)
REVERT: B   14 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8920 (tpp80)
REVERT: C   19 ARG cc_start: 0.7997 (ppt170) cc_final: 0.7761 (ppt170)
REVERT: C   20 LEU cc_start: 0.8164 (mt) cc_final: 0.7883 (mm)
REVERT: C   33 LYS cc_start: 0.8316 (tttt) cc_final: 0.8108 (ttmt)
REVERT: C   83 MET cc_start: 0.8713 (mtm) cc_final: 0.8051 (mtm)
REVERT: E    8 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7214 (tpm170)
REVERT: E  118 ASP cc_start: 0.8325 (p0) cc_final: 0.8021 (p0)
REVERT: F  221 MET cc_start: 0.7727 (ttp) cc_final: 0.7372 (ttp)
REVERT: F  342 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8283 (ttp80)
REVERT: F  386 MET cc_start: 0.7687 (tmm) cc_final: 0.7468 (tpp)
  outliers start: 3
  outliers final: 3
  residues processed: 190
  average time/residue: 0.3027
  time to fit residues: 73.9446
Evaluate side-chains
  135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 132
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  269 TYR
Chi-restraints excluded: chain F residue  325 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 98 optimal weight:    0.2980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 392 GLN
A 404 ASN
E  88 ASN
F  41 HIS
** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 292 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.093598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.071000 restraints weight = 26119.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.073171 restraints weight = 13678.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.074598 restraints weight = 9261.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9114  Z= 0.192
  Angle     :  0.629   7.225  12345  Z= 0.345
  Chirality :  0.045   0.203   1364
  Planarity :  0.005   0.050   1574
  Dihedral  :  6.180  32.717   1229
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.65 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.22), residues: 1102
  helix: -2.29 (0.21), residues: 408
  sheet: -1.06 (0.34), residues: 232
  loop : -2.54 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 243 
 HIS   0.005   0.001   HIS F 220 
 PHE   0.027   0.002   PHE F 222 
 TYR   0.017   0.001   TYR A 157 
 ARG   0.004   0.000   ARG F 317 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.4974 (pm20)
REVERT: A  225 GLU cc_start: 0.6471 (tt0) cc_final: 0.6171 (tp30)
REVERT: A  361 LEU cc_start: 0.8470 (tt) cc_final: 0.8223 (tt)
REVERT: B    3 ASP cc_start: 0.8997 (m-30) cc_final: 0.8774 (m-30)
REVERT: C   18 LEU cc_start: 0.8870 (tp) cc_final: 0.8510 (tt)
REVERT: C   20 LEU cc_start: 0.8373 (mt) cc_final: 0.8034 (mt)
REVERT: C   33 LYS cc_start: 0.8305 (tttt) cc_final: 0.8075 (ttmt)
REVERT: C   67 ARG cc_start: 0.7623 (ptp90) cc_final: 0.7334 (ptp90)
REVERT: C   83 MET cc_start: 0.8681 (mtm) cc_final: 0.8338 (mtp)
REVERT: D   18 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8454 (tp40)
  outliers start: 17
  outliers final: 9
  residues processed: 172
  average time/residue: 0.2669
  time to fit residues: 59.7514
Evaluate side-chains
  149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain F residue  325 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 99 optimal weight:    0.3980
   chunk 45 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    2.8788

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

Flipped N/Q/H residues before XYZ refinement:
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 320 ASN
C  31 ASN
E 311 HIS
F  23 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.091110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.068893 restraints weight = 27066.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.070998 restraints weight = 14086.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.072367 restraints weight = 9542.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9114  Z= 0.299
  Angle     :  0.662   9.391  12345  Z= 0.357
  Chirality :  0.045   0.201   1364
  Planarity :  0.004   0.049   1574
  Dihedral  :  5.847  25.390   1226
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.38 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.23), residues: 1102
  helix: -1.60 (0.23), residues: 420
  sheet: -0.74 (0.35), residues: 224
  loop : -2.49 (0.25), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 243 
 HIS   0.006   0.001   HIS F 357 
 PHE   0.032   0.002   PHE F 222 
 TYR   0.020   0.002   TYR A 211 
 ARG   0.006   0.001   ARG F 317 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5327 (pm20)
REVERT: A  225 GLU cc_start: 0.6527 (tt0) cc_final: 0.6208 (tp30)
