Starting phenix.real_space_refine
on Wed Feb  4 11:14:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pma_13526/02_2026/7pma_13526.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pma_13526/02_2026/7pma_13526.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2026/7pma_13526.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2026/7pma_13526.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2026/7pma_13526.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pma_13526/02_2026/7pma_13526.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      2      5.21       5
     S      62      5.16       5
     C    6412      2.51       5
     N    1710      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10066
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1059
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 5987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 732, 5987
          Classifications: {'peptide': 732}
          Link IDs: {'PTRANS': 27, 'TRANS': 704}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.89, per 1000 atoms: 0.19
  Number of scatterers: 10066
  At special positions: 0
  Unit cell: (102.82, 142.04, 149.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      62     16.00
     P       4     15.00
     Mg      2     11.99
     O    1876      8.00
     N    1710      7.00
     C    6412      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " TRP H   1 " - " ALA H   7 "
      " DTH H   4 " - " ALA H   3 "
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 355.2 milliseconds
  

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTH H   4 "
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 14 sheets defined
      55.2% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 20
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.054A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   ASP B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 56 through 63
    Processing helix  chain 'B' and resid 67 through 79
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 87 through 95
    Processing helix  chain 'B' and resid 105 through 116
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 140 through 150
    Processing helix  chain 'A' and resid 81 through 95
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 3.696A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 184
      removed outlier: 3.693A  pdb=" N   PHE A 180 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 207
      removed outlier: 3.740A  pdb=" N   ASN A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 245 through 250
      removed outlier: 3.505A  pdb=" N   VAL A 250 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 269
      removed outlier: 4.051A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 4.371A  pdb=" N   THR A 276 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 3.624A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 315
      removed outlier: 4.367A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASN A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.887A  pdb=" N   GLY A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 376
    Processing helix  chain 'A' and resid 392 through 424
      removed outlier: 3.699A  pdb=" N   LYS A 421 " --> pdb=" O   ASP A 417 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA A 422 " --> pdb=" O   HIS A 418 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A 423 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 479
    Processing helix  chain 'A' and resid 483 through 487
      removed outlier: 3.837A  pdb=" N   LEU A 486 " --> pdb=" O   PRO A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
      removed outlier: 3.504A  pdb=" N   ILE A 496 " --> pdb=" O   ASN A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 3.561A  pdb=" N   LYS A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 532
    Processing helix  chain 'A' and resid 563 through 569
      removed outlier: 3.505A  pdb=" N   LYS A 567 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
      removed outlier: 3.550A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 3.839A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 635 through 653
      removed outlier: 3.724A  pdb=" N   ALA A 653 " --> pdb=" O   GLU A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 685
    Processing helix  chain 'A' and resid 686 through 696
    Processing helix  chain 'A' and resid 704 through 712
      removed outlier: 4.053A  pdb=" N   SER A 709 " --> pdb=" O   GLN A 705 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ARG A 710 " --> pdb=" O   GLU A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 736
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 754 through 792
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 92
      removed outlier: 3.769A  pdb=" N   MET C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.921A  pdb=" N   HIS C 101 " --> pdb=" O   PRO C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 4.017A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   MET C 123 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE C 124 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
      removed outlier: 3.827A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 194
    Processing helix  chain 'C' and resid 195 through 197
      No H-bonds generated for 'chain 'C' and resid 195 through 197'
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.960A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 252 through 263
      removed outlier: 3.589A  pdb=" N   CYS C 257 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
      Proline residue:  C 258  - end of helix
      removed outlier: 4.145A  pdb=" N   LEU C 261 " --> pdb=" O   CYS C 257 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   PHE C 262 " --> pdb=" O   PRO C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 285
      removed outlier: 3.830A  pdb=" N   LYS C 284 " --> pdb=" O   ASN C 280 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   CYS C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 296
      removed outlier: 3.574A  pdb=" N   ARG C 290 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 4.344A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 321
      removed outlier: 3.791A  pdb=" N   ALA C 319 " --> pdb=" O   LYS C 315 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU C 320 " --> pdb=" O   GLU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 349
      removed outlier: 4.397A  pdb=" N   VAL C 339 " --> pdb=" O   ARG C 335 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   TRP C 340 " --> pdb=" O   LYS C 336 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER C 348 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU C 349 " --> pdb=" O   ILE C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 354
      removed outlier: 3.536A  pdb=" N   GLN C 353 " --> pdb=" O   LEU C 349 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLN C 354 " --> pdb=" O   SER C 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 349 through 354'
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 368 through 374
      removed outlier: 3.725A  pdb=" N   ARG C 372 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.532A  pdb=" N   VAL B  65 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 17
      removed outlier: 3.972A  pdb=" N   ALA A  11 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ASP A  17 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL A  21 " --> pdb=" O   ASP A  17 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
      removed outlier: 3.534A  pdb=" N   SER A 162 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN A 157 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY A 163 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER A 431 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209
    Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344
      removed outlier: 6.640A  pdb=" N   SER A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 381
    Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703
    Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31
      removed outlier: 3.674A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASN C  12 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241

    521 hydrogen bonds defined for protein.
