Starting phenix.real_space_refine
on Fri Dec 27 17:49:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rq7_24629/12_2024/7rq7_24629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rq7_24629/12_2024/7rq7_24629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rq7_24629/12_2024/7rq7_24629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rq7_24629/12_2024/7rq7_24629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rq7_24629/12_2024/7rq7_24629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rq7_24629/12_2024/7rq7_24629.cif"
  }
  resolution = 3.95
  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=   0.004 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4206      2.51       5
     N    1049      2.21       5
     O    1085      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6380
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3186
          Classifications: {'peptide': 430}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 410}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 3194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3194
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 411}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 4.38, per 1000 atoms: 0.69
  Number of scatterers: 6380
  At special positions: 0
  Unit cell: (85.936, 111.088, 73.36, 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      40     16.00
     O    1085      8.00
     N    1049      7.00
     C    4206      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      78.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 71
      removed outlier: 3.869A  pdb=" N   THR A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 85
      removed outlier: 3.564A  pdb=" N   LEU A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   CYS A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 101
      removed outlier: 3.556A  pdb=" N   LYS A  99 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.528A  pdb=" N   GLU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 141
      removed outlier: 3.911A  pdb=" N   VAL A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   THR A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 165
      removed outlier: 3.615A  pdb=" N   GLN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 156 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 188
      removed outlier: 3.749A  pdb=" N   HIS A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   THR A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLY A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 202
      removed outlier: 3.650A  pdb=" N   LEU A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 233
      removed outlier: 3.556A  pdb=" N   GLY A 221 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 251
    Processing helix  chain 'A' and resid 252 through 284
      removed outlier: 3.664A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.813A  pdb=" N   ASN A 270 " --> pdb=" O   GLY A 266 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   LYS A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU A 279 " --> pdb=" O   GLY A 275 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
      removed outlier: 4.124A  pdb=" N   LEU A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   CYS A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 325
      removed outlier: 3.940A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 347
      removed outlier: 3.703A  pdb=" N   VAL A 334 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 379
      removed outlier: 4.146A  pdb=" N   THR A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.890A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 385 through 392
      removed outlier: 4.176A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 402
      removed outlier: 3.998A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 416
    Processing helix  chain 'A' and resid 422 through 431
      removed outlier: 3.617A  pdb=" N   ILE A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   THR A 428 " --> pdb=" O   PRO A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 440
      removed outlier: 3.536A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 3.782A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 460
      No H-bonds generated for 'chain 'A' and resid 459 through 460'
    Processing helix  chain 'B' and resid 31 through 31
      No H-bonds generated for 'chain 'B' and resid 31 through 31'
    Processing helix  chain 'B' and resid 32 through 46
    Processing helix  chain 'B' and resid 47 through 71
      removed outlier: 3.988A  pdb=" N   THR B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 85
      removed outlier: 3.823A  pdb=" N   THR B  80 " --> pdb=" O   PRO B  76 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 100
      removed outlier: 3.557A  pdb=" N   GLY B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
      removed outlier: 3.625A  pdb=" N   GLY B 105 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 116
      removed outlier: 3.775A  pdb=" N   ILE B 112 " --> pdb=" O   GLY B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 136
      Proline residue:  B 129  - end of helix
      removed outlier: 3.907A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   PHE B 133 " --> pdb=" O   PRO B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 148 through 166
      removed outlier: 3.822A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 190
      removed outlier: 3.601A  pdb=" N   GLY B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 202
      removed outlier: 3.805A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   PHE B 199 " --> pdb=" O   ALA B 195 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 231
      removed outlier: 3.591A  pdb=" N   GLY B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TYR B 229 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 250
      No H-bonds generated for 'chain 'B' and resid 248 through 250'
    Processing helix  chain 'B' and resid 251 through 284
      removed outlier: 4.192A  pdb=" N   TYR B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
    Processing helix  chain 'B' and resid 287 through 309
      removed outlier: 3.688A  pdb=" N   CYS B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 325
      removed outlier: 3.692A  pdb=" N   ALA B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 3.762A  pdb=" N   LEU B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 379
      removed outlier: 3.802A  pdb=" N   ALA B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
    Processing helix  chain 'B' and resid 386 through 392
      removed outlier: 4.092A  pdb=" N   ALA B 392 " --> pdb=" O   THR B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 401
      removed outlier: 3.865A  pdb=" N   LEU B 397 " --> pdb=" O   GLY B 393 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU B 398 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 407
    Processing helix  chain 'B' and resid 408 through 416
      removed outlier: 3.872A  pdb=" N   VAL B 412 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B 413 " --> pdb=" O   ILE B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 440
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 4.080A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU B 457 " --> pdb=" O   LEU B 453 " (cutoff:3.500A)

    397 hydrogen bonds defined for protein.
