Starting phenix.real_space_refine
on Sat Jul  4 03:26:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8by2_16319/07_2026/8by2_16319_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8by2_16319/07_2026/8by2_16319.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8by2_16319/07_2026/8by2_16319_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8by2_16319/07_2026/8by2_16319_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8by2_16319/07_2026/8by2_16319.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8by2_16319/07_2026/8by2_16319.map"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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: 7
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     P       4      5.49       5
     S      56      5.16       5
     C    5572      2.51       5
     N    1433      2.21       5
     O    1487      1.98       5
     H    8802      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 17356
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 8598
          Classifications: {'peptide': 548}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 529}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 8568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 8568
          Classifications: {'peptide': 546}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 527}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 94
          Ad-hoc single atom residues: {'  K': 1}
          Unusual residues: {'AMP%rna2p': 1, 'GSH': 1, 'PGW': 1}
          Classifications: {'RNA_mixed': 1, 'undetermined': 2}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 2}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 94
          Ad-hoc single atom residues: {'  K': 1}
          Unusual residues: {'AMP%rna2p': 1, 'GSH': 1, 'PGW': 1}
          Classifications: {'RNA_mixed': 1, 'undetermined': 2}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 2}
          Chain breaks: 1
  Time building chain proxies: 3.02, per 1000 atoms: 0.17
  Number of scatterers: 17356
  At special positions: 0
  Unit cell: (93.03, 73.538, 110.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     K       2     19.00
     S      56     16.00
     P       4     15.00
     O    1487      8.00
     N    1433      7.00
     C    5572      6.00
     H    8802      1.00
    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: 1.58
  Conformation dependent library (CDL) restraints added in 469.9 milliseconds
  

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1992

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      78.3% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 26
      Proline residue:  A  21  - end of helix
    Processing helix  chain 'A' and resid 29 through 42
    Processing helix  chain 'A' and resid 53 through 72
    Processing helix  chain 'A' and resid 75 through 82
    Processing helix  chain 'A' and resid 82 through 109
      removed outlier: 4.369A  pdb=" N   ALA A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   LEU A 100 " --> pdb=" O   ILE A  96 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LEU A 103 " --> pdb=" O   GLY A  99 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   PHE A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 123
      removed outlier: 3.727A  pdb=" N   GLU A 116 " --> pdb=" O   TRP A 112 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   LEU A 117 " --> pdb=" O   GLN A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 138
    Processing helix  chain 'A' and resid 142 through 171
      removed outlier: 4.362A  pdb=" N   ILE A 160 " --> pdb=" O   ASP A 156 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
      removed outlier: 3.893A  pdb=" N   ILE A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      Proline residue:  A 167  - end of helix
      removed outlier: 3.818A  pdb=" N   THR A 171 " --> pdb=" O   PRO A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 177
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 4.160A  pdb=" N   LEU A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 202
      removed outlier: 3.533A  pdb=" N   ARG A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 212
      removed outlier: 3.590A  pdb=" N   VAL A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 238
    Processing helix  chain 'A' and resid 240 through 255
      removed outlier: 3.602A  pdb=" N   GLY A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 283
      Proline residue:  A 267  - end of helix
      removed outlier: 4.114A  pdb=" N   GLY A 270 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   LEU A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER A 283 " --> pdb=" O   GLY A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 316
      removed outlier: 3.681A  pdb=" N   LEU A 299 " --> pdb=" O   ARG A 295 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLY A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ILE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS A 307 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   ARG A 316 " --> pdb=" O   TRP A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 333
      removed outlier: 3.849A  pdb=" N   PHE A 328 " --> pdb=" O   GLN A 324 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 348
      removed outlier: 3.877A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   MET A 348 " --> pdb=" O   GLY A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 370