    1479 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: 1.18

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1671
        1.32 -     1.44: 2728
        1.44 -     1.56: 5775
        1.56 -     1.69: 6
        1.69 -     1.81: 100
  Bond restraints: 10280
  Sorted by residual:
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.450  0.122 2.00e-02 2.50e+03 3.73e+01
  bond pdb=" C   EEP H   2 "
       pdb=" O   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.263  1.201  0.062 2.00e-02 2.50e+03 9.59e+00
  bond pdb=" CA  TRP H   1 "
       pdb=" C   TRP H   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.463  0.062 2.10e-02 2.27e+03 8.64e+00
  bond pdb=" C   HYP H   6 "
       pdb=" N   ALA H   7 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.40e-02 5.10e+03 8.47e+00
  bond pdb=" CE1 HIC C  73 "
       pdb=" NE2 HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.347  1.402 -0.055 2.00e-02 2.50e+03 7.47e+00
  ... (remaining 10275 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 13529
        2.38 -     4.75: 295
        4.75 -     7.13: 50
        7.13 -     9.50: 7
        9.50 -    11.88: 6
  Bond angle restraints: 13887
  Sorted by residual:
  angle pdb=" C   HYP H   6 "
        pdb=" N   ALA H   7 "
        pdb=" CA  ALA H   7 "
      ideal   model   delta    sigma   weight residual
     121.70  109.82   11.88 1.80e+00 3.09e-01 4.36e+01
  angle pdb=" C   LYS A 668 "
        pdb=" N   PHE A 669 "
        pdb=" CA  PHE A 669 "
      ideal   model   delta    sigma   weight residual
     122.48  130.29   -7.81 1.77e+00 3.19e-01 1.95e+01
  angle pdb=" N   HYP H   6 "
        pdb=" CA  HYP H   6 "
        pdb=" CB  HYP H   6 "
      ideal   model   delta    sigma   weight residual
     103.00  107.79   -4.79 1.10e+00 8.26e-01 1.90e+01
  angle pdb=" C   TRP H   1 "
        pdb=" CA  TRP H   1 "
        pdb=" CB  TRP H   1 "
      ideal   model   delta    sigma   weight residual
     110.10  102.08    8.02 1.90e+00 2.77e-01 1.78e+01
  angle pdb=" CD2 TRP H   1 "
        pdb=" CE2 TRP H   1 "
        pdb=" CZ2 TRP H   1 "
      ideal   model   delta    sigma   weight residual
     122.40  118.28    4.12 1.00e+00 1.00e+00 1.70e+01
  ... (remaining 13882 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.82: 6024
       31.82 -    63.65: 128
       63.65 -    95.47: 40
       95.47 -   127.29: 3
      127.29 -   159.12: 2
  Dihedral angle restraints: 6197
    sinusoidal: 2549
      harmonic: 3648
  Sorted by residual:
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   99.12 -159.12     1      2.00e+01 2.50e-03 4.64e+01
  dihedral pdb=" O2A ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" PB  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   75.39 -135.39     1      2.00e+01 2.50e-03 4.11e+01
  dihedral pdb=" C5' ADP C 401 "
           pdb=" O5' ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" O2A ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  175.57  124.43     1      2.00e+01 2.50e-03 3.76e+01
  ... (remaining 6194 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1068
       0.044 -    0.089: 300
       0.089 -    0.133: 119
       0.133 -    0.177: 21
       0.177 -    0.222: 9
  Chirality restraints: 1517
  Sorted by residual:
  chirality pdb=" CA  TYR A  10 "
            pdb=" N   TYR A  10 "
            pdb=" C   TYR A  10 "
            pdb=" CB  TYR A  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  MET A 478 "
            pdb=" N   MET A 478 "
            pdb=" C   MET A 478 "
            pdb=" CB  MET A 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CG  LEU B 113 "
            pdb=" CB  LEU B 113 "
            pdb=" CD1 LEU B 113 "
            pdb=" CD2 LEU B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1514 not shown)

  Planarity restraints: 1772
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 248 "   -0.111 9.50e-02 1.11e+02   6.47e-02 2.29e+01
        pdb=" NE  ARG A 248 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 248 "   -0.079 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 248 "    0.028 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 248 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C  89 "   -0.022 2.00e-02 2.50e+03   4.41e-02 1.94e+01
        pdb=" C   THR C  89 "    0.076 2.00e-02 2.50e+03
        pdb=" O   THR C  89 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   PHE C  90 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 231 "    0.233 9.50e-02 1.11e+02   1.08e-01 1.45e+01
        pdb=" NE  ARG A 231 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 231 "   -0.051 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 231 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 231 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1769 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 12