    1179 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: 1.70

  Time building geometry restraints manager: 1.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1549
        1.33 -     1.45: 1247
        1.45 -     1.57: 3651
        1.57 -     1.69: 1
        1.69 -     1.81: 74
  Bond restraints: 6522
  Sorted by residual:
  bond pdb=" C   THR A  31 "
       pdb=" N   PRO A  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.391 -0.057 2.34e-02 1.83e+03 6.00e+00
  bond pdb=" N   LEU B  33 "
       pdb=" CA  LEU B  33 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.030 1.27e-02 6.20e+03 5.64e+00
  bond pdb=" CA  LEU B 421 "
       pdb=" CB  LEU B 421 "
    ideal  model  delta    sigma   weight residual
    1.531  1.595 -0.065 3.28e-02 9.30e+02 3.89e+00
  bond pdb=" C   LEU A 423 "
       pdb=" N   PRO A 424 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 2.34e-02 1.83e+03 3.14e+00
  bond pdb=" C   PRO B  32 "
       pdb=" O   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.237  1.216  0.022 1.26e-02 6.30e+03 2.95e+00
  ... (remaining 6517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 8564
        2.23 -     4.46: 242
        4.46 -     6.69: 36
        6.69 -     8.93: 22
        8.93 -    11.16: 3
  Bond angle restraints: 8867
  Sorted by residual:
  angle pdb=" N   VAL A 144 "
        pdb=" CA  VAL A 144 "
        pdb=" C   VAL A 144 "
      ideal   model   delta    sigma   weight residual
     111.91  107.45    4.46 8.90e-01 1.26e+00 2.52e+01
  angle pdb=" C   CYS A  85 "
        pdb=" N   SER A  86 "
        pdb=" CA  SER A  86 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" C   GLY B 106 "
        pdb=" N   SER B 107 "
        pdb=" CA  SER B 107 "
      ideal   model   delta    sigma   weight residual
     121.54  129.01   -7.47 1.91e+00 2.74e-01 1.53e+01
  angle pdb=" N   ILE B 109 "
        pdb=" CA  ILE B 109 "
        pdb=" C   ILE B 109 "
      ideal   model   delta    sigma   weight residual
     108.88  116.73   -7.85 2.16e+00 2.14e-01 1.32e+01
  angle pdb=" CA  ILE B 109 "
        pdb=" C   ILE B 109 "
        pdb=" N   PRO B 110 "
      ideal   model   delta    sigma   weight residual
     118.88  124.40   -5.52 1.54e+00 4.22e-01 1.28e+01
  ... (remaining 8862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3350
       17.83 -    35.66: 336
       35.66 -    53.49: 61
       53.49 -    71.32: 5
       71.32 -    89.16: 5
  Dihedral angle restraints: 3757
    sinusoidal: 1386
      harmonic: 2371
  Sorted by residual:
  dihedral pdb=" CA  ILE B 239 "
           pdb=" C   ILE B 239 "
           pdb=" N   ASP B 240 "
           pdb=" CA  ASP B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.80  -26.20     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  ILE A 109 "
           pdb=" C   ILE A 109 "
           pdb=" N   PRO A 110 "
           pdb=" CA  PRO A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.50   25.50     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  ALA B 311 "
           pdb=" C   ALA B 311 "
           pdb=" N   THR B 312 "
           pdb=" CA  THR B 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.58   23.42     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 3754 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 691
       0.047 -    0.095: 262
       0.095 -    0.142: 82
       0.142 -    0.189: 15
       0.189 -    0.237: 2
  Chirality restraints: 1052
  Sorted by residual:
  chirality pdb=" CB  VAL A 144 "
