Starting phenix.real_space_refine
on Mon Nov 17 17:03:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5tv4_8469/11_2025/5tv4_8469.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5tv4_8469/11_2025/5tv4_8469.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5tv4_8469/11_2025/5tv4_8469.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5tv4_8469/11_2025/5tv4_8469.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5tv4_8469/11_2025/5tv4_8469.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5tv4_8469/11_2025/5tv4_8469.cif"
  }
  resolution = 4.2
  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
-------------------------------------------------------------------------------
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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      16      5.16       5
     C    4040      2.51       5
     N    1234      2.21       5
     O    1254      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6548
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3205
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 375}
          Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555}
          Unresolved chain links: 1
          Unresolved chain link angles: 11
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 1255
          Unresolved non-hydrogen angles: 1592
          Unresolved non-hydrogen dihedrals: 1004
          Unresolved non-hydrogen chiralities: 134
          Planarities with less than four sites: {'GLN:plan1': 17, 'PHE:plan': 13, 'ARG:plan': 29, 'ASN:plan1': 19, 'ASP:plan': 26, 'TYR:plan': 11, 'GLU:plan': 28, 'TRP:plan': 1, 'HIS:plan': 6}
          Unresolved non-hydrogen planarities: 654
    Chain: "B"
      Number of atoms: 3180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3180
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 386}
          Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555}
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 1279
          Unresolved non-hydrogen angles: 1619
          Unresolved non-hydrogen dihedrals: 1021
          Unresolved non-hydrogen chiralities: 144
          Planarities with less than four sites: {'GLN:plan1': 17, 'PHE:plan': 16, 'ARG:plan': 28, 'ASP:plan': 26, 'GLU:plan': 28, 'TYR:plan': 8, 'TRP:plan': 1, 'ASN:plan1': 17, 'HIS:plan': 6}
          Unresolved non-hydrogen planarities: 640
    Chain: "C"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 91
          Unusual residues: {'GMH': 3, 'KDO': 2, 'PA1': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 6
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 12
          Unusual residues: {'PO4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 9
    Chain: "B"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 60
          Unusual residues: {'DAO': 1, 'FTT': 4, 'MYR': 1, 'PO4': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'FTT:plan-1': 4, 'MYR:plan-1': 1, 'DAO:plan-1': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 1.71, per 1000 atoms: 0.26
  Number of scatterers: 6548
  At special positions: 0
  Unit cell: (91.02, 84.87, 134.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P       4     15.00
     O    1254      8.00
     N    1234      7.00
     C    4040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=7, symmetry=0
  Links applied
    ?1-6
      " PA1 C   1 " - " PA1 C   2 "
    ?2-4
      " KDO C   3 " - " KDO C   7 "
    ?2-6
      " PA1 C   2 " - " KDO C   3 "
    ALPHA1-3
      " GMH C   4 " - " GMH C   5 "
    ALPHA1-5
      " KDO C   3 " - " GMH C   4 "
    ALPHA1-7
      " GMH C   5 " - " GMH C   6 "
  Number of additional bonds: simple=7, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 420.7 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2130

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 5 sheets defined
      69.4% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 24 through 48
    Processing helix  chain 'A' and resid 49 through 54
    Processing helix  chain 'A' and resid 62 through 65
    Processing helix  chain 'A' and resid 66 through 110
      removed outlier: 3.754A  pdb=" N   VAL A  70 " --> pdb=" O   TRP A  66 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE A  76 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   MET A  98 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 120 through 148
      removed outlier: 3.736A  pdb=" N   ALA A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   SER A 137 " --> pdb=" O   GLU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.642A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   MET A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 173
    Processing helix  chain 'A' and resid 174 through 193
    Processing helix  chain 'A' and resid 195 through 213
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 251
      removed outlier: 3.894A  pdb=" N   LYS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.820A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 280 through 323
      removed outlier: 3.619A  pdb=" N   ILE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A 289 " --> pdb=" O   THR A 285 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 4.091A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.993A  pdb=" N   LEU A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 419
    Processing helix  chain 'A' and resid 432 through 437
