Starting phenix.real_space_refine
on Wed Feb 12 06:31:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8l_36073/02_2025/8j8l_36073_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8l_36073/02_2025/8j8l_36073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8l_36073/02_2025/8j8l_36073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8l_36073/02_2025/8j8l_36073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8l_36073/02_2025/8j8l_36073_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8l_36073/02_2025/8j8l_36073_neut.cif"
  }
  resolution = 3.56
  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=  -0.003 sd=   0.039
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      27      5.16       5
     C    4809      2.51       5
     N    1187      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7361
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3656
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3579
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 24, 'TRANS': 438}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Classifications: {'peptide': 1}
  Time building chain proxies: 4.66, per 1000 atoms: 0.63
  Number of scatterers: 7361
  At special positions: 0
  Unit cell: (99.645, 83.22, 129.21, 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      27     16.00
     O    1338      8.00
     N    1187      7.00
     C    4809      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 1.87
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1718

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      58.7% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 179 through 207
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.756A  pdb=" N   HIS A 221 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 222'
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 4.445A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 287 through 302
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.575A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.728A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.624A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.615A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 450 through 460
      removed outlier: 3.628A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR A 460 " --> pdb=" O   LEU A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 532
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
      removed outlier: 3.660A  pdb=" N   VAL B  70 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 79
      removed outlier: 3.946A  pdb=" N   LEU B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.536A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLU B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 124
      removed outlier: 4.000A  pdb=" N   GLU B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 158
      removed outlier: 4.789A  pdb=" N   ARG B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      Proline residue:  B 142  - end of helix
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.756A  pdb=" N   ALA B 171 " --> pdb=" O   PRO B 167 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS B 172 " --> pdb=" O   GLU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
      removed outlier: 3.678A  pdb=" N   ALA B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 245
      No H-bonds generated for 'chain 'B' and resid 243 through 245'
    Processing helix  chain 'B' and resid 246 through 251
    Processing helix  chain 'B' and resid 269 through 298
      removed outlier: 3.627A  pdb=" N   ASN B 273 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 3.645A  pdb=" N   HIS B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY B 321 " --> pdb=" O   ASN B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 357
      removed outlier: 4.647A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 389
      removed outlier: 4.003A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 422
      removed outlier: 3.929A  pdb=" N   SER B 401 " --> pdb=" O   ILE B 397 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE B 416 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TRP B 417 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 451
      removed outlier: 4.270A  pdb=" N   PHE B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 476
      removed outlier: 3.865A  pdb=" N   ILE B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B 465 " --> pdb=" O   GLY B 461 " (cutoff:3.500A)
      Proline residue:  B 470  - end of helix
      removed outlier: 3.895A  pdb=" N   GLY B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 500
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
