Starting phenix.real_space_refine
on Tue Feb 11 20:05:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9h_35272/02_2025/8i9h_35272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9h_35272/02_2025/8i9h_35272.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i9h_35272/02_2025/8i9h_35272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9h_35272/02_2025/8i9h_35272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9h_35272/02_2025/8i9h_35272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9h_35272/02_2025/8i9h_35272.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4161      2.51       5
     N    1063      2.21       5
     O    1253      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6514
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
    Chain: "E"
      Number of atoms: 1462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1462
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 11, 'TRANS': 171}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.30, per 1000 atoms: 0.66
  Number of scatterers: 6514
  At special positions: 0
  Unit cell: (105.439, 86.96, 109.787, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1253      8.00
     N    1063      7.00
     C    4161      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 322 "
      " NAG B   1 " - " ASN A  53 "
      " NAG C   1 " - " ASN A  90 "
      " NAG D   1 " - " ASN A 103 "
      " NAG F   1 " - " ASN A 432 "
      " NAG G   1 " - " ASN A 546 "
      " NAG H   1 " - " ASN E 343 "
  Time building additional restraints: 1.81
  Conformation dependent library (CDL) restraints added in 832.7 milliseconds
  

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1472

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      50.1% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 31
      removed outlier: 3.885A  pdb=" N   LYS A  26 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LYS A  31 " --> pdb=" O   THR A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 52
      removed outlier: 4.038A  pdb=" N   TYR A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
      removed outlier: 3.854A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 91 through 102
      removed outlier: 3.829A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.558A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 155
      removed outlier: 3.789A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 171
      removed outlier: 3.800A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 4.571A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.552A  pdb=" N   TYR A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
      removed outlier: 4.317A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 249
      removed outlier: 4.422A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 305 through 319
      removed outlier: 3.778A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 4.025A  pdb=" N   ASN A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 4.040A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.554A  pdb=" N   LEU A 392 " --> pdb=" O   PRO A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 3.801A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
      removed outlier: 3.690A  pdb=" N   SER A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLY A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 444
      removed outlier: 3.603A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.099A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN A 531 " --> pdb=" O   GLU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.526A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.709A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG A 559 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 570
    Processing helix  chain 'A' and resid 581 through 596
      removed outlier: 3.558A  pdb=" N   LEU A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'E' and resid 337 through 341
      removed outlier: 3.702A  pdb=" N   GLU E 340 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 349 through 353
    Processing helix  chain 'E' and resid 364 through 368
      removed outlier: 4.094A  pdb=" N   VAL E 367 " --> pdb=" O   ASP E 364 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 390
    Processing helix  chain 'E' and resid 403 through 410
      removed outlier: 3.842A  pdb=" N   GLU E 406 " --> pdb=" O   ARG E 403 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   SER E 408 " --> pdb=" O   ASN E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 438 through 443
      removed outlier: 3.570A  pdb=" N   ASP E 442 " --> pdb=" O   SER E 438 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER E 443 " --> pdb=" O   ASN E 439 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 438 through 443'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.323A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 3.704A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358
      removed outlier: 4.461A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE E 434 " --> pdb=" O   VAL E 511 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454
      removed outlier: 3.684A  pdb=" N   GLN E 493 " --> pdb=" O   TYR E 453 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474

    243 hydrogen bonds defined for protein.
    666 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: 1.76