      removed outlier: 3.817A  pdb=" N   ILE A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 5.689A  pdb=" N   ARG A 441 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLU A 443 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 459 through 465
    Processing helix  chain 'A' and resid 468 through 472
    Processing helix  chain 'A' and resid 482 through 497
    Processing helix  chain 'A' and resid 512 through 528
    Processing helix  chain 'A' and resid 538 through 545
    Processing helix  chain 'A' and resid 561 through 567
      removed outlier: 3.521A  pdb=" N   LEU A 565 " --> pdb=" O   THR A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'B' and resid 12 through 21
      removed outlier: 4.059A  pdb=" N   TRP B  17 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 24 through 49
      removed outlier: 3.799A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 55
    Processing helix  chain 'B' and resid 60 through 109
      removed outlier: 3.728A  pdb=" N   LEU B  64 " --> pdb=" O   ASP B  60 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 113 through 118
    Processing helix  chain 'B' and resid 120 through 162
    Processing helix  chain 'B' and resid 164 through 173
    Processing helix  chain 'B' and resid 174 through 213
      removed outlier: 3.979A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 251
      removed outlier: 3.706A  pdb=" N   PHE B 230 " --> pdb=" O   GLU B 226 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS B 232 " --> pdb=" O   LYS B 228 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   VAL B 233 " --> pdb=" O   ARG B 229 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 246 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA B 247 " --> pdb=" O   LYS B 243 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 276
      removed outlier: 4.102A  pdb=" N   LEU B 257 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   ILE B 258 " --> pdb=" O   ILE B 254 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA B 259 " --> pdb=" O   ILE B 255 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LEU B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      Proline residue:  B 273  - end of helix
      removed outlier: 3.549A  pdb=" N   MET B 276 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 287
      removed outlier: 3.952A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 308
      Proline residue:  B 297  - end of helix
      removed outlier: 3.764A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 323
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 3.693A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 417
    Processing helix  chain 'B' and resid 446 through 456
      removed outlier: 4.510A  pdb=" N   ILE B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 463
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 512 through 527
    Processing helix  chain 'B' and resid 540 through 545
      removed outlier: 3.921A  pdb=" N   LYS B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B 545 " --> pdb=" O   THR B 541 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 540 through 545'
    Processing helix  chain 'B' and resid 561 through 567
      removed outlier: 3.904A  pdb=" N   GLU B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 570 through 579
      removed outlier: 4.202A  pdb=" N   GLN B 574 " --> pdb=" O   GLY B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 367
      removed outlier: 5.316A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   ASN A 363 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG A 345 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   LYS A 365 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   GLU A 343 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ASP A 341 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 374
      removed outlier: 6.407A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 552
      removed outlier: 6.773A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 344 through 347
      removed outlier: 4.942A  pdb=" N   ARG B 345 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 364 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 421
      removed outlier: 6.905A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    536 hydrogen bonds defined for protein.
    1572 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: 1.06

  Time building geometry restraints manager: 1.00 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: 2305
        1.34 -     1.46: 775
        1.46 -     1.57: 3475
        1.57 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 6586
  Sorted by residual:
  bond pdb=" C5  PA1 C   2 "
       pdb=" O5  PA1 C   2 "
    ideal  model  delta    sigma   weight residual
    1.417  1.533 -0.116 2.00e-02 2.50e+03 3.38e+01
  bond pdb=" O3  PO4 A 608 "
       pdb=" P   PO4 A 608 "
    ideal  model  delta    sigma   weight residual
    1.569  1.464  0.105 2.00e-02 2.50e+03 2.75e+01
  bond pdb=" O3  PO4 A 610 "
       pdb=" P   PO4 A 610 "
    ideal  model  delta    sigma   weight residual
    1.569  1.466  0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" O1  PO4 A 610 "
       pdb=" P   PO4 A 610 "
    ideal  model  delta    sigma   weight residual
    1.565  1.464  0.101 2.00e-02 2.50e+03 2.58e+01
  bond pdb=" O3  PO4 A 609 "
       pdb=" P   PO4 A 609 "
    ideal  model  delta    sigma   weight residual