      removed outlier: 3.590A  pdb=" N   PHE A 467 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.853A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 545
      removed outlier: 3.568A  pdb=" N   PHE A 545 " --> pdb=" O   SER A 553 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 621 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   GLY A 622 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   SER A 599 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 626 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 575 through 576
      removed outlier: 3.569A  pdb=" N   LEU A 575 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1095 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: 1.95

  Time building geometry restraints manager: 2.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2166
        1.34 -     1.46: 1276
        1.46 -     1.58: 4060
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7542
  Sorted by residual:
  bond pdb=" C   DAH B 601 "
       pdb=" OXT DAH B 601 "
    ideal  model  delta    sigma   weight residual
    1.360  1.257  0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" C4  NAG F   1 "
       pdb=" O4  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.409  1.477 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.64e+00
  bond pdb=" C3  NAG F   1 "
       pdb=" O3  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.435 -0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" CB  DAH B 601 "
       pdb=" CG  DAH B 601 "
    ideal  model  delta    sigma   weight residual
    1.487  1.517 -0.030 2.00e-02 2.50e+03 2.24e+00
  ... (remaining 7537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 10027
        2.03 -     4.06: 197
        4.06 -     6.09: 37
        6.09 -     8.12: 7
        8.12 -    10.15: 3
  Bond angle restraints: 10271
  Sorted by residual:
  angle pdb=" C   LEU B 138 "
        pdb=" N   ILE B 139 "
        pdb=" CA  ILE B 139 "
      ideal   model   delta    sigma   weight residual
     123.16  119.05    4.11 1.06e+00 8.90e-01 1.50e+01
  angle pdb=" N   ILE B 429 "
        pdb=" CA  ILE B 429 "
        pdb=" C   ILE B 429 "
      ideal   model   delta    sigma   weight residual
     113.22  117.46   -4.24 1.23e+00 6.61e-01 1.19e+01
  angle pdb=" CA  DAH B 601 "
        pdb=" C   DAH B 601 "
        pdb=" O   DAH B 601 "
      ideal   model   delta    sigma   weight residual
     128.96  118.81   10.15 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" N   PRO B 428 "
        pdb=" CA  PRO B 428 "
        pdb=" C   PRO B 428 "
      ideal   model   delta    sigma   weight residual
     112.47  119.32   -6.85 2.06e+00 2.36e-01 1.11e+01
  angle pdb=" N   GLU B  78 "
        pdb=" CA  GLU B  78 "
        pdb=" C   GLU B  78 "
      ideal   model   delta    sigma   weight residual
     114.31  110.14    4.17 1.29e+00 6.01e-01 1.05e+01
  ... (remaining 10266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.38: 4227
       25.38 -    50.76: 234
       50.76 -    76.14: 31
       76.14 -   101.53: 15
      101.53 -   126.91: 11
  Dihedral angle restraints: 4518
    sinusoidal: 1845
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" C2  NAG D   2 "
           pdb=" C1  NAG D   2 "
           pdb=" O5  NAG D   2 "
           pdb=" C5  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   63.95 -126.91     1      3.00e+01 1.11e-03 1.71e+01
  dihedral pdb=" C2  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   56.03  119.08     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" O3  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.45  176.99  118.46     1      3.00e+01 1.11e-03 1.57e+01
  ... (remaining 4515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.279: 1209
       0.279 -    0.558: 1
       0.558 -    0.837: 1
       0.837 -    1.117: 0
       1.117 -    1.396: 1
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.70    0.30 2.00e-02 2.50e+03 2.22e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-02 2.50e+03 1.35e+02
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.43e+01
  ... (remaining 1209 not shown)

  Planarity restraints: 1275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.328 2.00e-02 2.50e+03   2.82e-01 9.96e+02
        pdb=" C7  NAG D   2 "   -0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.026 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.490 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.211 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.300 2.00e-02 2.50e+03   2.52e-01 7.94e+02
        pdb=" C7  NAG D   1 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.431 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "   -0.294 2.00e-02 2.50e+03   2.50e-01 7.79e+02
        pdb=" C7  NAG F   1 "    0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "    0.430 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1272 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 873