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2061
        1.34 -     1.46: 1712
        1.46 -     1.58: 2864
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6695
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.95e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 3.96e+00
  bond pdb=" CA  ASN A 149 "
       pdb=" C   ASN A 149 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 1.41e-02 5.03e+03 3.54e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.43e+00
  bond pdb=" CA  HIS E 339 "
       pdb=" C   HIS E 339 "
    ideal  model  delta    sigma   weight residual
    1.522  1.496  0.025 1.72e-02 3.38e+03 2.18e+00
  ... (remaining 6690 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 8525
        1.32 -     2.64: 474
        2.64 -     3.96: 71
        3.96 -     5.28: 22
        5.28 -     6.60: 5
  Bond angle restraints: 9097
  Sorted by residual:
  angle pdb=" N   ILE A  21 "
        pdb=" CA  ILE A  21 "
        pdb=" C   ILE A  21 "
      ideal   model   delta    sigma   weight residual
     112.29  107.52    4.77 9.40e-01 1.13e+00 2.57e+01
  angle pdb=" N   GLU A 197 "
        pdb=" CA  GLU A 197 "
        pdb=" CB  GLU A 197 "
      ideal   model   delta    sigma   weight residual
     114.17  109.20    4.97 1.14e+00 7.69e-01 1.90e+01
  angle pdb=" CA  PRO A 138 "
        pdb=" C   PRO A 138 "
        pdb=" N   GLN A 139 "
      ideal   model   delta    sigma   weight residual
     116.45  119.77   -3.32 8.50e-01 1.38e+00 1.52e+01
  angle pdb=" CA  PRO A 138 "
        pdb=" C   PRO A 138 "
        pdb=" O   PRO A 138 "
      ideal   model   delta    sigma   weight residual
     121.38  118.61    2.77 7.70e-01 1.69e+00 1.30e+01
  angle pdb=" N   ASP A 509 "
        pdb=" CA  ASP A 509 "
        pdb=" C   ASP A 509 "
      ideal   model   delta    sigma   weight residual
     111.52  116.55   -5.03 1.40e+00 5.10e-01 1.29e+01
  ... (remaining 9092 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3526
       17.99 -    35.98: 434
       35.98 -    53.97: 130
       53.97 -    71.95: 19
       71.95 -    89.94: 7
  Dihedral angle restraints: 4116
    sinusoidal: 1824
      harmonic: 2292
  Sorted by residual:
  dihedral pdb=" CA  CYS A 344 "
           pdb=" C   CYS A 344 "
           pdb=" N   HIS A 345 "
           pdb=" CA  HIS A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.27   32.73     1      1.00e+01 1.00e-02 1.52e+01
  dihedral pdb=" CA  GLY A 337 "
           pdb=" C   GLY A 337 "
           pdb=" N   ASN A 338 "
           pdb=" CA  ASN A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.64  -19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 4113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 889
       0.079 -    0.158: 92
       0.158 -    0.237: 3
       0.237 -    0.316: 1
       0.316 -    0.395: 1
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A  90 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.89e+00
  chirality pdb=" C4  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" C5  NAG D   1 "
            pdb=" O4  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.25   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.30   -0.20 2.00e-01 2.50e+01 9.66e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 372 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO E 373 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO E 373 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E 373 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 462 "   -0.028 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO E 463 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO E 463 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 463 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "   -0.026 5.00e-02 4.00e+02   3.86e-02 2.39e+00
        pdb=" N   PRO A 583 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1165 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 184
        2.69 -     3.24: 6348
        3.24 -     3.79: 9469
        3.79 -     4.35: 11957
        4.35 -     4.90: 20385
  Nonbonded interactions: 48343
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 111 "
            pdb=" OD1 ASP A 111 "
     model   vdw
     2.135 3.120
  nonbonded pdb=" O   ASN E 439 "
            pdb=" OG  SER E 443 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER E 349 "
            pdb=" O   LEU E 452 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASP A 382 "
            pdb=" OH  TYR A 385 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" NH2 ARG E 357 "
            pdb=" O   ILE E 358 "
     model   vdw
     2.277 3.120
  ... (remaining 48338 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:             1.620
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.350
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
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      :  0.006   0.056   6695  Z= 0.415
  Angle     :  0.708   6.601   9097  Z= 0.391
  Chirality :  0.050   0.395    986
  Planarity :  0.004   0.044   1161
  Dihedral  : 16.884  89.943   2626
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 19.24 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.33 (0.24), residues: 774
  helix: -2.10 (0.23), residues: 359
  sheet: -2.11 (0.64), residues: 48
  loop : -3.87 (0.24), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.012   0.002   PHE E 400 
 TYR   0.017   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 169 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 87
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8352 (tptp)
REVERT: A  115 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7492 (tpt170)
REVERT: A  154 ASN cc_start: 0.8106 (m-40) cc_final: 0.7866 (t0)
REVERT: A  156 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8576 (tt)
REVERT: A  224 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6804 (mp0)
REVERT: A  367 ASP cc_start: 0.6928 (p0) cc_final: 0.6700 (p0)
REVERT: E  414 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9015 (tp40)
REVERT: E  466 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7425 (ptm160)
  outliers start: 52
  outliers final: 41
  residues processed: 134
  average time/residue: 0.1895
  time to fit residues: 34.1963
Evaluate side-chains
  120 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 76
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  432 ASN
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  418 ILE
Chi-restraints excluded: chain E residue  425 LEU
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  500 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0570
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0010
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.4104