    1.569  1.468  0.101 2.00e-02 2.50e+03 2.54e+01
  ... (remaining 6581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 8813
        3.24 -     6.49: 238
        6.49 -     9.73: 18
        9.73 -    12.98: 2
       12.98 -    16.22: 3
  Bond angle restraints: 9074
  Sorted by residual:
  angle pdb=" N   GLN B 309 "
        pdb=" CA  GLN B 309 "
        pdb=" C   GLN B 309 "
      ideal   model   delta    sigma   weight residual
     113.88  106.52    7.36 1.23e+00 6.61e-01 3.58e+01
  angle pdb=" C6  PA1 C   2 "
        pdb=" C5  PA1 C   2 "
        pdb=" O5  PA1 C   2 "
      ideal   model   delta    sigma   weight residual
     107.26   91.04   16.22 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" CA  SER A 300 "
        pdb=" C   SER A 300 "
        pdb=" N   LEU A 301 "
      ideal   model   delta    sigma   weight residual
     118.17  125.27   -7.10 1.33e+00 5.65e-01 2.85e+01
  angle pdb=" N   GLY B 311 "
        pdb=" CA  GLY B 311 "
        pdb=" C   GLY B 311 "
      ideal   model   delta    sigma   weight residual
     113.24  106.46    6.78 1.31e+00 5.83e-01 2.68e+01
  angle pdb=" C   ARG A 333 "
        pdb=" N   VAL A 334 "
        pdb=" CA  VAL A 334 "
      ideal   model   delta    sigma   weight residual
     121.70  131.00   -9.30 1.80e+00 3.09e-01 2.67e+01
  ... (remaining 9069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.23: 3780
       25.23 -    50.45: 108
       50.45 -    75.68: 27
       75.68 -   100.90: 15
      100.90 -   126.13: 20
  Dihedral angle restraints: 3950
    sinusoidal: 676
      harmonic: 3274
  Sorted by residual:
  dihedral pdb=" CA  TYR B 351 "
           pdb=" C   TYR B 351 "
           pdb=" N   PRO B 352 "
           pdb=" CA  PRO B 352 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.03   40.97     0      5.00e+00 4.00e-02 6.72e+01
  dihedral pdb=" CA  ASP B 498 "
           pdb=" C   ASP B 498 "
           pdb=" N   SER B 499 "
           pdb=" CA  SER B 499 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.68  -38.32     0      5.00e+00 4.00e-02 5.87e+01
  dihedral pdb=" CA  SER B 278 "
           pdb=" C   SER B 278 "
           pdb=" N   LEU B 279 "
           pdb=" CA  LEU B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.85  -37.15     0      5.00e+00 4.00e-02 5.52e+01
  ... (remaining 3947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.141: 1164
       0.141 -    0.283: 38
       0.283 -    0.424: 0
       0.424 -    0.566: 0
       0.566 -    0.707: 1
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" C1  GMH C   6 "
            pdb=" O7  GMH C   5 "
            pdb=" C2  GMH C   6 "
            pdb=" O5  GMH C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.32    0.08 2.00e-02 2.50e+03 1.64e+01
  chirality pdb=" C1  GMH C   5 "
            pdb=" O3  GMH C   4 "
            pdb=" C2  GMH C   5 "
            pdb=" O5  GMH C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.48   -0.08 2.00e-02 2.50e+03 1.55e+01
  chirality pdb=" C5  PA1 C   2 "
            pdb=" C4  PA1 C   2 "
            pdb=" C6  PA1 C   2 "
            pdb=" O5  PA1 C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -3.20    0.71 2.00e-01 2.50e+01 1.25e+01
  ... (remaining 1200 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 414 "    0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   SER B 414 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   SER B 414 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 415 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  97 "   -0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   VAL A  97 "    0.040 2.00e-02 2.50e+03
        pdb=" O   VAL A  97 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A  98 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 519 "    0.011 2.00e-02 2.50e+03   2.29e-02 5.23e+00
        pdb=" C   ILE A 519 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A 519 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLN A 520 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 31
        2.19 -     2.87: 3065
        2.87 -     3.54: 10210
        3.54 -     4.22: 13785
        4.22 -     4.90: 21636
  Nonbonded interactions: 48727
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  77 "
            pdb=" CG2 THR A  81 "
     model   vdw
     1.511 3.460
  nonbonded pdb=" O4  PA1 C   2 "
            pdb=" P   PO4 B 601 "
     model   vdw
     1.577 3.400
  nonbonded pdb=" O4  GMH C   5 "
            pdb=" P   PO4 A 610 "
     model   vdw
     1.580 3.400
  nonbonded pdb=" O1  PA1 C   1 "
            pdb=" P   PO4 A 608 "
     model   vdw
     1.591 3.400
  nonbonded pdb=" O4  GMH C   4 "
            pdb=" P   PO4 A 609 "
     model   vdw
     1.600 3.400
  ... (remaining 48722 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 11 through 27 or (resid 28 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 29 through 31 or (resid 32 through 35 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 36 through 40 or (res \ 
id 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (r \ 
esid 43 through 44 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 50 or (resid 51 through 54 and (name N or name CA or name C or \ 
 name O or name CB )) or (resid 55 through 65 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 66 through 79 or (resid 80 and (name N or name C \ 