    Processing helix  chain 'A' and resid 370 through 382
      removed outlier: 3.689A  pdb=" N   LEU A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 419
      removed outlier: 3.558A  pdb=" N   ILE A 413 " --> pdb=" O   ARG A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 439
      removed outlier: 3.510A  pdb=" N   HIS A 434 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLU A 436 " --> pdb=" O   ASP A 433 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ARG A 439 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 459
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 499 through 510
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 536 through 560
      removed outlier: 3.645A  pdb=" N   MET A 560 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 19
    Processing helix  chain 'B' and resid 19 through 27
      removed outlier: 3.550A  pdb=" N   ALA B  23 " --> pdb=" O   ILE B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 41
    Processing helix  chain 'B' and resid 51 through 72
      removed outlier: 3.954A  pdb=" N   ILE B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   LEU B  56 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 82
    Processing helix  chain 'B' and resid 89 through 109
      removed outlier: 3.734A  pdb=" N   GLN B  93 " --> pdb=" O   GLY B  89 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY B  99 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 123
      removed outlier: 3.860A  pdb=" N   GLU B 116 " --> pdb=" O   TRP B 112 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   LEU B 117 " --> pdb=" O   GLN B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 138
    Processing helix  chain 'B' and resid 142 through 165
      removed outlier: 4.265A  pdb=" N   ILE B 160 " --> pdb=" O   ASP B 156 " (cutoff:3.500A)
      Proline residue:  B 161  - end of helix
    Processing helix  chain 'B' and resid 165 through 170
      removed outlier: 3.512A  pdb=" N   LEU B 169 " --> pdb=" O   MET B 165 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ALA B 170 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 165 through 170'
    Processing helix  chain 'B' and resid 176 through 202
      removed outlier: 3.795A  pdb=" N   ALA B 191 " --> pdb=" O   LYS B 187 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 212
    Processing helix  chain 'B' and resid 217 through 236
      removed outlier: 3.749A  pdb=" N   GLU B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 255
      removed outlier: 3.633A  pdb=" N   GLY B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 266
    Processing helix  chain 'B' and resid 267 through 269
      No H-bonds generated for 'chain 'B' and resid 267 through 269'
    Processing helix  chain 'B' and resid 270 through 284
      removed outlier: 4.252A  pdb=" N   PHE B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 292
    Processing helix  chain 'B' and resid 292 through 316
      removed outlier: 3.876A  pdb=" N   ILE B 296 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU B 300 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   PHE B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ARG B 316 " --> pdb=" O   TRP B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 333
    Processing helix  chain 'B' and resid 337 through 349
      removed outlier: 3.808A  pdb=" N   VAL B 341 " --> pdb=" O   GLU B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 370
    Processing helix  chain 'B' and resid 370 through 383
      removed outlier: 3.783A  pdb=" N   LEU B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLN B 383 " --> pdb=" O   ASN B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 420
      removed outlier: 3.865A  pdb=" N   ILE B 413 " --> pdb=" O   ARG B 409 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR B 414 " --> pdb=" O   PHE B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 440
      removed outlier: 4.090A  pdb=" N   LYS B 440 " --> pdb=" O   THR B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 457
      removed outlier: 4.247A  pdb=" N   LEU B 456 " --> pdb=" O   ARG B 452 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   GLU B 457 " --> pdb=" O   MET B 453 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 452 through 457'
    Processing helix  chain 'B' and resid 458 through 460
      No H-bonds generated for 'chain 'B' and resid 458 through 460'
    Processing helix  chain 'B' and resid 473 through 488
    Processing helix  chain 'B' and resid 499 through 510
      removed outlier: 3.600A  pdb=" N   ARG B 505 " --> pdb=" O   ASP B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 534
    Processing helix  chain 'B' and resid 536 through 560
    Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 447
      removed outlier: 3.687A  pdb=" N   LYS A 444 " --> pdb=" O   MET A 425 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL A 402 " --> pdb=" O   VAL A 426 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   LEU A 428 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE A 404 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 497
    Processing sheet with id=AA3, first strand: chain 'B' and resid 444 through 447
      removed outlier: 4.075A  pdb=" N   LYS B 444 " --> pdb=" O   MET B 425 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL B 466 " --> pdb=" O   ARG B 401 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 496 through 497

    572 hydrogen bonds defined for protein.