REVERT: C   20 LEU cc_start: 0.8411 (mt) cc_final: 0.8152 (mt)
REVERT: C   33 LYS cc_start: 0.8206 (tttt) cc_final: 0.7988 (ttmt)
REVERT: C   83 MET cc_start: 0.8684 (mtm) cc_final: 0.8345 (mtm)
REVERT: F   13 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8694 (mpp80)
REVERT: F  342 ARG cc_start: 0.8745 (tmm-80) cc_final: 0.8379 (tmm-80)
  outliers start: 29
  outliers final: 19
  residues processed: 168
  average time/residue: 0.2461
  time to fit residues: 55.0539
Evaluate side-chains
  150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue   31 ASN
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  325 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 97 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 300 ASN
E 230 ASN
E 311 HIS
F 279 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.093699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.071062 restraints weight = 26444.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.073230 restraints weight = 13770.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.074674 restraints weight = 9321.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9114  Z= 0.167
  Angle     :  0.591   8.540  12345  Z= 0.314
  Chirality :  0.043   0.182   1364
  Planarity :  0.004   0.042   1574
  Dihedral  :  5.307  22.451   1226
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 21.01 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.24), residues: 1102
  helix: -1.00 (0.24), residues: 418
  sheet: -0.33 (0.36), residues: 210
  loop : -2.36 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 243 
 HIS   0.003   0.001   HIS E 311 
 PHE   0.015   0.001   PHE F 222 
 TYR   0.025   0.001   TYR A 211 
 ARG   0.004   0.000   ARG F 333 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TYR cc_start: 0.7220 (t80) cc_final: 0.6617 (t80)
REVERT: A  213 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5606 (pm20)
REVERT: C   20 LEU cc_start: 0.8321 (mt) cc_final: 0.8001 (mt)
REVERT: C   33 LYS cc_start: 0.8173 (tttt) cc_final: 0.7965 (ttmt)
REVERT: C   83 MET cc_start: 0.8656 (mtm) cc_final: 0.8092 (mtm)
REVERT: D   18 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8569 (tp40)
REVERT: F   13 ARG cc_start: 0.8900 (mtt180) cc_final: 0.8665 (mpp80)
REVERT: F  342 ARG cc_start: 0.8677 (tmm-80) cc_final: 0.8364 (tmm-80)
  outliers start: 28
  outliers final: 18
  residues processed: 174
  average time/residue: 0.2347
  time to fit residues: 55.3654
Evaluate side-chains
  158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  234 PHE
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  291 LEU
Chi-restraints excluded: chain F residue  325 THR
Chi-restraints excluded: chain F residue  334 VAL
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  371 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 101 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
E 230 ASN
E 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.093346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.070833 restraints weight = 26371.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.072984 restraints weight = 13811.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.074391 restraints weight = 9389.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9114  Z= 0.191
  Angle     :  0.600   8.283  12345  Z= 0.315
  Chirality :  0.043   0.180   1364
  Planarity :  0.004   0.039   1574
  Dihedral  :  5.092  21.516   1226
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.48 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.24), residues: 1102
  helix: -0.72 (0.25), residues: 420
  sheet: -0.23 (0.36), residues: 210
  loop : -2.27 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 243 
 HIS   0.003   0.001   HIS E  54 
 PHE   0.014   0.001   PHE F 222 
 TYR   0.019   0.001   TYR A 211 
 ARG   0.008   0.000   ARG E  96 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.7907 (pt0) cc_final: 0.7646 (pm20)
REVERT: C   20 LEU cc_start: 0.8327 (mt) cc_final: 0.8029 (mt)
REVERT: C   33 LYS cc_start: 0.8109 (tttt) cc_final: 0.7905 (ttmt)
REVERT: C   34 MET cc_start: 0.7995 (mtp) cc_final: 0.7626 (mtt)
REVERT: C   83 MET cc_start: 0.8625 (mtm) cc_final: 0.8041 (mtm)
REVERT: D   18 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8609 (tp40)
REVERT: F   13 ARG cc_start: 0.8901 (mtt180) cc_final: 0.8669 (mpp80)
  outliers start: 30
  outliers final: 24
  residues processed: 168
  average time/residue: 0.2380
  time to fit residues: 53.9364
Evaluate side-chains
  161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue   31 ASN
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  234 PHE