A or name C or name O or name CB )) or resid 81 through 83 or (resid 84 through  \ 
86 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resi \ 
d 88 through 90 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 91 through 94 or (resid 95 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 102 through 103 or (resid 104 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 105 through 112 or (resid 113 thro \ 
ugh 121 and (name N or name CA or name C or name O or name CB )) or resid 122 or \ 
 (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 
4 through 144 or (resid 145 through 147 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 148 through 152 or (resid 153 through 154 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 155 or (resid 156 through  \ 
160 and (name N or name CA or name C or name O or name CB )) or resid 161 throug \ 
h 171 or (resid 172 through 175 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 176 through 179 or (resid 180 through 187 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 188 through 191 or (resid 192 thro \ 
ugh 200 and (name N or name CA or name C or name O or name CB )) or resid 201 th \ 
rough 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 221 through 232 or (resid 233 through 236 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 237 through 239 or (resid 240 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 241 or (resid 242 through  \ 
249 and (name N or name CA or name C or name O or name CB )) or resid 250 throug \ 
h 252 or (resid 253 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 256 or (resid 257 through 262 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 263 through 264 or (resid 265 through 271 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 272 through 274 or (resid  \ 
275 through 281 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 282 through 302 or (resid 303 through 306 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 307 through 311 or (resid 312 through 318 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 319 through 321 or (re \ 
sid 322 through 330 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 331 through 608))
  selection = (chain 'B' and (resid 11 through 17 or (resid 18 through 19 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 20 through 21 or (resid 22 through \ 
 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 
 36 or (resid 37 through 41 and (name N or name CA or name C or name O or name C \ 
B )) or resid 42 through 81 or (resid 82 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 83 through 84 or (resid 85 through 86 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 87 through 96 or (resid 97 th \ 
rough 99 and (name N or name CA or name C or name O or name CB )) or resid 100 t \ 
hrough 102 or (resid 103 through 104 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 105 through 108 or (resid 109 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 110 through 129 or (resid 130 through 133 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 134 or (resid \ 
 135 through 140 and (name N or name CA or name C or name O or name CB )) or res \ 
id 141 through 143 or (resid 144 through 147 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 148 or (resid 149 and (name CA or name C or name  \ 
O or name CB )) or (resid 150 through 154 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 155 through 161 or (resid 162 through 165 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 166 through 181 or (resi \ 
d 182 through 187 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 188 through 196 or (resid 197 through 200 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 201 through 208 or (resid 209 through 212 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 213 through 216 or ( \ 
resid 217 through 220 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 221 through 224 or (resid 225 through 236 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 237 through 238 or (resid 239 through 240 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 241 through 251  \ 
or (resid 252 through 253 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 254 through 266 or (resid 267 through 271 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 272 through 282 or (resid 283 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 284 through 287 or (resi \ 
d 288 through 291 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 292 through 294 or (resid 295 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 296 through 304 or (resid 305 through 306 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 307 through 309 or (resid 310 an \ 
d (name N or name CA or name C or name O or name CB )) or (resid 311 through 318 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 319 through 3 \ 
20 or (resid 321 through 330 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 331 through 601))
}

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:             0.450
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.150
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5888
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      :  0.010   0.474   6599  Z= 0.747
  Angle     :  1.294  16.223   9092  Z= 0.753
  Chirality :  0.064   0.707   1203
  Planarity :  0.005   0.045   1225
  Dihedral  : 20.358 126.129   1820
  Min Nonbonded Distance : 1.511

Molprobity Statistics.
