Starting phenix.real_space_refine
on Mon Mar 11 02:04:13 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga3_29885/03_2024/8ga3_29885.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga3_29885/03_2024/8ga3_29885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga3_29885/03_2024/8ga3_29885.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga3_29885/03_2024/8ga3_29885.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga3_29885/03_2024/8ga3_29885.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga3_29885/03_2024/8ga3_29885.pdb"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.090
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     Cl      4      4.86       5
     C    4336      2.51       5
     N    1085      2.21       5
     O    1123      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   27": "OE1" <-> "OE2"
    Residue "A ARG   28": "NH1" <-> "NH2"
    Residue "A ASP   73": "OD1" <-> "OD2"
    Residue "A GLU  103": "OE1" <-> "OE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  120": "NH1" <-> "NH2"
    Residue "A ARG  123": "NH1" <-> "NH2"
    Residue "A GLU  203": "OE1" <-> "OE2"
    Residue "A ARG  205": "NH1" <-> "NH2"
    Residue "A ARG  209": "NH1" <-> "NH2"
    Residue "A TYR  210": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  229": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  240": "OD1" <-> "OD2"
    Residue "A GLU  414": "OE1" <-> "OE2"
    Residue "A GLU  457": "OE1" <-> "OE2"
    Residue "A GLU  459": "OE1" <-> "OE2"
    Residue "B GLU   27": "OE1" <-> "OE2"
    Residue "B ARG   28": "NH1" <-> "NH2"
    Residue "B ASP   73": "OD1" <-> "OD2"
    Residue "B GLU  113": "OE1" <-> "OE2"
    Residue "B ARG  120": "NH1" <-> "NH2"
    Residue "B ARG  123": "NH1" <-> "NH2"
    Residue "B GLU  172": "OE1" <-> "OE2"
    Residue "B GLU  203": "OE1" <-> "OE2"
    Residue "B ARG  205": "NH1" <-> "NH2"
    Residue "B ARG  209": "NH1" <-> "NH2"
    Residue "B GLU  235": "OE1" <-> "OE2"
    Residue "B ASP  240": "OD1" <-> "OD2"
    Residue "B ASP  246": "OD1" <-> "OD2"
    Residue "B ASP  278": "OD1" <-> "OD2"
    Residue "B PHE  357": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  385": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 6590
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3295
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3291
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.45, per 1000 atoms: 0.83
  Number of scatterers: 6590
  At special positions: 0
  Unit cell: (73.425, 89.925, 110.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      4     17.00
     S      42     16.00
     O    1123      8.00
     N    1085      7.00
     C    4336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS B 249 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 249 " - pdb=" SG  CYS B 230 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.23
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 0 sheets defined
      72.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 28
      removed outlier: 3.655A  pdb=" N   ARG A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLN A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A  26 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 49
      removed outlier: 3.814A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLY A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 58
    Processing helix  chain 'A' and resid 60 through 64
      removed outlier: 3.733A  pdb=" N   ARG A  64 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 4.019A  pdb=" N   THR A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 102 through 105
      removed outlier: 3.615A  pdb=" N   GLY A 105 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 102 through 105'
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 3.596A  pdb=" N   LEU A 128 " --> pdb=" O   TRP A 124 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
      removed outlier: 3.564A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 166
      removed outlier: 3.888A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 190
      removed outlier: 3.677A  pdb=" N   ALA A 179 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 202
      removed outlier: 3.899A  pdb=" N   ILE A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.570A  pdb=" N   SER A 225 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TYR A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 280
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 280 through 285
      removed outlier: 4.065A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.752A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.654A  pdb=" N   LEU A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 326
      removed outlier: 3.532A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 4.708A  pdb=" N   ARG A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 358 through 363
    Processing helix  chain 'A' and resid 363 through 379
      removed outlier: 3.647A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 401
      removed outlier: 3.590A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 417