    1701 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: 3.91

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8796
        1.03 -     1.23: 14
        1.23 -     1.42: 3426
        1.42 -     1.62: 5156
        1.62 -     1.81: 108
  Bond restraints: 17500
  Sorted by residual:
  bond pdb=" C4' AMP A 602 "
       pdb=" O4' AMP A 602 "
    ideal  model  delta    sigma   weight residual
    1.426  1.454 -0.028 2.00e-02 2.50e+03 1.93e+00
  bond pdb=" C4' AMP B 602 "
       pdb=" O4' AMP B 602 "
    ideal  model  delta    sigma   weight residual
    1.426  1.453 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C3  GSH A 603 "
       pdb=" CA3 GSH A 603 "
    ideal  model  delta    sigma   weight residual
    1.552  1.527  0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" C3  GSH B 603 "
       pdb=" CA3 GSH B 603 "
    ideal  model  delta    sigma   weight residual
    1.552  1.527  0.025 2.00e-02 2.50e+03 1.52e+00
  bond pdb=" C4  AMP B 602 "
       pdb=" C5  AMP B 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.465  0.025 2.00e-02 2.50e+03 1.50e+00
  ... (remaining 17495 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 31485
        1.92 -     3.84: 182
        3.84 -     5.76: 38
        5.76 -     7.67: 1
        7.67 -     9.59: 3
  Bond angle restraints: 31709
  Sorted by residual:
  angle pdb=" N   VAL B  86 "
        pdb=" CA  VAL B  86 "
        pdb=" C   VAL B  86 "
      ideal   model   delta    sigma   weight residual
     113.53  109.10    4.43 9.80e-01 1.04e+00 2.04e+01
  angle pdb=" C1' AMP B 602 "
        pdb=" C2' AMP B 602 "
        pdb=" C3' AMP B 602 "
      ideal   model   delta    sigma   weight residual
     111.00  101.41    9.59 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" C1' AMP A 602 "
        pdb=" C2' AMP A 602 "
        pdb=" C3' AMP A 602 "
      ideal   model   delta    sigma   weight residual
     111.00  101.56    9.44 3.00e+00 1.11e-01 9.91e+00
  angle pdb=" C2' AMP B 602 "
        pdb=" C3' AMP B 602 "
        pdb=" C4' AMP B 602 "
      ideal   model   delta    sigma   weight residual
     111.00  103.26    7.74 3.00e+00 1.11e-01 6.65e+00
  angle pdb=" C2' AMP A 602 "
        pdb=" C3' AMP A 602 "
        pdb=" C4' AMP A 602 "
      ideal   model   delta    sigma   weight residual
     111.00  103.39    7.61 3.00e+00 1.11e-01 6.43e+00
  ... (remaining 31704 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.00: 7706
       35.00 -    70.00: 400
       70.00 -   105.01: 22
      105.01 -   140.01: 3
      140.01 -   175.01: 4
  Dihedral angle restraints: 8135
    sinusoidal: 4563
      harmonic: 3572
  Sorted by residual:
  dihedral pdb=" C5' AMP B 602 "
           pdb=" O5' AMP B 602 "
           pdb=" P   AMP B 602 "
           pdb=" O3P AMP B 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   66.55 -126.54     1      2.00e+01 2.50e-03 3.83e+01
  dihedral pdb=" O01 PGW B 604 "
           pdb=" C01 PGW B 604 "
           pdb=" C02 PGW B 604 "
           pdb=" O03 PGW B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.30 -115.71  175.01     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C03 PGW B 604 "
           pdb=" C01 PGW B 604 "
           pdb=" C02 PGW B 604 "
           pdb=" O03 PGW B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.35  120.45  174.90     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 8132 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1141
       0.040 -    0.080: 186
       0.080 -    0.121: 63
       0.121 -    0.161: 4
       0.161 -    0.201: 2
  Chirality restraints: 1396
  Sorted by residual:
  chirality pdb=" C3' AMP B 602 "
            pdb=" C2' AMP B 602 "
            pdb=" C4' AMP B 602 "
            pdb=" O3' AMP B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.71    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" C3' AMP A 602 "
            pdb=" C2' AMP A 602 "
            pdb=" C4' AMP A 602 "
            pdb=" O3' AMP A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.71    0.20 2.00e-01 2.50e+01 9.98e-01
  chirality pdb=" CA  ILE A 494 "
            pdb=" N   ILE A 494 "
            pdb=" C   ILE A 494 "
            pdb=" CB  ILE A 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1393 not shown)

  Planarity restraints: 2512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  GSH A 603 "   -0.003 2.00e-02 2.50e+03   2.41e-02 7.25e+00
        pdb=" CA2 GSH A 603 "    0.021 2.00e-02 2.50e+03
        pdb=" CA3 GSH A 603 "    0.029 2.00e-02 2.50e+03
        pdb=" N3  GSH A 603 "   -0.039 2.00e-02 2.50e+03