  All-atom Clashscore : 46.64
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 13.14 %
    Favored  : 86.16 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 11.06 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 7.69 %
    Twisted General : 0.72 %

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: -5.82 (0.16), residues: 1134
  helix: -3.92 (0.11), residues: 718
  sheet: -3.39 (0.83), residues: 23
  loop : -3.35 (0.23), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 238 
 TYR   0.028   0.002   TYR B 268 
 PHE   0.036   0.003   PHE A 220 
 TRP   0.017   0.003   TRP B  17 
 HIS   0.021   0.006   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00828 ( 6586)
  covalent geometry    : angle       1.26350 ( 9074)
  hydrogen bonds       : bond        0.19166 (  536)
  hydrogen bonds       : angle      12.63068 ( 1572)
  glycosidic custom    : bond        0.02010 (    5)
  glycosidic custom    : angle       6.50724 (   15)
  Misc. bond           : bond        0.18511 (    7)
  link_ALPHA1-3        : bond        0.00816 (    1)
  link_ALPHA1-3        : angle       6.10918 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 LEU cc_start: 0.7112 (tt) cc_final: 0.6893 (tt)
REVERT: A  302 THR cc_start: 0.7128 (p) cc_final: 0.6889 (p)
REVERT: B   75 MET cc_start: 0.5168 (mmp) cc_final: 0.4866 (mmp)
REVERT: B   98 MET cc_start: 0.7031 (mmt) cc_final: 0.6768 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0823
  time to fit residues: 14.7462
Evaluate side-chains
  91 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.0870
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:   50.0000
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
B 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.109686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.093902 restraints weight = 31365.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.094320 restraints weight = 23255.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.094767 restraints weight = 20365.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.096548 restraints weight = 15848.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.096220 restraints weight = 12052.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6599  Z= 0.195
  Angle     :  0.855  10.940   9092  Z= 0.439
  Chirality :  0.048   0.220   1203
  Planarity :  0.005   0.046   1225
  Dihedral  : 16.072 127.623   1365
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.41 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.85 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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: -2.69 (0.22), residues: 1134
  helix: -1.24 (0.17), residues: 726
  sheet: -3.51 (0.68), residues: 32
  loop : -2.47 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 238 
 TYR   0.009   0.001   TYR B 130 
 PHE   0.037   0.003   PHE A 161 
 TRP   0.013   0.002   TRP B  17 
 HIS   0.003   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6586)
  covalent geometry    : angle       0.83065 ( 9074)
  hydrogen bonds       : bond        0.06163 (  536)
  hydrogen bonds       : angle       6.73786 ( 1572)
  glycosidic custom    : bond        0.01774 (    5)
  glycosidic custom    : angle       4.89823 (   15)
  Misc. bond           : bond        0.00063 (    7)
  link_ALPHA1-3        : bond        0.00876 (    1)
  link_ALPHA1-3        : angle       2.96653 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 THR cc_start: 0.7221 (p) cc_final: 0.6919 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 119
  average time/residue: 0.0666
  time to fit residues: 11.0264
Evaluate side-chains
  89 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:   40.0000
   chunk 90 optimal weight:    0.2980
   chunk 98 optimal weight:    0.5980
   chunk 110 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 38 optimal weight:   50.0000
   chunk 77 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
B 134 GLN
B 223 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.109472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.094187 restraints weight = 31622.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.094398 restraints weight = 24153.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.094614 restraints weight = 22490.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.095272 restraints weight = 18804.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.095381 restraints weight = 15019.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6599  Z= 0.152
  Angle     :  0.697   9.272   9092  Z= 0.352
  Chirality :  0.044   0.139   1203
  Planarity :  0.004   0.060   1225
  Dihedral  : 13.146 104.329   1365
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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: -1.16 (0.24), residues: 1134
  helix:  0.14 (0.18), residues: 747
  sheet: -3.68 (0.49), residues: 54
  loop : -2.22 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 148 
 TYR   0.013   0.001   TYR B 268 
 PHE   0.026   0.002   PHE A 161 
 TRP   0.017   0.002   TRP A  66 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6586)
  covalent geometry    : angle       0.67552 ( 9074)
  hydrogen bonds       : bond        0.05011 (  536)
  hydrogen bonds       : angle       5.70753 ( 1572)
  glycosidic custom    : bond        0.01304 (    5)
  glycosidic custom    : angle       3.75053 (   15)
  Misc. bond           : bond        0.00054 (    7)
  link_ALPHA1-3        : bond        0.00457 (    1)
  link_ALPHA1-3        : angle       4.48895 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 ILE cc_start: 0.9063 (mt) cc_final: 0.8552 (pt)
REVERT: A  302 THR cc_start: 0.7300 (p) cc_final: 0.7068 (p)