            pdb=" CA  VAL A 144 "
            pdb=" CG1 VAL A 144 "
            pdb=" CG2 VAL A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  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    2.87   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CB  VAL B  97 "
            pdb=" CA  VAL B  97 "
            pdb=" CG1 VAL B  97 "
            pdb=" CG2 VAL B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.26e-01
  ... (remaining 1049 not shown)

  Planarity restraints: 1109
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "    0.045 5.00e-02 4.00e+02   6.73e-02 7.24e+00
        pdb=" N   PRO A 150 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 157 "    0.013 2.00e-02 2.50e+03   2.61e-02 6.80e+00
        pdb=" CG  ASN B 157 "   -0.045 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 157 "    0.017 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 157 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 128 "   -0.040 5.00e-02 4.00e+02   5.98e-02 5.72e+00
        pdb=" N   PRO B 129 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1106 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 2184
        2.86 -     3.37: 6372
        3.37 -     3.88: 10484
        3.88 -     4.39: 11817
        4.39 -     4.90: 19870
  Nonbonded interactions: 50727
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 320 "
            pdb=" OG1 THR B 324 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OD1 ASN B 270 "
            pdb=" OG  SER B 401 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" N   THR B  31 "
            pdb=" CD  PRO B  32 "
     model   vdw
     2.363 3.520
  nonbonded pdb=" O   SER A 446 "
            pdb=" OG  SER A 446 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" OG1 THR B 365 "
            pdb=" O   ALA B 390 "
     model   vdw
     2.368 3.040
  ... (remaining 50722 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 31 through 460)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.840
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
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   0.065   6522  Z= 0.316
  Angle     :  0.950  11.158   8867  Z= 0.496
  Chirality :  0.055   0.237   1052
  Planarity :  0.007   0.067   1109
  Dihedral  : 14.605  89.155   2263
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  8.16 %
    Favored  : 91.52 %
  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: -5.29 (0.19), residues: 857
  helix: -3.13 (0.13), residues: 616
  sheet:  None (None), residues: 0
  loop : -4.01 (0.28), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  59 
 HIS   0.005   0.001   HIS B 175 
 PHE   0.017   0.001   PHE B 357 
 TYR   0.010   0.001   TYR A 445 
 ARG   0.002   0.000   ARG A 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 218
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8377 (mmmt)
REVERT: A   94 TYR cc_start: 0.8957 (m-80) cc_final: 0.8632 (m-10)
REVERT: A  166 PHE cc_start: 0.8206 (m-80) cc_final: 0.7925 (m-10)
REVERT: A  250 ASN cc_start: 0.7779 (m110) cc_final: 0.7475 (m-40)
REVERT: A  293 LEU cc_start: 0.8672 (mm) cc_final: 0.8118 (pp)
REVERT: A  336 ILE cc_start: 0.8967 (mt) cc_final: 0.8710 (mt)
REVERT: A  342 ILE cc_start: 0.9005 (tp) cc_final: 0.8710 (tp)
REVERT: A  420 GLN cc_start: 0.8767 (pm20) cc_final: 0.8375 (pm20)
REVERT: B   62 ASN cc_start: 0.8663 (t0) cc_final: 0.8441 (t0)
REVERT: B   96 LEU cc_start: 0.8646 (mt) cc_final: 0.8284 (mm)
REVERT: B  158 ILE cc_start: 0.9338 (mm) cc_final: 0.9137 (mm)