    Processing helix  chain 'A' and resid 422 through 439
      removed outlier: 3.516A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 457
      removed outlier: 3.706A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 67
      removed outlier: 3.559A  pdb=" N   PHE B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TRP B  59 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   MET B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA B  67 " --> pdb=" O   GLN B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 99
      removed outlier: 4.236A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 117
      removed outlier: 4.223A  pdb=" N   ALA B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
      Proline residue:  B 129  - end of helix
      removed outlier: 3.667A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 139
    Processing helix  chain 'B' and resid 140 through 142
      No H-bonds generated for 'chain 'B' and resid 140 through 142'
    Processing helix  chain 'B' and resid 148 through 166
      removed outlier: 3.591A  pdb=" N   VAL B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 188
      removed outlier: 3.629A  pdb=" N   LEU B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA B 182 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.775A  pdb=" N   ILE B 197 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 231
      removed outlier: 3.575A  pdb=" N   PHE B 219 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 280
      Proline residue:  B 267  - end of helix
      removed outlier: 3.866A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 309
      removed outlier: 3.873A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 324
      removed outlier: 3.587A  pdb=" N   THR B 324 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 346
      removed outlier: 3.516A  pdb=" N   PHE B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 351
      removed outlier: 3.528A  pdb=" N   SER B 350 " --> pdb=" O   CYS B 347 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY B 351 " --> pdb=" O   PHE B 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 347 through 351'
    Processing helix  chain 'B' and resid 357 through 362
    Processing helix  chain 'B' and resid 363 through 373
      removed outlier: 3.661A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 383
      removed outlier: 3.707A  pdb=" N   TYR B 382 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 379 through 383'
    Processing helix  chain 'B' and resid 387 through 395
      removed outlier: 4.002A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 401
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 418 through 422
    Processing helix  chain 'B' and resid 423 through 440
      removed outlier: 3.679A  pdb=" N   ALA B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 461
      removed outlier: 3.776A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 454 " --> pdb=" O   ALA B 450 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU B 461 " --> pdb=" O   GLU B 457 " (cutoff:3.500A)

    336 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 3.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2062
        1.34 -     1.46: 1227
        1.46 -     1.57: 3365
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 6730
  Sorted by residual:
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.336  1.385 -0.049 1.23e-02 6.61e+03 1.59e+01
  bond pdb=" CA  ILE B 109 "
       pdb=" C   ILE B 109 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 8.80e-03 1.29e+04 2.26e+00
  bond pdb=" C   ILE A 109 "
       pdb=" N   PRO A 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.25e-02 6.40e+03 2.01e+00
  bond pdb=" C   LEU B 423 "
       pdb=" N   PRO B 424 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.017 1.25e-02 6.40e+03 1.81e+00
  bond pdb=" C   ARG B 205 "
       pdb=" N   PRO B 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 9.40e-03 1.13e+04 1.74e+00
  ... (remaining 6725 not shown)

  Histogram of bond angle deviations from ideal:
       98.23 -   105.38: 160
      105.38 -   112.53: 3277
      112.53 -   119.67: 2507
      119.67 -   126.82: 3108
      126.82 -   133.97: 95
  Bond angle restraints: 9147
  Sorted by residual:
  angle pdb=" N   LEU B 411 "
        pdb=" CA  LEU B 411 "
        pdb=" C   LEU B 411 "
      ideal   model   delta    sigma   weight residual
     114.62  108.19    6.43 1.14e+00 7.69e-01 3.18e+01
  angle pdb=" C   LEU B 319 "
        pdb=" N   ILE B 320 "
        pdb=" CA  ILE B 320 "
      ideal   model   delta    sigma   weight residual
     120.33  123.85   -3.52 8.00e-01 1.56e+00 1.94e+01
  angle pdb=" CA  ILE B 320 "
        pdb=" C   ILE B 320 "
        pdb=" N   PRO B 321 "
      ideal   model   delta    sigma   weight residual
     120.83  123.41   -2.58 6.10e-01 2.69e+00 1.79e+01
  angle pdb=" C   GLY B 108 "
        pdb=" N   ILE B 109 "
        pdb=" CA  ILE B 109 "
      ideal   model   delta    sigma   weight residual
     120.24  122.73   -2.49 6.30e-01 2.52e+00 1.57e+01