        pdb=" O2  GSH A 603 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 316 "    0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO B 317 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 317 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 317 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 302 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.15e+00
        pdb=" C   GLY A 302 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLY A 302 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A 303 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2509 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.32: 4096
        2.32 -     3.02: 47036
        3.02 -     3.73: 60637
        3.73 -     4.43: 91336
        4.43 -     5.14: 145154
  Nonbonded interactions: 348259
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A  93 "
            pdb="HE22 GLN A 155 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" OD1 ASP A  51 "
            pdb=" H   SER A  54 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" O   ARG B 212 "
            pdb=" HE  ARG B 212 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" OD1 ASP B 429 "
            pdb=" H   HIS B 430 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" OE1 GLU A 512 "
            pdb=" H   GLU A 512 "
     model   vdw
     1.662 2.450
  ... (remaining 348254 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 385 or resid 400 through 604))
  selection = (chain 'B' and (resid 1 through 126 or (resid 127 and (name N or name CA or name \ 
 C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB  \ 
or name HG21 or name HG22 or name HG23)) or resid 128 through 604))
}

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:             1.960
  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:             0.110
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.280
  Find NCS groups from input model:        0.280
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
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      :  0.002   0.028   8698  Z= 0.119
  Angle     :  0.572   9.593  11751  Z= 0.274
  Chirality :  0.035   0.201   1396
  Planarity :  0.004   0.066   1457
  Dihedral  : 19.760 175.012   3244
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.83 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.27), residues: 1086
  helix:  2.27 (0.19), residues: 799
  sheet: -0.61 (0.64), residues: 60
  loop : -2.29 (0.38), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 208 
 TYR   0.019   0.001   TYR A 538 
 PHE   0.008   0.001   PHE A 410 
 TRP   0.007   0.001   TRP B  44 
 HIS   0.003   0.001   HIS B 259 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 8698)
  covalent geometry    : angle       0.57217 /  0.27 (11751)
  hydrogen bonds       : bond        0.06895 /  5.08 (  572)
  hydrogen bonds       : angle       4.08771 /  2.99 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  135 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1926
  time to fit residues: 37.2697
Evaluate side-chains
  131 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.3322

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.139831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112380 restraints weight = 35441.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.80
r_work: 0.3218 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.0426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8698  Z= 0.150
  Angle     :  0.545   6.444  11751  Z= 0.268
  Chirality :  0.035   0.137   1396
  Planarity :  0.004   0.058   1457
  Dihedral  : 14.970 175.186   1322
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 24.37 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.27), residues: 1086
  helix:  2.10 (0.19), residues: 800
  sheet: -0.62 (0.64), residues: 60
  loop : -2.30 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 496 
 TYR   0.016   0.002   TYR B 257 
 PHE   0.010   0.001   PHE A 410 
 TRP   0.011   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 259 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 8698)
  covalent geometry    : angle       0.54458 /  0.27 (11751)
  hydrogen bonds       : bond        0.03831 /  2.57 (  572)
  hydrogen bonds       : angle       3.77852 /  2.80 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  145 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 ASP cc_start: 0.8905 (m-30) cc_final: 0.8650 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 140
  average time/residue: 0.1954
  time to fit residues: 38.1188
Evaluate side-chains