        2.37 -     3.00: 5465
        3.00 -     3.63: 15172
        3.63 -     4.27: 22395
        4.27 -     4.90: 37952
  Nonbonded interactions: 80996
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.732 3.620
  nonbonded pdb="MG    MG A1901 "
            pdb=" O1B ADP A1902 "
     model   vdw
     2.060 2.170
  nonbonded pdb=" O2B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     2.073 2.170
  nonbonded pdb="MG    MG A1901 "
            pdb=" O3B ADP A1902 "
     model   vdw
     2.155 2.170
  nonbonded pdb=" O   PHE A 698 "
            pdb=" NH1 ARG A 701 "
     model   vdw
     2.184 3.120
  ... (remaining 80991 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.310
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.122  10282  Z= 0.216
  Angle     :  0.887  11.880  13893  Z= 0.516
  Chirality :  0.051   0.222   1517
  Planarity :  0.008   0.108   1770
  Dihedral  : 15.928 159.118   3839
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.21), residues: 1218
  helix: -1.28 (0.17), residues: 572
  sheet:  0.60 (0.37), residues: 165
  loop : -0.16 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.080   0.012   ARG A 248 
 TYR   0.035   0.006   TYR A 113 
 PHE   0.029   0.002   PHE A 673 
 TRP   0.059   0.003   TRP A 484 
 HIS   0.006   0.001   HIS B 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (10280)
  covalent geometry    : angle       0.88298 (13887)
  hydrogen bonds       : bond        0.16761 (  519)
  hydrogen bonds       : angle       7.40991 ( 1479)
  link_TRANS           : bond        0.00886 (    2)
  link_TRANS           : angle       4.26422 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 ILE cc_start: 0.8764 (pt) cc_final: 0.8528 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 157
  average time/residue: 0.0905
  time to fit residues: 20.0977
Evaluate side-chains
  90 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0370
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 123 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 264 GLN
A 354 HIS
A 373 HIS
A 395 HIS
A 410 ASN
** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
A 533 ASN
A 642 ASN
A 652 ASN
** C  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.067088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.047499 restraints weight = 45785.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.049177 restraints weight = 22352.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.050329 restraints weight = 13811.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.051083 restraints weight = 9792.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.051565 restraints weight = 7684.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10282  Z= 0.157
  Angle     :  0.717  11.512  13893  Z= 0.367
  Chirality :  0.045   0.298   1517
  Planarity :  0.004   0.048   1770
  Dihedral  : 10.308 167.300   1392
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.88 %
    Favored  : 93.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.07 (0.23), residues: 1218
  helix:  0.97 (0.20), residues: 592
  sheet:  0.85 (0.38), residues: 166
  loop :  0.53 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  95 
 TYR   0.015   0.002   TYR A 711 
 PHE   0.030   0.002   PHE A 360 
 TRP   0.016   0.002   TRP C 356 
 HIS   0.005   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10280)
  covalent geometry    : angle       0.71641 (13887)
  hydrogen bonds       : bond        0.04509 (  519)
  hydrogen bonds       : angle       5.34828 ( 1479)
  link_TRANS           : bond        0.00191 (    2)
  link_TRANS           : angle       1.07448 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.7288 (tp40) cc_final: 0.7046 (tp-100)
REVERT: A  305 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7960 (ptp)
REVERT: C  217 CYS cc_start: 0.8630 (m) cc_final: 0.7881 (m)
  outliers start: 7
  outliers final: 3
  residues processed: 109
  average time/residue: 0.0845
  time to fit residues: 13.2834
Evaluate side-chains
  85 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 101 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 122 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0870
   chunk 112 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.067131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.047803 restraints weight = 45870.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.049509 restraints weight = 22210.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.050575 restraints weight = 13624.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.051337 restraints weight = 9767.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.051731 restraints weight = 7682.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10282  Z= 0.126