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 102 GLN
A 239 HIS
A 340 GLN
A 374 HIS
A 378 HIS
A 437 ASN
A 472 GLN
A 505 HIS
A 522 GLN
A 535 HIS
A 599 ASN
** E 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 450 ASN
E 487 ASN
** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.103868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.085845 restraints weight = 11231.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.089148 restraints weight = 5475.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.091422 restraints weight = 3342.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6695  Z= 0.165
  Angle     :  0.618  14.091   9097  Z= 0.299
  Chirality :  0.045   0.323    986
  Planarity :  0.004   0.059   1161
  Dihedral  :  9.550  58.841   1192
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 21.72 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.10 (0.27), residues: 774
  helix: -0.99 (0.27), residues: 363
  sheet: -1.54 (0.67), residues: 49
  loop : -3.36 (0.26), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 265 
 PHE   0.013   0.001   PHE A 428 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 219 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 80
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8455 (tptp)
REVERT: A   82 MET cc_start: 0.7793 (ttp) cc_final: 0.6927 (tmm)
REVERT: A  201 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8159 (t70)
REVERT: A  340 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7551 (mm110)
REVERT: A  474 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8504 (mmm)
REVERT: E  414 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9022 (tp40)
REVERT: E  466 ARG cc_start: 0.8347 (ptm160) cc_final: 0.8049 (ptm160)
  outliers start: 38
  outliers final: 20
  residues processed: 110
  average time/residue: 0.1541
  time to fit residues: 23.8758
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  467 ASP
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0570
   chunk 61 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0870
   chunk 38 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0470
   overall best weight:    0.2574

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 340 GLN
E 339 HIS
E 487 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.106815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.088151 restraints weight = 11439.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.091529 restraints weight = 5628.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.093817 restraints weight = 3461.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6695  Z= 0.138
  Angle     :  0.573  15.187   9097  Z= 0.274
  Chirality :  0.043   0.296    986
  Planarity :  0.004   0.056   1161
  Dihedral  :  7.895  59.631   1143
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 22.59 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.28), residues: 774
  helix: -0.30 (0.29), residues: 355
  sheet: -1.21 (0.70), residues: 48
  loop : -3.00 (0.27), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.011   0.001   PHE A 428 
 TYR   0.009   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 582 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8930 (tmtt) cc_final: 0.8681 (tppt)
REVERT: A   82 MET cc_start: 0.7666 (ttp) cc_final: 0.6727 (tmm)
REVERT: A  201 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8034 (t0)
REVERT: A  249 MET cc_start: 0.8141 (ttp) cc_final: 0.7903 (tmm)
REVERT: A  306 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7406 (tpp-160)
REVERT: A  340 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7573 (mm110)
REVERT: A  479 GLU cc_start: 0.8422 (tp30) cc_final: 0.8211 (tp30)
REVERT: E  414 GLN cc_start: 0.9258 (mm-40) cc_final: 0.9011 (tp40)
  outliers start: 30
  outliers final: 17
  residues processed: 104
  average time/residue: 0.1512
  time to fit residues: 22.5053
Evaluate side-chains
  94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 21 optimal weight:    0.0370
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0010
   overall best weight:    1.0070

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
E 409 GLN
E 477 ASN
E 487 ASN
E 493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.105088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.086612 restraints weight = 11664.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.089869 restraints weight = 5829.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.092066 restraints weight = 3629.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6695  Z= 0.228
  Angle     :  0.590  15.068   9097  Z= 0.280
  Chirality :  0.045   0.296    986
  Planarity :  0.004   0.056   1161
  Dihedral  :  7.499  58.747   1138
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 23.47 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.29), residues: 774
  helix: -0.07 (0.29), residues: 359
  sheet: -1.07 (0.71), residues: 48
  loop : -2.92 (0.27), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.004   0.001   HIS A 265 
 PHE   0.010   0.001   PHE A 327 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 582 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 82
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8632 (tppt)
REVERT: A   82 MET cc_start: 0.7670 (ttp) cc_final: 0.6650 (tmm)
REVERT: A  201 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8019 (t0)
REVERT: A  249 MET cc_start: 0.8163 (ttp) cc_final: 0.7883 (tmm)
REVERT: A  306 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7455 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8529 (tp30) cc_final: 0.8269 (tp30)
REVERT: E  414 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8958 (tp40)
  outliers start: 30
  outliers final: 19
  residues processed: 108
  average time/residue: 0.1472
  time to fit residues: 22.6362
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0000
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.3390