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  323 ASP
Chi-restraints excluded: chain F residue  211 LYS
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  291 LEU
Chi-restraints excluded: chain F residue  325 THR
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  371 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 23 optimal weight:    0.3980
   chunk 63 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 106 optimal weight:    0.1980
   chunk 70 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
E 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.092960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.070378 restraints weight = 26509.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.072515 restraints weight = 13943.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.073902 restraints weight = 9489.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9114  Z= 0.212
  Angle     :  0.611   7.360  12345  Z= 0.323
  Chirality :  0.044   0.187   1364
  Planarity :  0.004   0.039   1574
  Dihedral  :  4.987  21.179   1226
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 22.79 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.24), residues: 1102
  helix: -0.52 (0.25), residues: 422
  sheet: -0.11 (0.36), residues: 208
  loop : -2.21 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 243 
 HIS   0.003   0.001   HIS F 357 
 PHE   0.015   0.001   PHE F 376 
 TYR   0.012   0.001   TYR A 157 
 ARG   0.004   0.000   ARG F 342 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.7906 (pt0) cc_final: 0.7655 (pm20)
REVERT: A  197 MET cc_start: 0.8547 (mtt) cc_final: 0.8097 (mtt)
REVERT: C   20 LEU cc_start: 0.8371 (mt) cc_final: 0.8069 (mt)
REVERT: C   83 MET cc_start: 0.8632 (mtm) cc_final: 0.8075 (mtm)
REVERT: D   18 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8615 (tp40)
REVERT: D   20 LYS cc_start: 0.8463 (tmmt) cc_final: 0.7823 (tmmt)
REVERT: F   13 ARG cc_start: 0.8974 (mtt180) cc_final: 0.8713 (mpp80)
  outliers start: 38
  outliers final: 33
  residues processed: 171
  average time/residue: 0.2087
  time to fit residues: 49.2385
Evaluate side-chains
  166 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue   31 ASN
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue   93 ILE
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  223 THR
Chi-restraints excluded: chain E residue  234 PHE
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  323 ASP
Chi-restraints excluded: chain F residue  211 LYS
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  291 LEU
Chi-restraints excluded: chain F residue  325 THR
Chi-restraints excluded: chain F residue  334 VAL
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  371 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 59 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0010
   chunk 106 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
E  88 ASN
E 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.094219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.071645 restraints weight = 26544.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.073876 restraints weight = 13690.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.075318 restraints weight = 9205.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9114  Z= 0.162
  Angle     :  0.604   9.771  12345  Z= 0.314
  Chirality :  0.043   0.192   1364
  Planarity :  0.003   0.038   1574
  Dihedral  :  4.743  19.791   1226
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.74 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.24), residues: 1102
  helix: -0.29 (0.26), residues: 420
  sheet: -0.06 (0.37), residues: 205
  loop : -2.11 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 243 
 HIS   0.002   0.001   HIS F 362 
 PHE   0.010   0.001   PHE F 376 
 TYR   0.025   0.001   TYR A 211 
 ARG   0.003   0.000   ARG C 105 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.8531 (mtt) cc_final: 0.8078 (mtt)
REVERT: C   20 LEU cc_start: 0.8451 (mt) cc_final: 0.8167 (mt)
REVERT: C   67 ARG cc_start: 0.7700 (ptp90) cc_final: 0.7460 (ptp90)
REVERT: C   83 MET cc_start: 0.8604 (mtm) cc_final: 0.8069 (mtm)
REVERT: D   18 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8679 (tp40)
REVERT: E   93 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8874 (tt)
REVERT: F   13 ARG cc_start: 0.8921 (mtt180) cc_final: 0.8687 (mpp80)
  outliers start: 33
  outliers final: 25
  residues processed: 175
  average time/residue: 0.2189
  time to fit residues: 52.5382
Evaluate side-chains