  Angle     :  0.632  12.191  13893  Z= 0.317
  Chirality :  0.043   0.205   1517
  Planarity :  0.004   0.044   1770
  Dihedral  :  9.257 179.762   1391
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  6.82 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.63 (0.24), residues: 1218
  helix:  1.57 (0.22), residues: 598
  sheet:  0.99 (0.39), residues: 164
  loop :  0.65 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  95 
 TYR   0.011   0.001   TYR A 477 
 PHE   0.019   0.001   PHE A 360 
 TRP   0.011   0.001   TRP C 356 
 HIS   0.006   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10280)
  covalent geometry    : angle       0.63209 (13887)
  hydrogen bonds       : bond        0.03838 (  519)
  hydrogen bonds       : angle       4.93685 ( 1479)
  link_TRANS           : bond        0.00295 (    2)
  link_TRANS           : angle       1.08337 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8109 (ptp)
REVERT: A  418 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8455 (m90)
REVERT: C   82 MET cc_start: 0.8538 (tpt) cc_final: 0.8128 (tpp)
REVERT: C  217 CYS cc_start: 0.8690 (m) cc_final: 0.7874 (m)
REVERT: C  225 ASN cc_start: 0.8931 (m-40) cc_final: 0.8184 (t0)
  outliers start: 18
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0781
  time to fit residues: 11.6398
Evaluate side-chains
  81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0170
   chunk 75 optimal weight:    0.2980
   chunk 97 optimal weight:    1.9990
   chunk 122 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.066552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.047381 restraints weight = 45969.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.049053 restraints weight = 22150.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.050154 restraints weight = 13585.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.050873 restraints weight = 9636.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.051350 restraints weight = 7565.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10282  Z= 0.135
  Angle     :  0.609   9.754  13893  Z= 0.304
  Chirality :  0.042   0.196   1517
  Planarity :  0.004   0.038   1770
  Dihedral  :  8.685 166.498   1391
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  7.94 %
    Favored  : 90.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.24), residues: 1218
  helix:  1.77 (0.22), residues: 592
  sheet:  1.15 (0.39), residues: 163
  loop :  0.67 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 779 
 TYR   0.010   0.001   TYR A 658 
 PHE   0.027   0.001   PHE A 360 
 TRP   0.009   0.001   TRP A 484 
 HIS   0.009   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10280)
  covalent geometry    : angle       0.60902 (13887)
  hydrogen bonds       : bond        0.03647 (  519)
  hydrogen bonds       : angle       4.86598 ( 1479)
  link_TRANS           : bond        0.00236 (    2)
  link_TRANS           : angle       0.97679 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 GLU cc_start: 0.8733 (mp0) cc_final: 0.8432 (mp0)
REVERT: A  418 HIS cc_start: 0.8918 (OUTLIER) cc_final: 0.8702 (m170)
REVERT: A  520 ASP cc_start: 0.8302 (m-30) cc_final: 0.7907 (m-30)
REVERT: C   72 GLU cc_start: 0.8381 (tt0) cc_final: 0.8154 (tt0)
REVERT: C  132 MET cc_start: 0.9044 (tmm) cc_final: 0.8571 (tmm)
REVERT: C  217 CYS cc_start: 0.8673 (m) cc_final: 0.7900 (m)
REVERT: C  225 ASN cc_start: 0.8875 (m-40) cc_final: 0.8151 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 93
  average time/residue: 0.0736
  time to fit residues: 10.2325
Evaluate side-chains
  82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 89 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.066266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.046885 restraints weight = 45843.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.048537 restraints weight = 22336.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.049662 restraints weight = 13859.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.050350 restraints weight = 9861.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.050878 restraints weight = 7806.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10282  Z= 0.137
  Angle     :  0.597   9.893  13893  Z= 0.293
  Chirality :  0.041   0.193   1517
  Planarity :  0.004   0.036   1770
  Dihedral  :  8.042 146.542   1391
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.31 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.24), residues: 1218
  helix:  1.73 (0.22), residues: 600
  sheet:  1.07 (0.39), residues: 163
  loop :  0.68 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.008   0.001   TYR A 179 
 PHE   0.024   0.001   PHE A 360 
 TRP   0.009   0.001   TRP C 356 