REVERT: B  271 LYS cc_start: 0.9205 (mttt) cc_final: 0.8947 (mmtp)
REVERT: B  414 GLU cc_start: 0.7777 (tp30) cc_final: 0.7562 (tp30)
REVERT: B  434 LEU cc_start: 0.8806 (tt) cc_final: 0.8544 (pp)
  outliers start: 2
  outliers final: 1
  residues processed: 220
  average time/residue: 0.1837
  time to fit residues: 53.0862
Evaluate side-chains
  164 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 ASN
A 250 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6522  Z= 0.299
  Angle     :  0.737   8.298   8867  Z= 0.368
  Chirality :  0.044   0.225   1052
  Planarity :  0.005   0.044   1109
  Dihedral  :  5.666  51.019    909
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.52 %
    Favored  : 78.49 %
  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: -2.82 (0.25), residues: 857
  helix: -1.25 (0.19), residues: 622
  sheet:  None (None), residues: 0
  loop : -3.26 (0.32), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 124 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.017   0.001   PHE B 379 
 TYR   0.009   0.001   TYR A 445 
 ARG   0.005   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8593 (mmmt)
REVERT: A  258 LEU cc_start: 0.8774 (tp) cc_final: 0.8509 (tp)
REVERT: A  350 SER cc_start: 0.9131 (p) cc_final: 0.8929 (p)
REVERT: A  420 GLN cc_start: 0.8845 (pm20) cc_final: 0.8557 (pm20)
REVERT: A  456 GLN cc_start: 0.8120 (tp40) cc_final: 0.7903 (tp40)
REVERT: B   62 ASN cc_start: 0.8696 (t0) cc_final: 0.8489 (t0)
REVERT: B   91 MET cc_start: 0.8345 (mpp) cc_final: 0.7927 (mpp)
REVERT: B  153 GLN cc_start: 0.8953 (tt0) cc_final: 0.8141 (tm-30)
REVERT: B  250 ASN cc_start: 0.7612 (t0) cc_final: 0.7345 (t0)
REVERT: B  271 LYS cc_start: 0.9260 (mttt) cc_final: 0.9017 (mmtp)
REVERT: B  382 TYR cc_start: 0.7635 (m-80) cc_final: 0.7025 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 193
  average time/residue: 0.1694
  time to fit residues: 43.9310
Evaluate side-chains
  174 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 163
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0770
   chunk 53 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7142

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6522  Z= 0.198
  Angle     :  0.675   9.131   8867  Z= 0.331
  Chirality :  0.041   0.131   1052
  Planarity :  0.004   0.038   1109
  Dihedral  :  5.330  48.812    909
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 22.92 %
    Favored  : 74.25 %
  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: -1.87 (0.27), residues: 857
  helix: -0.54 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -2.94 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A  70 
 PHE   0.023   0.001   PHE B 379 
 TYR   0.009   0.001   TYR A  94 
 ARG   0.002   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 182
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8578 (mmmt)
REVERT: A  350 SER cc_start: 0.9225 (p) cc_final: 0.8908 (p)
REVERT: A  420 GLN cc_start: 0.8741 (pm20) cc_final: 0.8138 (pm20)
REVERT: B   62 ASN cc_start: 0.8685 (t0) cc_final: 0.8466 (t0)
REVERT: B  124 TRP cc_start: 0.8306 (p90) cc_final: 0.8080 (p90)
REVERT: B  153 GLN cc_start: 0.8877 (tt0) cc_final: 0.8452 (tm-30)
REVERT: B  250 ASN cc_start: 0.7539 (t0) cc_final: 0.7022 (t0)
REVERT: B  271 LYS cc_start: 0.9227 (mttt) cc_final: 0.8921 (mmtp)
REVERT: B  382 TYR cc_start: 0.7487 (m-80) cc_final: 0.6899 (m-80)
REVERT: B  416 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8502 (p)
REVERT: B  442 LYS cc_start: 0.8399 (mppt) cc_final: 0.8162 (mppt)