  161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue   93 ILE
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  223 THR
Chi-restraints excluded: chain E residue  234 PHE
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  323 ASP
Chi-restraints excluded: chain F residue  211 LYS
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  325 THR
Chi-restraints excluded: chain F residue  364 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 27 optimal weight:    0.2980
   chunk 8 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 94 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
E  88 ASN
E 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.092649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.070157 restraints weight = 26873.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.072322 restraints weight = 13985.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.073729 restraints weight = 9471.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9114  Z= 0.218
  Angle     :  0.620   8.131  12345  Z= 0.325
  Chirality :  0.044   0.181   1364
  Planarity :  0.004   0.038   1574
  Dihedral  :  4.799  20.461   1226
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.95 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.25), residues: 1102
  helix: -0.18 (0.26), residues: 420
  sheet: -0.12 (0.36), residues: 214
  loop : -2.14 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 243 
 HIS   0.004   0.001   HIS F 357 
 PHE   0.015   0.002   PHE F 376 
 TYR   0.013   0.001   TYR C  95 
 ARG   0.002   0.000   ARG F 342 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 134
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.8549 (mtt) cc_final: 0.8109 (mtt)
REVERT: C   20 LEU cc_start: 0.8351 (mt) cc_final: 0.8072 (mt)
REVERT: C   83 MET cc_start: 0.8624 (mtm) cc_final: 0.8104 (mtm)
REVERT: E  118 ASP cc_start: 0.8105 (p0) cc_final: 0.7824 (p0)
REVERT: F   13 ARG cc_start: 0.8997 (mtt180) cc_final: 0.8660 (mpp80)
  outliers start: 35
  outliers final: 32
  residues processed: 162
  average time/residue: 0.2255
  time to fit residues: 50.0256
Evaluate side-chains
  159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 MET
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  148 TYR
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue   31 ASN
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue   93 ILE
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  223 THR
Chi-restraints excluded: chain E residue  234 PHE
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  323 ASP
Chi-restraints excluded: chain F residue  211 LYS
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  325 THR
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  371 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
C 123 GLN
E 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.092632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.070237 restraints weight = 26860.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.072384 restraints weight = 13962.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.073769 restraints weight = 9463.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9114  Z= 0.215
  Angle     :  0.626   9.407  12345  Z= 0.327
  Chirality :  0.044   0.182   1364
  Planarity :  0.004   0.038   1574
  Dihedral  :  4.791  20.857   1226
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 23.63 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.25), residues: 1102
  helix: -0.13 (0.26), residues: 423
  sheet: -0.13 (0.35), residues: 219
  loop : -2.06 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 243 
 HIS   0.003   0.001   HIS F 357 
 PHE   0.016   0.001   PHE C 103 
 TYR   0.022   0.001   TYR A 211 
 ARG   0.005   0.000   ARG C  67 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.7622 (mp10) cc_final: 0.7132 (pm20)
REVERT: A  197 MET cc_start: 0.8545 (mtt) cc_final: 0.8107 (mtt)
REVERT: A  299 MET cc_start: 0.5085 (mmp) cc_final: 0.4660 (mmp)
REVERT: C   20 LEU cc_start: 0.8404 (mt) cc_final: 0.8170 (mt)
REVERT: C   67 ARG cc_start: 0.7403 (ptp90) cc_final: 0.7073 (ptp90)
REVERT: C   83 MET cc_start: 0.8628 (mtm) cc_final: 0.8131 (mtm)
REVERT: E  118 ASP cc_start: 0.8088 (p0) cc_final: 0.7807 (p0)
REVERT: E  241 PHE cc_start: 0.9076 (p90) cc_final: 0.8715 (p90)
REVERT: F   13 ARG cc_start: 0.8988 (mtt180) cc_final: 0.8661 (mpp80)
  outliers start: 38
  outliers final: 32
  residues processed: 160
  average time/residue: 0.2176
  time to fit residues: 48.6203
Evaluate side-chains
  159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 MET