  angle pdb=" C   THR B 211 "
        pdb=" N   LEU B 212 "
        pdb=" CA  LEU B 212 "
      ideal   model   delta    sigma   weight residual
     121.54  129.01   -7.47 1.91e+00 2.74e-01 1.53e+01
  ... (remaining 9142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3426
       17.85 -    35.70: 395
       35.70 -    53.55: 59
       53.55 -    71.40: 10
       71.40 -    89.24: 3
  Dihedral angle restraints: 3893
    sinusoidal: 1447
      harmonic: 2446
  Sorted by residual:
  dihedral pdb=" CB  CYS A 230 "
           pdb=" SG  CYS A 230 "
           pdb=" SG  CYS B 249 "
           pdb=" CB  CYS B 249 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.98  -60.98     1      1.00e+01 1.00e-02 4.94e+01
  dihedral pdb=" CA  CYS A 249 "
           pdb=" C   CYS A 249 "
           pdb=" N   ASN A 250 "
           pdb=" CA  ASN A 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.86   27.14     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  ASP A 118 "
           pdb=" C   ASP A 118 "
           pdb=" N   GLN A 119 "
           pdb=" CA  GLN A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.25  -26.75     0      5.00e+00 4.00e-02 2.86e+01
  ... (remaining 3890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 891
       0.063 -    0.125: 169
       0.125 -    0.188: 18
       0.188 -    0.250: 4
       0.250 -    0.313: 2
  Chirality restraints: 1084
  Sorted by residual:
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CB  THR B  31 "
            pdb=" CA  THR B  31 "
            pdb=" OG1 THR B  31 "
            pdb=" CG2 THR B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  THR B  31 "
            pdb=" N   THR B  31 "
            pdb=" C   THR B  31 "
            pdb=" CB  THR B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1081 not shown)

  Planarity restraints: 1147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "    0.045 5.00e-02 4.00e+02   6.66e-02 7.09e+00
        pdb=" N   PRO B 359 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 266 "    0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO A 267 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 423 "   -0.043 5.00e-02 4.00e+02   6.41e-02 6.56e+00
        pdb=" N   PRO A 424 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 424 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 424 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1144 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2042
        2.81 -     3.34: 5683
        3.34 -     3.86: 11120
        3.86 -     4.38: 13691
        4.38 -     4.90: 22872
  Nonbonded interactions: 55408
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" O   ARG A 147 "
            pdb=" OG1 THR A 151 "
     model   vdw
     2.295 2.440
  nonbonded pdb=" O   LEU B 435 "
            pdb=" OG1 THR B 439 "
     model   vdw
     2.319 2.440
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLY B 141 "
     model   vdw
     2.320 2.440
  nonbonded pdb=" O   LEU A 345 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.327 2.440
  ... (remaining 55403 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 19 through 20 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 21 through 461 or resid 501 through 502))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.460
  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:             0.000
  Extract box with map and model:          3.860
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     26.270
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6730  Z= 0.307
  Angle     :  0.888   9.996   9147  Z= 0.471
  Chirality :  0.051   0.313   1084
  Planarity :  0.007   0.067   1147
  Dihedral  : 14.759  89.245   2343
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  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: -6.60 (0.16), residues: 882
  helix: -4.64 (0.08), residues: 604
  sheet:  None (None), residues: 0
  loop : -3.13 (0.29), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP B 291 
 HIS   0.007   0.002   HIS B 284 
 PHE   0.009   0.001   PHE A 219 
 TYR   0.019   0.002   TYR A 210 
 ARG   0.003   0.000   ARG A  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8663 (m-30) cc_final: 0.8459 (m-30)
REVERT: A  174 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6544 (mtp180)
REVERT: B  290 LYS cc_start: 0.7985 (mttp) cc_final: 0.7784 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.2275
  time to fit residues: 28.8703
Evaluate side-chains
  74 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0010
   chunk 44 optimal weight:    0.0010
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6730  Z= 0.172
  Angle     :  0.605   8.096   9147  Z= 0.305
  Chirality :  0.041   0.154   1084
  Planarity :  0.006   0.044   1147
  Dihedral  :  5.404  23.772    934
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.53 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.49 (0.22), residues: 882
  helix: -2.80 (0.16), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.88 (0.32), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 291 
 HIS   0.004   0.001   HIS A 383 