  outliers start: 18
  outliers final: 6
  residues processed: 192
  average time/residue: 0.1687
  time to fit residues: 43.5095
Evaluate side-chains
  179 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 172
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 456 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6522  Z= 0.189
  Angle     :  0.667   9.336   8867  Z= 0.324
  Chirality :  0.041   0.126   1052
  Planarity :  0.004   0.035   1109
  Dihedral  :  5.130  49.416    909
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.49 %
    Favored  : 72.53 %
  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: -1.34 (0.28), residues: 857
  helix: -0.07 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop : -2.94 (0.33), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A  70 
 PHE   0.025   0.001   PHE B 438 
 TYR   0.008   0.001   TYR A  94 
 ARG   0.002   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 174
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8395 (mmmt)
REVERT: A   65 MET cc_start: 0.7972 (mmp) cc_final: 0.7579 (ptp)
REVERT: A  153 GLN cc_start: 0.8833 (tt0) cc_final: 0.8583 (tt0)
REVERT: A  350 SER cc_start: 0.9240 (p) cc_final: 0.8918 (p)
REVERT: A  420 GLN cc_start: 0.8590 (pm20) cc_final: 0.8001 (pm20)
REVERT: B   62 ASN cc_start: 0.8693 (t0) cc_final: 0.8453 (t0)
REVERT: B   91 MET cc_start: 0.7944 (mtt) cc_final: 0.7494 (mpp)
REVERT: B  153 GLN cc_start: 0.8820 (tt0) cc_final: 0.7924 (tm-30)
REVERT: B  250 ASN cc_start: 0.7481 (t0) cc_final: 0.6969 (t0)
REVERT: B  271 LYS cc_start: 0.9200 (mttt) cc_final: 0.8899 (mmtp)
REVERT: B  276 MET cc_start: 0.8921 (tpp) cc_final: 0.8662 (tpp)
REVERT: B  382 TYR cc_start: 0.7385 (m-80) cc_final: 0.6723 (m-80)
REVERT: B  414 GLU cc_start: 0.8160 (tp30) cc_final: 0.7874 (tp30)
REVERT: B  416 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8474 (p)
REVERT: B  421 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8758 (pp)
  outliers start: 19
  outliers final: 11
  residues processed: 188
  average time/residue: 0.1638
  time to fit residues: 41.4894
Evaluate side-chains
  186 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 1 optimal weight:    0.5980
   chunk 61 optimal weight:    0.4980
   chunk 34 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 0 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6522  Z= 0.195
  Angle     :  0.684  10.856   8867  Z= 0.329
  Chirality :  0.041   0.126   1052
  Planarity :  0.004   0.039   1109
  Dihedral  :  5.050  47.460    909
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 25.90 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.03 (0.29), residues: 857
  helix:  0.15 (0.22), residues: 615
  sheet:  None (None), residues: 0
  loop : -2.80 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A  70 
 PHE   0.024   0.001   PHE B 438 
 TYR   0.007   0.001   TYR A 210 
 ARG   0.003   0.000   ARG A 403 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8384 (mt) cc_final: 0.8045 (mt)
REVERT: A   55 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8401 (mmmt)
REVERT: A   83 PHE cc_start: 0.8262 (t80) cc_final: 0.7950 (t80)
REVERT: A  153 GLN cc_start: 0.8809 (tt0) cc_final: 0.8535 (tt0)
REVERT: A  253 TRP cc_start: 0.8177 (p-90) cc_final: 0.7787 (p-90)
REVERT: A  350 SER cc_start: 0.9237 (p) cc_final: 0.8878 (p)
REVERT: A  420 GLN cc_start: 0.8513 (pm20) cc_final: 0.7974 (pm20)
REVERT: B   62 ASN cc_start: 0.8682 (t0) cc_final: 0.8454 (t0)