REVERT: B  109 MET cc_start: 0.7992 (ptp) cc_final: 0.7389 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0749
  time to fit residues: 11.1096
Evaluate side-chains
  90 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0370
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 103 optimal weight:   50.0000
   chunk 31 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.0664

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.109480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.095843 restraints weight = 31785.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.095497 restraints weight = 35065.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.095559 restraints weight = 32043.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.095673 restraints weight = 29394.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.095795 restraints weight = 27254.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.4921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6599  Z= 0.135
  Angle     :  0.649   8.003   9092  Z= 0.323
  Chirality :  0.043   0.143   1203
  Planarity :  0.003   0.032   1225
  Dihedral  : 11.933 104.725   1365
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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: -0.26 (0.25), residues: 1134
  helix:  0.82 (0.19), residues: 745
  sheet: -3.24 (0.50), residues: 67
  loop : -1.74 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 310 
 TYR   0.012   0.001   TYR B  83 
 PHE   0.027   0.002   PHE A 272 
 TRP   0.040   0.003   TRP A  66 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6586)
  covalent geometry    : angle       0.62587 ( 9074)
  hydrogen bonds       : bond        0.04446 (  536)
  hydrogen bonds       : angle       5.10254 ( 1572)
  glycosidic custom    : bond        0.01359 (    5)
  glycosidic custom    : angle       3.86249 (   15)
  Misc. bond           : bond        0.00114 (    7)
  link_ALPHA1-3        : bond        0.00018 (    1)
  link_ALPHA1-3        : angle       4.07342 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   35 ILE cc_start: 0.8878 (mt) cc_final: 0.8372 (pt)
REVERT: B  256 GLN cc_start: 0.7195 (mm110) cc_final: 0.6992 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0852
  time to fit residues: 12.3264
Evaluate side-chains
  88 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 93 optimal weight:   20.0000
   chunk 71 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 39 optimal weight:   30.0000
   chunk 31 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    3.7788

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.106244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.091457 restraints weight = 32322.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.091520 restraints weight = 25592.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.091888 restraints weight = 23473.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.092894 restraints weight = 19308.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.092778 restraints weight = 16624.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.5146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6599  Z= 0.171
  Angle     :  0.676   8.548   9092  Z= 0.342
  Chirality :  0.043   0.131   1203
  Planarity :  0.004   0.035   1225
  Dihedral  : 11.752 107.927   1365
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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: -0.05 (0.26), residues: 1134
  helix:  1.03 (0.19), residues: 743
  sheet: -3.00 (0.55), residues: 65
  loop : -1.84 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 238 
 TYR   0.015   0.001   TYR B  83 
 PHE   0.028   0.002   PHE A 161 
 TRP   0.021   0.002   TRP A  66 
 HIS   0.003   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6586)
  covalent geometry    : angle       0.65320 ( 9074)
  hydrogen bonds       : bond        0.04879 (  536)
  hydrogen bonds       : angle       5.04326 ( 1572)
  glycosidic custom    : bond        0.00979 (    5)
  glycosidic custom    : angle       3.90210 (   15)
  Misc. bond           : bond        0.00087 (    7)
  link_ALPHA1-3        : bond        0.00237 (    1)
  link_ALPHA1-3        : angle       4.05718 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   75 MET cc_start: 0.7353 (tmm) cc_final: 0.7130 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0651
  time to fit residues: 9.0197
Evaluate side-chains
  84 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 1 optimal weight:    0.3980
   chunk 26 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    2.2788

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.106911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.091452 restraints weight = 31979.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.092151 restraints weight = 24260.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.092889 restraints weight = 19816.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.093155 restraints weight = 16617.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.093501 restraints weight = 14857.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.5481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6599  Z= 0.136
  Angle     :  0.638   8.225   9092  Z= 0.320
  Chirality :  0.043   0.175   1203
  Planarity :  0.003   0.034   1225
  Dihedral  : 11.470 109.930   1365
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.33 (0.26), residues: 1134
  helix:  1.34 (0.19), residues: 744
  sheet: -2.60 (0.73), residues: 48
  loop : -1.89 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  78 
 TYR   0.017   0.001   TYR B  83 
 PHE   0.035   0.001   PHE A 272 
 TRP   0.016   0.002   TRP B  17 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6586)