        2.75 -     3.28: 7800
        3.28 -     3.82: 12211
        3.82 -     4.36: 13372
        4.36 -     4.90: 22899
  Nonbonded interactions: 57155
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 356 "
            pdb=" OG  SER A 359 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" NH2 ARG B 419 "
            pdb=" O   LYS B 422 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OD1 ASN A 366 "
            pdb=" C8  NAG D   2 "
     model   vdw
     2.219 3.460
  nonbonded pdb=" O   TYR A 251 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ILE B 268 "
            pdb=" ND2 ASN B 273 "
     model   vdw
     2.256 3.120
  ... (remaining 57150 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.960
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
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      :  0.004   0.103   7542  Z= 0.240
  Angle     :  0.694  10.145  10271  Z= 0.354
  Chirality :  0.062   1.396   1212
  Planarity :  0.016   0.282   1271
  Dihedral  : 17.563 126.907   2797
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  0.89 %
    Favored  : 98.22 %
  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:  0.16 (0.29), residues: 928
  helix:  1.32 (0.25), residues: 481
  sheet:  0.09 (0.67), residues: 59
  loop : -1.48 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 184 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.014   0.001   PHE B 402 
 TYR   0.015   0.001   TYR B 289 
 ARG   0.008   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8006 (m-30) cc_final: 0.7689 (m-30)
REVERT: B   84 LEU cc_start: 0.9120 (tp) cc_final: 0.8914 (tt)
REVERT: B  141 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8547 (mmp80)
REVERT: B  259 TYR cc_start: 0.8902 (m-80) cc_final: 0.8506 (m-80)
REVERT: B  383 MET cc_start: 0.8573 (tpp) cc_final: 0.7994 (mpp)
  outliers start: 7
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1733
  time to fit residues: 26.2177
Evaluate side-chains
  66 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 429 ASN
A 561 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.062794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.045826 restraints weight = 38508.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.047293 restraints weight = 20673.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.048242 restraints weight = 14489.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7542  Z= 0.195
  Angle     :  0.720  11.384  10271  Z= 0.335
  Chirality :  0.045   0.332   1212
  Planarity :  0.005   0.048   1271
  Dihedral  : 14.328 103.780   1159
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.55 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.28), residues: 928
  helix:  1.76 (0.24), residues: 492
  sheet: -0.30 (0.63), residues: 66
  loop : -1.20 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 325 
 HIS   0.006   0.001   HIS B 367 
 PHE   0.021   0.001   PHE A 190 
 TYR   0.015   0.002   TYR B 103 
 ARG   0.005   0.001   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9351 (pp)
REVERT: A  471 ASP cc_start: 0.8106 (m-30) cc_final: 0.7704 (m-30)
REVERT: A  508 MET cc_start: 0.9271 (ptp) cc_final: 0.8815 (ptp)
REVERT: B   47 GLN cc_start: 0.8250 (mm110) cc_final: 0.8034 (mm-40)
REVERT: B  120 MET cc_start: 0.9006 (ppp) cc_final: 0.8604 (ppp)
REVERT: B  141 ARG cc_start: 0.9201 (mmp80) cc_final: 0.8884 (mmp80)
REVERT: B  262 PHE cc_start: 0.9489 (m-10) cc_final: 0.9286 (m-80)
REVERT: B  267 MET cc_start: 0.9283 (mpp) cc_final: 0.8957 (pmm)
REVERT: B  365 MET cc_start: 0.8162 (mmm) cc_final: 0.7891 (mmm)
REVERT: B  383 MET cc_start: 0.9211 (tpp) cc_final: 0.8630 (mpp)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1578
  time to fit residues: 18.5661
Evaluate side-chains
  67 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0980
   chunk 48 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0970
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.063309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.046035 restraints weight = 39204.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.047528 restraints weight = 20905.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.048488 restraints weight = 14664.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7542  Z= 0.165
  Angle     :  0.644  12.245  10271  Z= 0.299
  Chirality :  0.041   0.233   1212
  Planarity :  0.005   0.056   1271
  Dihedral  : 13.326 110.283   1157
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 12.33 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.28), residues: 928
  helix:  1.96 (0.24), residues: 486
  sheet: -0.23 (0.64), residues: 66