 HIS   0.006   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10280)
  covalent geometry    : angle       0.59699 (13887)
  hydrogen bonds       : bond        0.03515 (  519)
  hydrogen bonds       : angle       4.78812 ( 1479)
  link_TRANS           : bond        0.00245 (    2)
  link_TRANS           : angle       0.92475 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7868 (tp-100)
REVERT: B   68 GLU cc_start: 0.8662 (mp0) cc_final: 0.8318 (mp0)
REVERT: A  135 MET cc_start: 0.8756 (mmm) cc_final: 0.8144 (mmm)
REVERT: A  418 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8500 (m90)
REVERT: A  477 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8491 (t80)
REVERT: A  702 TRP cc_start: 0.8048 (t-100) cc_final: 0.7615 (t-100)
REVERT: C  132 MET cc_start: 0.9065 (tmm) cc_final: 0.8585 (tmm)
REVERT: C  217 CYS cc_start: 0.8808 (m) cc_final: 0.8128 (m)
REVERT: C  225 ASN cc_start: 0.8876 (m-40) cc_final: 0.8153 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0718
  time to fit residues: 10.4489
Evaluate side-chains
  84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 54 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0470
   chunk 83 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0000
   chunk 91 optimal weight:    0.0970
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.2080

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

Flipped N/Q/H residues before XYZ refinement:
A 681 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  12 ASN
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.067657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.048251 restraints weight = 45888.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.049950 restraints weight = 22004.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.051127 restraints weight = 13551.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.051821 restraints weight = 9570.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.052348 restraints weight = 7580.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10282  Z= 0.102
  Angle     :  0.588  10.304  13893  Z= 0.285
  Chirality :  0.041   0.184   1517
  Planarity :  0.004   0.038   1770
  Dihedral  :  7.284 120.507   1391
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.06 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.90 (0.24), residues: 1218
  helix:  1.89 (0.22), residues: 588
  sheet:  1.03 (0.39), residues: 163
  loop :  0.67 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 257 
 TYR   0.010   0.001   TYR A 284 
 PHE   0.024   0.001   PHE A 360 
 TRP   0.008   0.001   TRP A 484 
 HIS   0.019   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (10280)
  covalent geometry    : angle       0.58782 (13887)
  hydrogen bonds       : bond        0.03254 (  519)
  hydrogen bonds       : angle       4.66049 ( 1479)
  link_TRANS           : bond        0.00176 (    2)
  link_TRANS           : angle       0.87646 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  477 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8511 (t80)
REVERT: A  702 TRP cc_start: 0.8123 (t-100) cc_final: 0.7662 (t-100)
REVERT: C  176 MET cc_start: 0.8257 (mmm) cc_final: 0.7918 (mmt)
REVERT: C  217 CYS cc_start: 0.8833 (m) cc_final: 0.8147 (m)
REVERT: C  225 ASN cc_start: 0.8844 (m-40) cc_final: 0.8129 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 96
  average time/residue: 0.0796
  time to fit residues: 11.5356
Evaluate side-chains
  82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0770
   chunk 70 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
A 681 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  12 ASN
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.066755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.047535 restraints weight = 45509.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.049210 restraints weight = 21847.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.050322 restraints weight = 13364.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.051058 restraints weight = 9470.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.051510 restraints weight = 7427.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10282  Z= 0.125
  Angle     :  0.611  11.004  13893  Z= 0.298
  Chirality :  0.041   0.182   1517
  Planarity :  0.004   0.037   1770
  Dihedral  :  7.071 111.662   1391
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.71 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.24), residues: 1218
  helix:  1.82 (0.22), residues: 602
  sheet:  0.97 (0.39), residues: 163
  loop :  0.64 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 343 
 TYR   0.009   0.001   TYR A 284 
 PHE   0.025   0.001   PHE A 360 
 TRP   0.009   0.001   TRP A 781 
 HIS   0.004   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10280)