 PHE   0.008   0.001   PHE A 379 
 TYR   0.008   0.001   TYR A 210 
 ARG   0.003   0.000   ARG B 167 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.6544 (mtt180) cc_final: 0.6213 (mtp180)
REVERT: A  186 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8127 (mp)
REVERT: A  294 MET cc_start: 0.7216 (ttp) cc_final: 0.6841 (ttt)
  outliers start: 8
  outliers final: 2
  residues processed: 73
  average time/residue: 0.1871
  time to fit residues: 18.6833
Evaluate side-chains
  66 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6730  Z= 0.220
  Angle     :  0.591   7.679   9147  Z= 0.293
  Chirality :  0.042   0.132   1084
  Planarity :  0.004   0.045   1147
  Dihedral  :  5.250  24.232    934
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.05 %
    Favored  : 85.28 %
  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: -3.22 (0.25), residues: 882
  helix: -1.78 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.66 (0.34), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.006   0.001   PHE B 307 
 TYR   0.010   0.001   TYR B  94 
 ARG   0.005   0.000   ARG B  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.7548 (ptt-90) cc_final: 0.7334 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6470 (mtt180) cc_final: 0.6142 (mtp180)
REVERT: A  186 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8187 (mp)
REVERT: A  294 MET cc_start: 0.7273 (ttp) cc_final: 0.6919 (ttt)
  outliers start: 11
  outliers final: 5
  residues processed: 69
  average time/residue: 0.1936
  time to fit residues: 18.2531
Evaluate side-chains
  65 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  287 ASN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6730  Z= 0.208
  Angle     :  0.573   7.952   9147  Z= 0.282
  Chirality :  0.042   0.174   1084
  Planarity :  0.004   0.046   1147
  Dihedral  :  5.128  23.686    934
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.11 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.27), residues: 882
  helix: -1.14 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.63 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.005   0.001   PHE A 379 
 TYR   0.008   0.001   TYR A 382 
 ARG   0.002   0.000   ARG A  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.7571 (ptt-90) cc_final: 0.7207 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6460 (mtt180) cc_final: 0.6130 (mtp180)
REVERT: A  186 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8213 (mp)
REVERT: A  294 MET cc_start: 0.7281 (ttp) cc_final: 0.6884 (ttt)
REVERT: B   65 MET cc_start: 0.7491 (mmt) cc_final: 0.7187 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 73
  average time/residue: 0.1838
  time to fit residues: 18.5986
Evaluate side-chains
  66 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  287 ASN
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0770
   chunk 72 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 43 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6730  Z= 0.188
  Angle     :  0.593  14.223   9147  Z= 0.290
  Chirality :  0.042   0.171   1084
  Planarity :  0.004   0.047   1147
  Dihedral  :  5.109  28.272    934
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.42 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.08 (0.28), residues: 882
  helix: -0.80 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.67 (0.34), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.017   0.001   PHE B  95 
 TYR   0.009   0.001   TYR A 229 
 ARG   0.002   0.000   ARG A  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.6440 (mtt180) cc_final: 0.6082 (mtp180)
REVERT: A  186 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8207 (mp)
REVERT: A  294 MET cc_start: 0.7317 (ttp) cc_final: 0.6941 (ttt)
  outliers start: 14
  outliers final: 8
  residues processed: 74
  average time/residue: 0.2012
  time to fit residues: 21.4215
Evaluate side-chains
  70 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0670
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6730  Z= 0.203
  Angle     :  0.586  12.387   9147  Z= 0.286
  Chirality :  0.042   0.151   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  5.054  27.834    934
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.78 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.28), residues: 882
  helix: -0.56 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.41 (0.34), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.020   0.001   PHE B  95 
 TYR   0.008   0.001   TYR A 229 
 ARG   0.003   0.000   ARG B 160 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.6445 (mtt180) cc_final: 0.6079 (mtp180)
REVERT: A  186 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8229 (mp)
REVERT: A  294 MET cc_start: 0.7319 (ttp) cc_final: 0.6935 (ttt)
  outliers start: 11
  outliers final: 9
  residues processed: 73
  average time/residue: 0.1794
  time to fit residues: 18.2573
Evaluate side-chains
  70 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.0980
   chunk 48 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6730  Z= 0.189
  Angle     :  0.567   8.203   9147  Z= 0.278