  139 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.137728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.110992 restraints weight = 35711.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.78
r_work: 0.3199 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.0584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8698  Z= 0.145
  Angle     :  0.540   6.177  11751  Z= 0.264
  Chirality :  0.035   0.143   1396
  Planarity :  0.004   0.054   1457
  Dihedral  : 14.475 175.610   1322
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 23.56 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.27), residues: 1086
  helix:  2.03 (0.19), residues: 800
  sheet: -0.70 (0.64), residues: 60
  loop : -2.34 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 439 
 TYR   0.014   0.002   TYR B 257 
 PHE   0.010   0.001   PHE B 328 
 TRP   0.011   0.001   TRP B  44 
 HIS   0.002   0.001   HIS A 502 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 ( 8698)
  covalent geometry    : angle       0.54021 /  0.26 (11751)
  hydrogen bonds       : bond        0.03997 /  2.69 (  572)
  hydrogen bonds       : angle       3.81332 /  2.82 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 ASP cc_start: 0.8900 (m-30) cc_final: 0.8685 (m-30)
REVERT: B  243 MET cc_start: 0.8325 (mmp) cc_final: 0.8115 (mmp)
  outliers start: 14
  outliers final: 13
  residues processed: 141
  average time/residue: 0.1973
  time to fit residues: 39.5128
Evaluate side-chains
  144 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.138615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112031 restraints weight = 35390.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.78
r_work: 0.3221 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.0644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8698  Z= 0.114
  Angle     :  0.531   6.115  11751  Z= 0.257
  Chirality :  0.035   0.143   1396
  Planarity :  0.004   0.053   1457
  Dihedral  : 14.113 174.924   1322
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 23.22 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.27), residues: 1086
  helix:  2.07 (0.19), residues: 800
  sheet: -0.70 (0.63), residues: 60
  loop : -2.31 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 439 
 TYR   0.010   0.001   TYR B 257 
 PHE   0.009   0.001   PHE A 410 
 TRP   0.010   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 8698)
  covalent geometry    : angle       0.53145 /  0.26 (11751)
  hydrogen bonds       : bond        0.03707 /  2.51 (  572)
  hydrogen bonds       : angle       3.74876 /  2.78 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  158 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 GLU cc_start: 0.8345 (tp30) cc_final: 0.8073 (tp30)
REVERT: B  216 ARG cc_start: 0.6939 (ptt90) cc_final: 0.6712 (ptm160)
REVERT: B  243 MET cc_start: 0.8307 (mmp) cc_final: 0.8068 (mmp)
  outliers start: 18
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1789
  time to fit residues: 37.7082
Evaluate side-chains
  150 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.139903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.112900 restraints weight = 35200.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.77
r_work: 0.3222 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.0674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8698  Z= 0.110
  Angle     :  0.530   6.142  11751  Z= 0.255
  Chirality :  0.035   0.143   1396
  Planarity :  0.004   0.051   1457
  Dihedral  : 13.531 174.657   1322
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 22.99 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.27), residues: 1086
  helix:  2.11 (0.19), residues: 799
  sheet: -0.69 (0.63), residues: 60
  loop : -2.27 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 439 
 TYR   0.010   0.001   TYR B 257 
 PHE   0.009   0.001   PHE A 410 
 TRP   0.009   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 8698)
  covalent geometry    : angle       0.52966 /  0.26 (11751)
  hydrogen bonds       : bond        0.03576 /  2.42 (  572)
  hydrogen bonds       : angle       3.72292 /  2.76 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  154 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.4062 (mp)
REVERT: B  216 ARG cc_start: 0.6899 (ptt90) cc_final: 0.6683 (ptm160)
  outliers start: 20
  outliers final: 17
  residues processed: 145
  average time/residue: 0.1858
  time to fit residues: 38.0114
Evaluate side-chains