REVERT: B   91 MET cc_start: 0.7822 (mtt) cc_final: 0.7425 (mpp)
REVERT: B  157 ASN cc_start: 0.8956 (m-40) cc_final: 0.8547 (m110)
REVERT: B  210 TYR cc_start: 0.7967 (m-10) cc_final: 0.7730 (m-10)
REVERT: B  250 ASN cc_start: 0.7451 (t0) cc_final: 0.6756 (t0)
REVERT: B  271 LYS cc_start: 0.9202 (mttt) cc_final: 0.8911 (mmtp)
REVERT: B  276 MET cc_start: 0.8757 (tpp) cc_final: 0.8490 (tpp)
REVERT: B  382 TYR cc_start: 0.7264 (m-80) cc_final: 0.6394 (m-80)
REVERT: B  414 GLU cc_start: 0.8202 (tp30) cc_final: 0.7948 (tp30)
REVERT: B  415 MET cc_start: 0.8140 (mtp) cc_final: 0.7908 (mtp)
REVERT: B  416 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8474 (p)
REVERT: B  421 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8792 (pp)
REVERT: B  442 LYS cc_start: 0.8413 (mppt) cc_final: 0.8193 (mppt)
  outliers start: 18
  outliers final: 12
  residues processed: 198
  average time/residue: 0.1669
  time to fit residues: 44.4822
Evaluate side-chains
  179 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    0.0370
   chunk 74 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    8.9990
   chunk 80 optimal weight:    0.4980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6522  Z= 0.200
  Angle     :  0.717  14.704   8867  Z= 0.344
  Chirality :  0.041   0.123   1052
  Planarity :  0.004   0.034   1109
  Dihedral  :  4.980  46.635    909
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 27.63 %
    Favored  : 69.54 %
  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: -0.79 (0.29), residues: 857
  helix:  0.30 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -2.66 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A  70 
 PHE   0.030   0.001   PHE B 379 
 TYR   0.008   0.001   TYR A 229 
 ARG   0.005   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 PHE cc_start: 0.8134 (t80) cc_final: 0.7836 (t80)
REVERT: A  253 TRP cc_start: 0.8198 (p-90) cc_final: 0.7816 (p-90)
REVERT: A  350 SER cc_start: 0.9229 (p) cc_final: 0.8932 (p)
REVERT: A  420 GLN cc_start: 0.8489 (pm20) cc_final: 0.7932 (pm20)
REVERT: B   62 ASN cc_start: 0.8669 (t0) cc_final: 0.8420 (t0)
REVERT: B  250 ASN cc_start: 0.7413 (t0) cc_final: 0.6801 (t0)
REVERT: B  271 LYS cc_start: 0.9166 (mttt) cc_final: 0.8900 (mmtp)
REVERT: B  276 MET cc_start: 0.8744 (tpp) cc_final: 0.8477 (tpp)
REVERT: B  382 TYR cc_start: 0.7129 (m-80) cc_final: 0.6275 (m-80)
REVERT: B  414 GLU cc_start: 0.8208 (tp30) cc_final: 0.7936 (tp30)
REVERT: B  421 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8787 (pp)
  outliers start: 18
  outliers final: 8
  residues processed: 186
  average time/residue: 0.1671
  time to fit residues: 42.0222
Evaluate side-chains
  172 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 70 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 82 optimal weight:    0.1980
   chunk 51 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6522  Z= 0.198
  Angle     :  0.723  14.001   8867  Z= 0.346
  Chirality :  0.041   0.244   1052
  Planarity :  0.004   0.036   1109
  Dihedral  :  4.917  45.072    909
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 28.89 %
    Favored  : 68.45 %
  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: -0.60 (0.29), residues: 857
  helix:  0.39 (0.22), residues: 618
  sheet:  None (None), residues: 0
  loop : -2.43 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A  70 
 PHE   0.025   0.001   PHE B 438 
 TYR   0.010   0.001   TYR B  94 
 ARG   0.005   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.8693 (tt0) cc_final: 0.8456 (tt0)