  covalent geometry    : angle       0.61081 (13887)
  hydrogen bonds       : bond        0.03288 (  519)
  hydrogen bonds       : angle       4.65689 ( 1479)
  link_TRANS           : bond        0.00252 (    2)
  link_TRANS           : angle       0.88766 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7463 (tt0)
REVERT: A  477 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8461 (t80)
REVERT: A  702 TRP cc_start: 0.8099 (t-100) cc_final: 0.7649 (t-100)
REVERT: C   44 MET cc_start: 0.7261 (tmm) cc_final: 0.6896 (tmm)
REVERT: C  217 CYS cc_start: 0.8888 (m) cc_final: 0.8188 (m)
REVERT: C  225 ASN cc_start: 0.8846 (m-40) cc_final: 0.8137 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 87
  average time/residue: 0.0722
  time to fit residues: 9.5753
Evaluate side-chains
  80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 102 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 118 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 455 ASN
A 681 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  12 ASN
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.066885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.047215 restraints weight = 45861.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.048913 restraints weight = 22244.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.050025 restraints weight = 13704.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.050770 restraints weight = 9722.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.051225 restraints weight = 7678.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10282  Z= 0.127
  Angle     :  0.619  12.182  13893  Z= 0.297
  Chirality :  0.041   0.230   1517
  Planarity :  0.004   0.038   1770
  Dihedral  :  6.935 108.272   1391
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  9.90 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.85 (0.24), residues: 1218
  helix:  1.88 (0.22), residues: 602
  sheet:  0.90 (0.39), residues: 163
  loop :  0.61 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  37 
 TYR   0.008   0.001   TYR A 284 
 PHE   0.025   0.001   PHE A 360 
 TRP   0.009   0.001   TRP A 781 
 HIS   0.005   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10280)
  covalent geometry    : angle       0.61885 (13887)
  hydrogen bonds       : bond        0.03299 (  519)
  hydrogen bonds       : angle       4.64755 ( 1479)
  link_TRANS           : bond        0.00262 (    2)
  link_TRANS           : angle       0.88270 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  477 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8467 (t80)
REVERT: A  648 MET cc_start: 0.9120 (mmm) cc_final: 0.8721 (tpp)
REVERT: A  702 TRP cc_start: 0.8165 (t-100) cc_final: 0.7705 (t-100)
REVERT: C  176 MET cc_start: 0.8169 (mmm) cc_final: 0.7803 (mmt)
REVERT: C  217 CYS cc_start: 0.8879 (m) cc_final: 0.8188 (m)
REVERT: C  225 ASN cc_start: 0.8847 (m-40) cc_final: 0.8140 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 85
  average time/residue: 0.0776
  time to fit residues: 10.0151
Evaluate side-chains
  79 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 61 optimal weight:    0.7980
   chunk 110 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0170
   chunk 83 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.067010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.047395 restraints weight = 45617.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.049079 restraints weight = 22093.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.050202 restraints weight = 13597.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.050956 restraints weight = 9662.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.051338 restraints weight = 7589.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10282  Z= 0.121
  Angle     :  0.636  12.722  13893  Z= 0.304
  Chirality :  0.041   0.230   1517
  Planarity :  0.004   0.038   1770
  Dihedral  :  6.812 104.816   1391
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.36 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.24), residues: 1218
  helix:  1.89 (0.22), residues: 596
  sheet:  0.88 (0.39), residues: 163
  loop :  0.66 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  37 
 TYR   0.012   0.001   TYR A 284 
 PHE   0.024   0.001   PHE A 360 
 TRP   0.021   0.001   TRP A 781 
 HIS   0.004   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10280)
  covalent geometry    : angle       0.63628 (13887)
  hydrogen bonds       : bond        0.03305 (  519)
  hydrogen bonds       : angle       4.67903 ( 1479)
  link_TRANS           : bond        0.00250 (    2)
  link_TRANS           : angle       0.87738 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.7665 (tp-100) cc_final: 0.7405 (tt0)