  loop : -1.14 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 477 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.018   0.001   PHE B 402 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.006   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8109 (m-30) cc_final: 0.7693 (m-30)
REVERT: A  508 MET cc_start: 0.9266 (ptp) cc_final: 0.8793 (ptp)
REVERT: B  120 MET cc_start: 0.9027 (ppp) cc_final: 0.8581 (ppp)
REVERT: B  141 ARG cc_start: 0.9239 (mmp80) cc_final: 0.9037 (mmp80)
REVERT: B  262 PHE cc_start: 0.9506 (m-10) cc_final: 0.9254 (m-80)
REVERT: B  267 MET cc_start: 0.9319 (mpp) cc_final: 0.8956 (pmm)
REVERT: B  365 MET cc_start: 0.8200 (mmm) cc_final: 0.7849 (mmm)
REVERT: B  383 MET cc_start: 0.9203 (tpp) cc_final: 0.8675 (mpp)
  outliers start: 7
  outliers final: 3
  residues processed: 77
  average time/residue: 0.1575
  time to fit residues: 18.0343
Evaluate side-chains
  68 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 59 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.062134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.044937 restraints weight = 39677.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.046405 restraints weight = 21270.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.047335 restraints weight = 14960.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7542  Z= 0.214
  Angle     :  0.650  10.504  10271  Z= 0.304
  Chirality :  0.041   0.249   1212
  Planarity :  0.004   0.047   1271
  Dihedral  : 12.260 110.659   1157
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.87 %
    Favored  : 83.99 %
  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:  0.96 (0.29), residues: 928
  helix:  2.03 (0.24), residues: 486
  sheet: -0.35 (0.65), residues: 66
  loop : -1.08 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.003   0.001   HIS A 266 
 PHE   0.015   0.001   PHE B 402 
 TYR   0.013   0.001   TYR B 472 
 ARG   0.006   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8117 (m-30) cc_final: 0.7698 (m-30)
REVERT: A  508 MET cc_start: 0.9278 (ptp) cc_final: 0.8951 (ptp)
REVERT: B   47 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7453 (mm-40)
REVERT: B  120 MET cc_start: 0.9065 (ppp) cc_final: 0.8610 (ppp)
REVERT: B  262 PHE cc_start: 0.9520 (m-80) cc_final: 0.9280 (m-80)
REVERT: B  267 MET cc_start: 0.9266 (mpp) cc_final: 0.8925 (pmm)
REVERT: B  365 MET cc_start: 0.8361 (mmm) cc_final: 0.7957 (mmm)
REVERT: B  383 MET cc_start: 0.9230 (tpp) cc_final: 0.8671 (mpp)
  outliers start: 9
  outliers final: 8
  residues processed: 71
  average time/residue: 0.1725
  time to fit residues: 17.5929
Evaluate side-chains
  66 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    0.0970
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.045140 restraints weight = 39721.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.046625 restraints weight = 21327.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.047547 restraints weight = 14987.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7542  Z= 0.184
  Angle     :  0.644  15.016  10271  Z= 0.297
  Chirality :  0.041   0.236   1212
  Planarity :  0.005   0.078   1271
  Dihedral  : 11.681 110.984   1157
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.12 %
    Favored  : 83.10 %
  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: 928
  helix:  2.09 (0.24), residues: 486
  sheet: -0.41 (0.64), residues: 66
  loop : -1.04 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 134 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.021   0.001   PHE B 402 
 TYR   0.011   0.001   TYR B 103 
 ARG   0.007   0.000   ARG B 355 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8104 (m-30) cc_final: 0.7665 (m-30)
REVERT: A  508 MET cc_start: 0.9256 (ptp) cc_final: 0.8946 (ptp)
REVERT: B   47 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7622 (mm-40)
REVERT: B  120 MET cc_start: 0.9102 (ppp) cc_final: 0.8606 (ppp)
REVERT: B  262 PHE cc_start: 0.9506 (m-80) cc_final: 0.9278 (m-80)
REVERT: B  267 MET cc_start: 0.9309 (mpp) cc_final: 0.8890 (pmm)
REVERT: B  365 MET cc_start: 0.8357 (mmm) cc_final: 0.6835 (mmp)
REVERT: B  383 MET cc_start: 0.9245 (tpp) cc_final: 0.8669 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 76
  average time/residue: 0.1742
  time to fit residues: 19.0889
Evaluate side-chains
  71 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.063316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.046278 restraints weight = 39603.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.047733 restraints weight = 21666.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.048644 restraints weight = 15431.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7542  Z= 0.173
  Angle     :  0.642  12.494  10271  Z= 0.295
  Chirality :  0.041   0.234   1212
  Planarity :  0.005   0.079   1271