REVERT: A  294 MET cc_start: 0.8607 (tmm) cc_final: 0.8272 (tmm)
REVERT: A  350 SER cc_start: 0.9175 (p) cc_final: 0.8940 (p)
REVERT: A  420 GLN cc_start: 0.8430 (pm20) cc_final: 0.7825 (pm20)
REVERT: A  421 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8340 (pp)
REVERT: B   91 MET cc_start: 0.7884 (mtt) cc_final: 0.7445 (mpp)
REVERT: B  161 MET cc_start: 0.8329 (ttp) cc_final: 0.7975 (ttm)
REVERT: B  271 LYS cc_start: 0.9100 (mttt) cc_final: 0.8827 (mmtp)
REVERT: B  276 MET cc_start: 0.8750 (tpp) cc_final: 0.8483 (tpp)
REVERT: B  421 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8943 (pp)
  outliers start: 17
  outliers final: 10
  residues processed: 180
  average time/residue: 0.1554
  time to fit residues: 38.5171
Evaluate side-chains
  174 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 162
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 65 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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: 0.7957
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6522  Z= 0.200
  Angle     :  0.727  13.471   8867  Z= 0.347
  Chirality :  0.041   0.122   1052
  Planarity :  0.004   0.037   1109
  Dihedral  :  4.834  42.489    909
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 29.83 %
    Favored  : 67.50 %
  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: -0.49 (0.30), residues: 857
  helix:  0.50 (0.22), residues: 625
  sheet:  None (None), residues: 0
  loop : -2.55 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A  70 
 PHE   0.031   0.001   PHE A  95 
 TYR   0.008   0.001   TYR A 229 
 ARG   0.004   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  153 GLN cc_start: 0.8722 (tt0) cc_final: 0.8419 (tt0)
REVERT: A  294 MET cc_start: 0.8710 (tmm) cc_final: 0.8381 (tmm)
REVERT: A  342 ILE cc_start: 0.9027 (tp) cc_final: 0.8793 (tp)
REVERT: A  350 SER cc_start: 0.9182 (p) cc_final: 0.8964 (p)
REVERT: A  420 GLN cc_start: 0.8426 (pm20) cc_final: 0.7842 (pm20)
REVERT: B  161 MET cc_start: 0.8352 (ttp) cc_final: 0.8085 (ttm)
REVERT: B  271 LYS cc_start: 0.9066 (mttt) cc_final: 0.8799 (mmtp)
REVERT: B  276 MET cc_start: 0.8690 (tpp) cc_final: 0.8434 (tpp)
REVERT: B  421 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8890 (pp)
  outliers start: 17
  outliers final: 11
  residues processed: 178
  average time/residue: 0.1504
  time to fit residues: 37.0383
Evaluate side-chains
  175 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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: 0.7968
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6522  Z= 0.211
  Angle     :  0.742  14.285   8867  Z= 0.351
  Chirality :  0.042   0.224   1052
  Planarity :  0.004   0.038   1109
  Dihedral  :  4.785  38.400    909
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 29.20 %
    Favored  : 67.82 %
  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: -0.47 (0.29), residues: 857
  helix:  0.51 (0.22), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.49 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 253 
 HIS   0.001   0.000   HIS A  70 
 PHE   0.038   0.001   PHE A 371 
 TYR   0.010   0.001   TYR B  94 
 ARG   0.005   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.9149 (tptm) cc_final: 0.8835 (tttt)
REVERT: A  153 GLN cc_start: 0.8745 (tt0) cc_final: 0.8461 (tt0)
REVERT: A  294 MET cc_start: 0.8742 (tmm) cc_final: 0.8354 (tmm)
REVERT: A  342 ILE cc_start: 0.9066 (tp) cc_final: 0.8802 (tp)