  covalent geometry    : angle       0.61538 ( 9074)
  hydrogen bonds       : bond        0.04482 (  536)
  hydrogen bonds       : angle       4.79535 ( 1572)
  glycosidic custom    : bond        0.01135 (    5)
  glycosidic custom    : angle       3.84572 (   15)
  Misc. bond           : bond        0.00072 (    7)
  link_ALPHA1-3        : bond        0.00142 (    1)
  link_ALPHA1-3        : angle       3.89032 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   75 MET cc_start: 0.7419 (tmm) cc_final: 0.7204 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0622
  time to fit residues: 9.2122
Evaluate side-chains
  86 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:   20.0000
   chunk 83 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 113 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 49 optimal weight:   50.0000
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.108068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.091824 restraints weight = 32112.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.092789 restraints weight = 23551.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.093566 restraints weight = 18387.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.094003 restraints weight = 15042.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.094564 restraints weight = 13028.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.5831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6599  Z= 0.131
  Angle     :  0.607   7.942   9092  Z= 0.302
  Chirality :  0.042   0.155   1203
  Planarity :  0.003   0.029   1225
  Dihedral  : 11.208 111.794   1365
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.58 (0.26), residues: 1134
  helix:  1.55 (0.19), residues: 752
  sheet: -2.59 (0.74), residues: 48
  loop : -1.91 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  78 
 TYR   0.007   0.001   TYR A  83 
 PHE   0.020   0.001   PHE B 288 
 TRP   0.012   0.002   TRP A  66 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6586)
  covalent geometry    : angle       0.58579 ( 9074)
  hydrogen bonds       : bond        0.04309 (  536)
  hydrogen bonds       : angle       4.59569 ( 1572)
  glycosidic custom    : bond        0.01078 (    5)
  glycosidic custom    : angle       3.57611 (   15)
  Misc. bond           : bond        0.00056 (    7)
  link_ALPHA1-3        : bond        0.00125 (    1)
  link_ALPHA1-3        : angle       3.87209 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   75 MET cc_start: 0.7519 (tmm) cc_final: 0.7296 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0686
  time to fit residues: 9.7911
Evaluate side-chains
  86 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 32 optimal weight:   40.0000
   chunk 31 optimal weight:    0.3980
   chunk 28 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 96 optimal weight:   30.0000
   chunk 4 optimal weight:   20.0000
   chunk 112 optimal weight:    0.4980
   chunk 98 optimal weight:   50.0000
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.108382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.092566 restraints weight = 32104.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.092940 restraints weight = 26588.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.093140 restraints weight = 23322.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.093331 restraints weight = 20117.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.093445 restraints weight = 19517.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.6117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6599  Z= 0.122
  Angle     :  0.597   7.438   9092  Z= 0.295
  Chirality :  0.042   0.145   1203
  Planarity :  0.003   0.026   1225
  Dihedral  : 10.896 112.468   1365
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.72 (0.26), residues: 1134
  helix:  1.66 (0.19), residues: 763
  sheet: -2.20 (0.72), residues: 49
  loop : -2.01 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 236 
 TYR   0.020   0.001   TYR B  83 
 PHE   0.015   0.001   PHE B 105 
 TRP   0.014   0.001   TRP B  17 
 HIS   0.002   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6586)
  covalent geometry    : angle       0.57666 ( 9074)
  hydrogen bonds       : bond        0.04014 (  536)
  hydrogen bonds       : angle       4.43205 ( 1572)
  glycosidic custom    : bond        0.01256 (    5)
  glycosidic custom    : angle       3.45008 (   15)
  Misc. bond           : bond        0.00051 (    7)
  link_ALPHA1-3        : bond        0.00028 (    1)
  link_ALPHA1-3        : angle       3.80428 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.6003 (m-30) cc_final: 0.4879 (p0)
REVERT: A  176 PRO cc_start: 0.7986 (Cg_exo) cc_final: 0.7783 (Cg_endo)
REVERT: B  109 MET cc_start: 0.8304 (mpp) cc_final: 0.8011 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0567
  time to fit residues: 8.7914
Evaluate side-chains
  90 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 108 optimal weight:    0.0000
   chunk 91 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:   40.0000
   chunk 73 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:   50.0000
   chunk 32 optimal weight:   30.0000
   chunk 71 optimal weight:    8.9990
   overall best weight:    4.3992

-------------------------------------------------------------------------------