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  148 TYR
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue   35 ASN
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue   93 ILE
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  223 THR
Chi-restraints excluded: chain E residue  234 PHE
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  323 ASP
Chi-restraints excluded: chain F residue  211 LYS
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  325 THR
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  371 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 106 optimal weight:    0.3980
   chunk 58 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 28 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
E 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.093591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.071176 restraints weight = 26687.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.073351 restraints weight = 13836.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.074784 restraints weight = 9356.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9114  Z= 0.180
  Angle     :  0.626  11.674  12345  Z= 0.322
  Chirality :  0.044   0.185   1364
  Planarity :  0.003   0.038   1574
  Dihedral  :  4.632  19.517   1226
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.95 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.25), residues: 1102
  helix: -0.03 (0.26), residues: 424
  sheet:  0.04 (0.37), residues: 205
  loop : -1.95 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 243 
 HIS   0.003   0.001   HIS F 357 
 PHE   0.011   0.001   PHE F 376 
 TYR   0.014   0.001   TYR A 157 
 ARG   0.004   0.000   ARG C  67 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.7797 (mp10) cc_final: 0.7301 (pm20)
REVERT: A  197 MET cc_start: 0.8570 (mtt) cc_final: 0.8120 (mtt)
REVERT: A  299 MET cc_start: 0.5065 (mmp) cc_final: 0.4193 (mmp)
REVERT: C   20 LEU cc_start: 0.8440 (mt) cc_final: 0.8223 (mt)
REVERT: C   34 MET cc_start: 0.8066 (mtp) cc_final: 0.7747 (mtt)
REVERT: C   83 MET cc_start: 0.8630 (mtm) cc_final: 0.8140 (mtm)
REVERT: E    8 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8202 (tpm170)
REVERT: E  118 ASP cc_start: 0.7987 (p0) cc_final: 0.7715 (p0)
REVERT: E  241 PHE cc_start: 0.9057 (p90) cc_final: 0.8683 (p90)
REVERT: F   13 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8641 (mpp80)
  outliers start: 34
  outliers final: 30
  residues processed: 170
  average time/residue: 0.2136
  time to fit residues: 50.0121
Evaluate side-chains
  164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 MET
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  148 TYR
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain C residue   31 ASN
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain E residue   59 TYR
Chi-restraints excluded: chain E residue   93 ILE
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  223 THR
Chi-restraints excluded: chain E residue  234 PHE
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  323 ASP
Chi-restraints excluded: chain F residue  211 LYS
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  291 LEU
Chi-restraints excluded: chain F residue  325 THR
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  371 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0050
   chunk 89 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.9800

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN
E 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.093409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.071164 restraints weight = 26826.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.073336 restraints weight = 13867.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.074756 restraints weight = 9381.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129   9114  Z= 0.252
  Angle     :  0.977  59.200  12345  Z= 0.580
  Chirality :  0.043   0.175   1364
  Planarity :  0.004   0.044   1574
  Dihedral  :  4.653  19.567   1226
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.26 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.25), residues: 1102
  helix: -0.02 (0.26), residues: 424
  sheet:  0.05 (0.37), residues: 205
  loop : -1.95 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 243 
 HIS   0.003   0.001   HIS F 357 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.015   0.001   TYR C  32 
 ARG   0.004   0.000   ARG C  67 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.18 seconds
wall clock time: 54 minutes 43.00 seconds (3283.00 seconds total)