REVERT: A  350 SER cc_start: 0.9149 (p) cc_final: 0.8887 (p)
REVERT: A  420 GLN cc_start: 0.8453 (pm20) cc_final: 0.7864 (pm20)
REVERT: B  271 LYS cc_start: 0.9091 (mttt) cc_final: 0.8806 (mmtp)
REVERT: B  276 MET cc_start: 0.8703 (tpp) cc_final: 0.8463 (tpp)
REVERT: B  420 GLN cc_start: 0.8950 (pm20) cc_final: 0.8664 (pm20)
REVERT: B  421 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8686 (pp)
REVERT: B  437 GLN cc_start: 0.7813 (tp40) cc_final: 0.7605 (tp40)
  outliers start: 19
  outliers final: 12
  residues processed: 172
  average time/residue: 0.1532
  time to fit residues: 36.4600
Evaluate side-chains
  172 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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: 0.8006
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6522  Z= 0.252
  Angle     :  0.776  15.035   8867  Z= 0.369
  Chirality :  0.044   0.204   1052
  Planarity :  0.004   0.038   1109
  Dihedral  :  4.915  38.443    909
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 30.77 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.43 (0.29), residues: 857
  helix:  0.54 (0.22), residues: 623
  sheet:  None (None), residues: 0
  loop : -2.47 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 253 
 HIS   0.002   0.000   HIS B 383 
 PHE   0.055   0.002   PHE A 371 
 TYR   0.011   0.001   TYR B  94 
 ARG   0.005   0.000   ARG B 147 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.9144 (tptm) cc_final: 0.8831 (tttt)
REVERT: A  153 GLN cc_start: 0.8792 (tt0) cc_final: 0.8484 (tt0)
REVERT: A  204 MET cc_start: 0.7698 (mmp) cc_final: 0.7217 (mmt)
REVERT: A  294 MET cc_start: 0.8745 (tmm) cc_final: 0.8404 (tmm)
REVERT: A  342 ILE cc_start: 0.9078 (tp) cc_final: 0.8788 (tp)
REVERT: A  350 SER cc_start: 0.9193 (p) cc_final: 0.8929 (p)
REVERT: A  420 GLN cc_start: 0.8488 (pm20) cc_final: 0.7869 (pm20)
REVERT: B  271 LYS cc_start: 0.9148 (mttt) cc_final: 0.8860 (mmtp)
REVERT: B  276 MET cc_start: 0.8773 (tpp) cc_final: 0.8542 (tpp)
REVERT: B  420 GLN cc_start: 0.9000 (pm20) cc_final: 0.8785 (pm20)
REVERT: B  421 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8776 (pp)
  outliers start: 15
  outliers final: 13
  residues processed: 165
  average time/residue: 0.1577
  time to fit residues: 35.8754
Evaluate side-chains
  171 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0770
   chunk 70 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6738

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.127642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.105801 restraints weight = 12031.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.108657 restraints weight = 7640.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.110640 restraints weight = 5688.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6522  Z= 0.205
  Angle     :  0.760  15.579   8867  Z= 0.357
  Chirality :  0.042   0.233   1052
  Planarity :  0.004   0.037   1109
  Dihedral  :  4.831  36.331    909
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 30.93 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.31 (0.29), residues: 857
  helix:  0.61 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -2.35 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 253 
 HIS   0.001   0.000   HIS B 175 
 PHE   0.051   0.002   PHE A 371 
 TYR   0.011   0.001   TYR B  94 
 ARG   0.004   0.000   ARG B 147 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1594.32 seconds
wall clock time: 29 minutes 56.35 seconds (1796.35 seconds total)