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 = 0.4016 r_free = 0.4016 target = 0.104853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.087984 restraints weight = 31982.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.088979 restraints weight = 23710.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.089771 restraints weight = 18687.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.090318 restraints weight = 15433.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.090477 restraints weight = 13299.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.6182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6599  Z= 0.180
  Angle     :  0.693  10.647   9092  Z= 0.348
  Chirality :  0.045   0.216   1203
  Planarity :  0.004   0.044   1225
  Dihedral  : 11.097 111.219   1365
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.52 (0.26), residues: 1134
  helix:  1.43 (0.19), residues: 766
  sheet: -2.23 (0.82), residues: 42
  loop : -1.97 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 236 
 TYR   0.015   0.002   TYR B  83 
 PHE   0.009   0.002   PHE A 157 
 TRP   0.010   0.002   TRP B  66 
 HIS   0.003   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6586)
  covalent geometry    : angle       0.67153 ( 9074)
  hydrogen bonds       : bond        0.04712 (  536)
  hydrogen bonds       : angle       4.76245 ( 1572)
  glycosidic custom    : bond        0.01008 (    5)
  glycosidic custom    : angle       3.81809 (   15)
  Misc. bond           : bond        0.00092 (    7)
  link_ALPHA1-3        : bond        0.00281 (    1)
  link_ALPHA1-3        : angle       4.06349 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: B  109 MET cc_start: 0.8739 (mpp) cc_final: 0.8159 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0481
  time to fit residues: 7.3035
Evaluate side-chains
  84 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:   50.0000
   chunk 108 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 36 optimal weight:   30.0000
   chunk 64 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   overall best weight:    1.8382

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.106130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.089897 restraints weight = 30865.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.090775 restraints weight = 23551.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.091335 restraints weight = 19037.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.091926 restraints weight = 16340.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.092259 restraints weight = 14200.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.6407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6599  Z= 0.127
  Angle     :  0.619   8.693   9092  Z= 0.306
  Chirality :  0.043   0.167   1203
  Planarity :  0.003   0.031   1225
  Dihedral  : 10.847 112.291   1365
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.76 (0.26), residues: 1134
  helix:  1.70 (0.19), residues: 766
  sheet: -2.17 (0.74), residues: 48
  loop : -2.09 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  78 
 TYR   0.006   0.001   TYR B 162 
 PHE   0.013   0.001   PHE B  23 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6586)
  covalent geometry    : angle       0.59930 ( 9074)
  hydrogen bonds       : bond        0.04201 (  536)
  hydrogen bonds       : angle       4.48907 ( 1572)
  glycosidic custom    : bond        0.01137 (    5)
  glycosidic custom    : angle       3.42231 (   15)
  Misc. bond           : bond        0.00058 (    7)
  link_ALPHA1-3        : bond        0.00000 (    1)
  link_ALPHA1-3        : angle       3.83757 (    3)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  157 PHE cc_start: 0.7548 (m-80) cc_final: 0.7178 (m-80)
REVERT: B  109 MET cc_start: 0.8836 (mpp) cc_final: 0.8266 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0480
  time to fit residues: 7.5242
Evaluate side-chains
  85 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 87 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0770
   chunk 60 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   chunk 38 optimal weight:   50.0000
   chunk 68 optimal weight:    7.9990
   chunk 41 optimal weight:   40.0000
   overall best weight:    3.6146

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.104759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.088154 restraints weight = 31910.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.089187 restraints weight = 23400.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.089991 restraints weight = 18156.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.090527 restraints weight = 14880.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.090956 restraints weight = 12801.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.6565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6599  Z= 0.157
  Angle     :  0.651   9.444   9092  Z= 0.326
  Chirality :  0.043   0.189   1203
  Planarity :  0.003   0.040   1225
  Dihedral  : 10.811 111.872   1365
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.73 (0.26), residues: 1134
  helix:  1.63 (0.19), residues: 771
  sheet: -2.42 (0.82), residues: 37
  loop : -2.02 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  78 
 TYR   0.007   0.001   TYR B 162 
 PHE   0.011   0.001   PHE B  23 
 TRP   0.010   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6586)
  covalent geometry    : angle       0.63179 ( 9074)
  hydrogen bonds       : bond        0.04481 (  536)
  hydrogen bonds       : angle       4.58032 ( 1572)
  glycosidic custom    : bond        0.01114 (    5)
  glycosidic custom    : angle       3.52832 (   15)
  Misc. bond           : bond        0.00109 (    7)
  link_ALPHA1-3        : bond        0.00056 (    1)
  link_ALPHA1-3        : angle       3.98629 (    3)

===============================================================================
Job complete
usr+sys time: 1070.98 seconds
wall clock time: 19 minutes 3.99 seconds (1143.99 seconds total)