REVERT: A  477 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8474 (t80)
REVERT: A  520 ASP cc_start: 0.8039 (m-30) cc_final: 0.7824 (m-30)
REVERT: A  702 TRP cc_start: 0.8147 (t-100) cc_final: 0.7682 (t-100)
REVERT: C  176 MET cc_start: 0.8190 (mmm) cc_final: 0.7872 (mmt)
REVERT: C  217 CYS cc_start: 0.8861 (m) cc_final: 0.8167 (m)
REVERT: C  225 ASN cc_start: 0.8845 (m-40) cc_final: 0.8142 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 81
  average time/residue: 0.0748
  time to fit residues: 9.0376
Evaluate side-chains
  81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  343 ARG
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  285 CYS
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 6 optimal weight:    0.4980
   chunk 102 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 775 GLN
C  12 ASN
C 161 HIS
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.066680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.047099 restraints weight = 45229.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.048773 restraints weight = 22008.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.049892 restraints weight = 13613.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.050611 restraints weight = 9702.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.051086 restraints weight = 7659.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10282  Z= 0.133
  Angle     :  0.655  12.209  13893  Z= 0.314
  Chirality :  0.041   0.215   1517
  Planarity :  0.004   0.037   1770
  Dihedral  :  6.738 102.281   1391
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.55 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.24), residues: 1218
  helix:  1.80 (0.22), residues: 602
  sheet:  0.80 (0.39), residues: 163
  loop :  0.58 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  37 
 TYR   0.012   0.001   TYR A 284 
 PHE   0.023   0.001   PHE A 360 
 TRP   0.028   0.002   TRP A 781 
 HIS   0.005   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10280)
  covalent geometry    : angle       0.65445 (13887)
  hydrogen bonds       : bond        0.03302 (  519)
  hydrogen bonds       : angle       4.71350 ( 1479)
  link_TRANS           : bond        0.00272 (    2)
  link_TRANS           : angle       0.87128 (    6)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  477 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8485 (t80)
REVERT: A  520 ASP cc_start: 0.7973 (m-30) cc_final: 0.7762 (m-30)
REVERT: A  702 TRP cc_start: 0.8163 (t-100) cc_final: 0.7698 (t-100)
REVERT: C  217 CYS cc_start: 0.8880 (m) cc_final: 0.8193 (m)
REVERT: C  225 ASN cc_start: 0.8843 (m-40) cc_final: 0.8151 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0688
  time to fit residues: 8.5204
Evaluate side-chains
  81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  285 CYS
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0770
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0170
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0010
   chunk 30 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 48 optimal weight:    0.3980
   overall best weight:    0.2582

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.066819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.047231 restraints weight = 46000.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.048930 restraints weight = 22420.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.050039 restraints weight = 13838.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.050793 restraints weight = 9882.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.051225 restraints weight = 7787.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.174  10282  Z= 0.234
  Angle     :  0.945  58.985  13893  Z= 0.530
  Chirality :  0.047   0.695   1517
  Planarity :  0.004   0.059   1770
  Dihedral  :  6.828 102.251   1391
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.64 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.46 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  1.74 (0.24), residues: 1218
  helix:  1.82 (0.22), residues: 601
  sheet:  0.75 (0.39), residues: 163
  loop :  0.56 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 343 
 TYR   0.010   0.001   TYR A 284 
 PHE   0.023   0.001   PHE A 360 
 TRP   0.025   0.002   TRP A 781 
 HIS   0.005   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (10280)
  covalent geometry    : angle       0.94470 (13887)
  hydrogen bonds       : bond        0.03273 (  519)
  hydrogen bonds       : angle       4.71944 ( 1479)
  link_TRANS           : bond        0.00259 (    2)
  link_TRANS           : angle       0.87352 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1652.25 seconds
wall clock time: 29 minutes 14.13 seconds (1754.13 seconds total)