  149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.139017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.112438 restraints weight = 35228.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.78
r_work: 0.3218 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.0717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8698  Z= 0.111
  Angle     :  0.525   6.202  11751  Z= 0.254
  Chirality :  0.035   0.143   1396
  Planarity :  0.004   0.051   1457
  Dihedral  : 13.062 174.695   1322
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 23.33 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.27), residues: 1086
  helix:  2.13 (0.19), residues: 800
  sheet: -0.69 (0.63), residues: 60
  loop : -2.31 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 439 
 TYR   0.010   0.001   TYR B 257 
 PHE   0.009   0.001   PHE A 410 
 TRP   0.009   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 8698)
  covalent geometry    : angle       0.52466 /  0.25 (11751)
  hydrogen bonds       : bond        0.03519 /  2.37 (  572)
  hydrogen bonds       : angle       3.72110 /  2.75 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.4063 (mp)
REVERT: B  216 ARG cc_start: 0.7006 (ptt90) cc_final: 0.6765 (ptm160)
  outliers start: 19
  outliers final: 16
  residues processed: 144
  average time/residue: 0.1704
  time to fit residues: 34.4138
Evaluate side-chains
  149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 4 optimal weight:    0.3980
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 350 ASN ** 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 = 0.3669 r_free = 0.3669 target = 0.137035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.110181 restraints weight = 35435.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.77
r_work: 0.3186 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8698  Z= 0.159
  Angle     :  0.559   6.563  11751  Z= 0.275
  Chirality :  0.036   0.141   1396
  Planarity :  0.004   0.056   1457
  Dihedral  : 12.867 175.788   1322
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 23.33 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.27), residues: 1086
  helix:  1.97 (0.19), residues: 798
  sheet: -0.69 (0.64), residues: 60
  loop : -2.34 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 439 
 TYR   0.012   0.002   TYR A 201 
 PHE   0.010   0.001   PHE B 328 
 TRP   0.012   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 430 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 8698)
  covalent geometry    : angle       0.55932 /  0.27 (11751)
  hydrogen bonds       : bond        0.04115 /  2.77 (  572)
  hydrogen bonds       : angle       3.88084 /  2.87 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  153 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 LEU cc_start: 0.4494 (OUTLIER) cc_final: 0.3948 (mp)
  outliers start: 20
  outliers final: 18
  residues processed: 144
  average time/residue: 0.2014
  time to fit residues: 40.0700
Evaluate side-chains
  149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 350 ASN ** 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 = 0.3684 r_free = 0.3684 target = 0.138271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111302 restraints weight = 35153.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.76
r_work: 0.3201 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8698  Z= 0.128
  Angle     :  0.548   6.420  11751  Z= 0.267
  Chirality :  0.035   0.145   1396
  Planarity :  0.004   0.062   1457
  Dihedral  : 12.743 175.220   1322
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 23.56 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.27), residues: 1086
  helix:  1.96 (0.19), residues: 804
  sheet: -0.68 (0.65), residues: 60
  loop : -2.39 (0.38), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 439 
 TYR   0.011   0.001   TYR B 257 
 PHE   0.009   0.001   PHE A 410 
 TRP   0.011   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 8698)
  covalent geometry    : angle       0.54800 /  0.27 (11751)
  hydrogen bonds       : bond        0.03845 /  2.59 (  572)
  hydrogen bonds       : angle       3.82123 /  2.82 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 LEU cc_start: 0.7012 (tt) cc_final: 0.6732 (tp)
REVERT: A  289 LEU cc_start: 0.4492 (OUTLIER) cc_final: 0.3961 (mp)
  outliers start: 18
  outliers final: 15
  residues processed: 144
  average time/residue: 0.1872
  time to fit residues: 37.4110
Evaluate side-chains
  150 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 350 ASN ** 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 = 0.3698 r_free = 0.3698 target = 0.139066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.112560 restraints weight = 35399.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.71