  Dihedral  : 11.190 110.577   1156
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.39 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.12 (0.29), residues: 928
  helix:  2.20 (0.24), residues: 483
  sheet: -0.42 (0.64), residues: 66
  loop : -1.02 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.008   0.001   HIS B 367 
 PHE   0.021   0.001   PHE B 402 
 TYR   0.008   0.001   TYR B 119 
 ARG   0.006   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8185 (m-30) cc_final: 0.7753 (m-30)
REVERT: A  508 MET cc_start: 0.9258 (ptp) cc_final: 0.8950 (ptp)
REVERT: B   47 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7803 (mm-40)
REVERT: B  120 MET cc_start: 0.9114 (ppp) cc_final: 0.8580 (ppp)
REVERT: B  262 PHE cc_start: 0.9492 (m-80) cc_final: 0.9264 (m-80)
REVERT: B  267 MET cc_start: 0.9304 (mpp) cc_final: 0.8886 (pmm)
REVERT: B  297 PHE cc_start: 0.8469 (t80) cc_final: 0.8118 (t80)
REVERT: B  365 MET cc_start: 0.8552 (mmm) cc_final: 0.7347 (mmp)
REVERT: B  383 MET cc_start: 0.9209 (tpp) cc_final: 0.8641 (mpp)
  outliers start: 14
  outliers final: 12
  residues processed: 80
  average time/residue: 0.1780
  time to fit residues: 20.0436
Evaluate side-chains
  77 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 58 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** 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 = 0.3407 r_free = 0.3407 target = 0.063192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.046832 restraints weight = 38829.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.048276 restraints weight = 21140.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.049190 restraints weight = 15010.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7542  Z= 0.163
  Angle     :  0.643  12.350  10271  Z= 0.293
  Chirality :  0.041   0.247   1212
  Planarity :  0.004   0.073   1271
  Dihedral  : 10.689 110.059   1156
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.92 %
    Favored  : 80.43 %
  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:  1.19 (0.29), residues: 928
  helix:  2.27 (0.24), residues: 483
  sheet: -0.43 (0.64), residues: 66
  loop : -0.98 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 319 
 PHE   0.022   0.001   PHE B 402 
 TYR   0.021   0.001   TYR A 251 
 ARG   0.008   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8142 (m-30) cc_final: 0.7698 (m-30)
REVERT: A  508 MET cc_start: 0.9262 (ptp) cc_final: 0.8961 (ptp)
REVERT: B   47 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7861 (mm-40)
REVERT: B  120 MET cc_start: 0.9119 (ppp) cc_final: 0.8557 (ppp)
REVERT: B  145 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8804 (mp10)
REVERT: B  262 PHE cc_start: 0.9452 (m-80) cc_final: 0.9239 (m-80)
REVERT: B  267 MET cc_start: 0.9239 (mpp) cc_final: 0.8793 (pmm)
REVERT: B  365 MET cc_start: 0.8625 (mmm) cc_final: 0.6972 (tpp)
REVERT: B  383 MET cc_start: 0.9160 (tpp) cc_final: 0.8566 (mpp)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1779
  time to fit residues: 19.5766
Evaluate side-chains
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  473 PHE
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 86 optimal weight:    9.9990
   chunk 67 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** 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 = 0.3379 r_free = 0.3379 target = 0.062338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.045523 restraints weight = 40147.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.046959 restraints weight = 22227.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.047863 restraints weight = 15905.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7542  Z= 0.209
  Angle     :  0.669  11.543  10271  Z= 0.306
  Chirality :  0.042   0.252   1212
  Planarity :  0.005   0.071   1271
  Dihedral  : 10.403 110.015   1156
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.79 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.29), residues: 928
  helix:  2.31 (0.24), residues: 484
  sheet: -0.45 (0.65), residues: 66
  loop : -0.96 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.018   0.001   TYR A 251 
 ARG   0.007   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8134 (m-30) cc_final: 0.7723 (m-30)
REVERT: A  508 MET cc_start: 0.9254 (ptp) cc_final: 0.8961 (ptp)
REVERT: B   47 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8054 (mm-40)
REVERT: B  120 MET cc_start: 0.9145 (ppp) cc_final: 0.8585 (ppp)
REVERT: B  262 PHE cc_start: 0.9436 (m-80) cc_final: 0.9235 (m-80)
REVERT: B  365 MET cc_start: 0.8613 (mmm) cc_final: 0.7071 (tpp)
  outliers start: 16
  outliers final: 11
  residues processed: 74
  average time/residue: 0.1656
  time to fit residues: 18.1127
Evaluate side-chains
  74 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  473 PHE