  Chirality :  0.042   0.153   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.991  27.080    934
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.08 %
    Favored  : 81.79 %
  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: -1.45 (0.28), residues: 882
  helix: -0.33 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.39 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.021   0.001   PHE B  95 
 TYR   0.006   0.001   TYR A 229 
 ARG   0.003   0.000   ARG B 160 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.6420 (mtt180) cc_final: 0.6067 (mtp180)
REVERT: A  186 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8212 (mp)
REVERT: A  294 MET cc_start: 0.7317 (ttp) cc_final: 0.6933 (ttt)
  outliers start: 14
  outliers final: 8
  residues processed: 74
  average time/residue: 0.2386
  time to fit residues: 23.5802
Evaluate side-chains
  70 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   chunk 57 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6730  Z= 0.178
  Angle     :  0.562   8.525   9147  Z= 0.274
  Chirality :  0.041   0.144   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.920  26.126    934
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.24 %
    Favored  : 81.79 %
  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: -1.17 (0.29), residues: 882
  helix: -0.10 (0.22), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.33 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.000   HIS A 383 
 PHE   0.021   0.001   PHE B  95 
 TYR   0.006   0.001   TYR A 229 
 ARG   0.003   0.000   ARG B 160 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.6425 (mtt180) cc_final: 0.6048 (mtp180)
REVERT: A  294 MET cc_start: 0.7314 (ttp) cc_final: 0.6940 (ttt)
  outliers start: 13
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1944
  time to fit residues: 19.4312
Evaluate side-chains
  69 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0040
   chunk 24 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.5794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6730  Z= 0.188
  Angle     :  0.558   8.360   9147  Z= 0.272
  Chirality :  0.041   0.146   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.909  26.955    934
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.39 %
    Favored  : 82.09 %
  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: -1.02 (0.29), residues: 882
  helix:  0.04 (0.22), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.30 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.022   0.001   PHE B  95 
 TYR   0.006   0.001   TYR A 229 
 ARG   0.003   0.000   ARG B 160 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 ARG cc_start: 0.6449 (mtt180) cc_final: 0.6080 (mtp180)
REVERT: A  294 MET cc_start: 0.7315 (ttp) cc_final: 0.6935 (ttt)
  outliers start: 10
  outliers final: 7
  residues processed: 73
  average time/residue: 0.1887
  time to fit residues: 18.9256
Evaluate side-chains
  69 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0970
   chunk 80 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0010
   chunk 42 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0000
   overall best weight:    0.2988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6730  Z= 0.156
  Angle     :  0.545   8.587   9147  Z= 0.267
  Chirality :  0.041   0.141   1084
  Planarity :  0.004   0.047   1147
  Dihedral  :  4.752  24.448    934
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.69 %
    Favored  : 82.25 %
  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: -0.70 (0.29), residues: 882
  helix:  0.30 (0.22), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.27 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 291 
 HIS   0.002   0.000   HIS A 383 
 PHE   0.020   0.001   PHE B  95 
 TYR   0.006   0.001   TYR A 229 
 ARG   0.003   0.000   ARG B 160 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 MET cc_start: 0.7295 (ttp) cc_final: 0.6916 (ttt)
  outliers start: 7
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1835
  time to fit residues: 16.2553
Evaluate side-chains
  63 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0670
   chunk 69 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.164428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.136794 restraints weight = 7115.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.88
r_work: 0.3437 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6730  Z= 0.186
  Angle     :  0.561   8.541   9147  Z= 0.274
  Chirality :  0.042   0.147   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.778  25.288    934
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 17.30 %
    Favored  : 81.64 %
  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: -0.68 (0.29), residues: 882
  helix:  0.33 (0.22), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.38 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.021   0.001   PHE B  95 
 TYR   0.014   0.001   TYR A 419 
 ARG   0.003   0.000   ARG B 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1711.67 seconds
wall clock time: 32 minutes 13.40 seconds (1933.40 seconds total)