r_work: 0.3229 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8698  Z= 0.115
  Angle     :  0.546   6.362  11751  Z= 0.265
  Chirality :  0.035   0.171   1396
  Planarity :  0.004   0.067   1457
  Dihedral  : 12.612 174.836   1322
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 23.45 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.27), residues: 1086
  helix:  2.02 (0.19), residues: 798
  sheet: -0.63 (0.65), residues: 60
  loop : -2.30 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 439 
 TYR   0.010   0.001   TYR B 257 
 PHE   0.008   0.001   PHE A 410 
 TRP   0.010   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 487 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 8698)
  covalent geometry    : angle       0.54582 /  0.26 (11751)
  hydrogen bonds       : bond        0.03697 /  2.51 (  572)
  hydrogen bonds       : angle       3.78622 /  2.80 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 ARG cc_start: 0.8049 (tmm160) cc_final: 0.7746 (ttp-110)
REVERT: A  289 LEU cc_start: 0.4392 (OUTLIER) cc_final: 0.3942 (mp)
  outliers start: 18
  outliers final: 17
  residues processed: 143
  average time/residue: 0.1892
  time to fit residues: 38.0321
Evaluate side-chains
  149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0570
   chunk 32 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.7700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 350 ASN ** 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 = 0.3700 r_free = 0.3700 target = 0.139293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.112798 restraints weight = 35273.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.70
r_work: 0.3238 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8698  Z= 0.108
  Angle     :  0.539   6.298  11751  Z= 0.260
  Chirality :  0.035   0.144   1396
  Planarity :  0.004   0.071   1457
  Dihedral  : 12.489 174.641   1322
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 23.33 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.27), residues: 1086
  helix:  2.03 (0.19), residues: 805
  sheet: -0.61 (0.65), residues: 60
  loop : -2.38 (0.38), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 439 
 TYR   0.009   0.001   TYR B 257 
 PHE   0.008   0.001   PHE A 410 
 TRP   0.009   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 8698)
  covalent geometry    : angle       0.53945 /  0.26 (11751)
  hydrogen bonds       : bond        0.03525 /  2.39 (  572)
  hydrogen bonds       : angle       3.75253 /  2.77 ( 1701)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 ARG cc_start: 0.8080 (tmm160) cc_final: 0.7785 (ttp-110)
REVERT: A  289 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3873 (mp)
REVERT: A  560 MET cc_start: 0.6984 (tpt) cc_final: 0.6733 (tpt)
  outliers start: 19
  outliers final: 16
  residues processed: 143
  average time/residue: 0.1772
  time to fit residues: 35.7730
Evaluate side-chains
  147 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  496 ARG
Chi-restraints excluded: chain B residue  560 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0270
   chunk 63 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0000
   chunk 79 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.0046

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.138882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.112410 restraints weight = 35501.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.70
r_work: 0.3228 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8698  Z= 0.123
  Angle     :  0.549   6.673  11751  Z= 0.266
  Chirality :  0.035   0.143   1396
  Planarity :  0.004   0.070   1457
  Dihedral  : 12.453 175.004   1322
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 23.56 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.27), residues: 1086
  helix:  2.04 (0.19), residues: 798
  sheet: -0.57 (0.66), residues: 60
  loop : -2.31 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 439 
 TYR   0.009   0.001   TYR B 257 
 PHE   0.009   0.001   PHE A 410 
 TRP   0.010   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 487 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 8698)
  covalent geometry    : angle       0.54934 /  0.27 (11751)
  hydrogen bonds       : bond        0.03661 /  2.48 (  572)
  hydrogen bonds       : angle       3.78277 /  2.80 ( 1701)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3552.85 seconds
wall clock time: 60 minutes 53.18 seconds (3653.18 seconds total)