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 77 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 66 optimal weight:   10.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** 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 = 0.3399 r_free = 0.3399 target = 0.063161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.046308 restraints weight = 40102.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.047785 restraints weight = 21725.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.048705 restraints weight = 15367.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7542  Z= 0.158
  Angle     :  0.670  11.447  10271  Z= 0.301
  Chirality :  0.042   0.261   1212
  Planarity :  0.004   0.063   1271
  Dihedral  : 10.041 109.739   1156
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.42 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.29), residues: 928
  helix:  2.25 (0.24), residues: 489
  sheet: -0.40 (0.65), residues: 66
  loop : -0.92 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.021   0.001   TYR A 251 
 ARG   0.007   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8166 (m-30) cc_final: 0.7751 (m-30)
REVERT: A  508 MET cc_start: 0.9273 (ptp) cc_final: 0.8977 (ptp)
REVERT: B  120 MET cc_start: 0.9144 (ppp) cc_final: 0.8597 (ppp)
REVERT: B  145 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8782 (mp10)
REVERT: B  262 PHE cc_start: 0.9398 (m-80) cc_final: 0.9191 (m-80)
REVERT: B  365 MET cc_start: 0.8567 (mmm) cc_final: 0.6965 (tpp)
REVERT: B  383 MET cc_start: 0.9161 (tpp) cc_final: 0.8602 (mpp)
  outliers start: 10
  outliers final: 8
  residues processed: 76
  average time/residue: 0.1695
  time to fit residues: 18.6528
Evaluate side-chains
  74 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  473 PHE
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** 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 = 0.3397 r_free = 0.3397 target = 0.062967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.046199 restraints weight = 39802.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.047645 restraints weight = 21534.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.048556 restraints weight = 15227.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7542  Z= 0.175
  Angle     :  0.683  11.488  10271  Z= 0.307
  Chirality :  0.042   0.260   1212
  Planarity :  0.004   0.064   1271
  Dihedral  :  9.741 109.525   1156
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.81 %
    Favored  : 79.80 %
  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:  1.26 (0.29), residues: 928
  helix:  2.20 (0.24), residues: 492
  sheet: -0.38 (0.65), residues: 66
  loop : -0.84 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.022   0.001   TYR A 251 
 ARG   0.007   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8149 (m-30) cc_final: 0.7725 (m-30)
REVERT: A  508 MET cc_start: 0.9268 (ptp) cc_final: 0.8972 (ptp)
REVERT: B  120 MET cc_start: 0.9145 (ppp) cc_final: 0.8602 (ppp)
REVERT: B  262 PHE cc_start: 0.9387 (m-80) cc_final: 0.9182 (m-80)
REVERT: B  365 MET cc_start: 0.8560 (mmm) cc_final: 0.6967 (tpp)
REVERT: B  383 MET cc_start: 0.9137 (tpp) cc_final: 0.8610 (mpp)
  outliers start: 11
  outliers final: 9
  residues processed: 74
  average time/residue: 0.2020
  time to fit residues: 21.4732
Evaluate side-chains
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   49 ASN
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  473 PHE
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 85 optimal weight:    0.0970
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** 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 = 0.3401 r_free = 0.3401 target = 0.063103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.046382 restraints weight = 39328.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.047829 restraints weight = 21343.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.048741 restraints weight = 15110.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7542  Z= 0.170
  Angle     :  0.686  11.356  10271  Z= 0.307
  Chirality :  0.043   0.302   1212
  Planarity :  0.004   0.055   1271
  Dihedral  :  9.370 109.487   1156
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.55 %
    Favored  : 79.92 %
  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:  1.31 (0.29), residues: 928
  helix:  2.24 (0.24), residues: 492
  sheet: -0.35 (0.65), residues: 66
  loop : -0.82 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.002   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.021   0.001   TYR A 251 
 ARG   0.007   0.000   ARG A 614 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2364.50 seconds
wall clock time: 43 minutes 11.71 seconds (2591.71 seconds total)