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN
E 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.103710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.085538 restraints weight = 11720.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.088684 restraints weight = 5773.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.090904 restraints weight = 3595.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6695  Z= 0.282
  Angle     :  0.648  24.241   9097  Z= 0.298
  Chirality :  0.047   0.293    986
  Planarity :  0.004   0.056   1161
  Dihedral  :  7.384  58.658   1138
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 23.91 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.29), residues: 774
  helix:  0.07 (0.29), residues: 359
  sheet: -0.98 (0.71), residues: 48
  loop : -2.88 (0.27), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.012   0.001   PHE A 327 
 TYR   0.013   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 219 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.584 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8993 (tmtt) cc_final: 0.8643 (tppt)
REVERT: A   82 MET cc_start: 0.7621 (ttp) cc_final: 0.6536 (tmm)
REVERT: A  190 MET cc_start: 0.8598 (tmm) cc_final: 0.8311 (ttt)
REVERT: A  201 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8067 (t0)
REVERT: A  249 MET cc_start: 0.8078 (ttp) cc_final: 0.7781 (tmm)
REVERT: A  306 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7457 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8554 (tp30) cc_final: 0.8253 (tp30)
REVERT: A  557 MET cc_start: 0.9045 (tmm) cc_final: 0.8750 (tmm)
REVERT: E  357 ARG cc_start: 0.7419 (ptm160) cc_final: 0.7100 (ptm-80)
REVERT: E  414 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8917 (tp40)
  outliers start: 30
  outliers final: 20
  residues processed: 98
  average time/residue: 0.1736
  time to fit residues: 23.4453
Evaluate side-chains
  101 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Chi-restraints excluded: chain E residue  477 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN
E 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.104517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.086635 restraints weight = 11424.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.089832 restraints weight = 5628.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.092024 restraints weight = 3463.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6695  Z= 0.231
  Angle     :  0.637  24.379   9097  Z= 0.292
  Chirality :  0.045   0.296    986
  Planarity :  0.004   0.056   1161
  Dihedral  :  7.055  58.543   1134
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.91 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.29), residues: 774
  helix:  0.20 (0.29), residues: 360
  sheet: -0.87 (0.72), residues: 48
  loop : -2.79 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.011   0.001   PHE A 327 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 219 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8959 (tmtt) cc_final: 0.8599 (tppt)
REVERT: A   82 MET cc_start: 0.7592 (ttp) cc_final: 0.6497 (tmm)
REVERT: A  190 MET cc_start: 0.8654 (tmm) cc_final: 0.8343 (ttt)
REVERT: A  201 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8034 (t0)
REVERT: A  249 MET cc_start: 0.8034 (ttp) cc_final: 0.7767 (tmm)
REVERT: A  293 VAL cc_start: 0.8006 (m) cc_final: 0.7783 (m)
REVERT: A  306 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7597 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8480 (tp30) cc_final: 0.8246 (tp30)
REVERT: A  557 MET cc_start: 0.9019 (tmm) cc_final: 0.8688 (tmm)
REVERT: E  357 ARG cc_start: 0.7382 (ptm160) cc_final: 0.7068 (ptm-80)
REVERT: E  414 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8911 (tp40)
  outliers start: 26
  outliers final: 22
  residues processed: 101
  average time/residue: 0.1629
  time to fit residues: 23.1112
Evaluate side-chains
  101 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0040
   chunk 74 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 19 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.2990

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.106973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.088946 restraints weight = 11289.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.092211 restraints weight = 5563.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.094454 restraints weight = 3415.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6695  Z= 0.145
  Angle     :  0.626  25.775   9097  Z= 0.277
  Chirality :  0.044   0.322    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  7.445  58.651   1134
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.91 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.30), residues: 774
  helix:  0.37 (0.29), residues: 362
  sheet: -0.76 (0.72), residues: 48
  loop : -2.58 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.009   0.001   PHE E 342 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.001   0.000   ARG A 219 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8533 (tppt)
REVERT: A   82 MET cc_start: 0.7570 (ttp) cc_final: 0.6510 (tmm)
REVERT: A  101 GLN cc_start: 0.8728 (tt0) cc_final: 0.8503 (tt0)
REVERT: A  201 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7898 (t0)
REVERT: A  249 MET cc_start: 0.8107 (ttp) cc_final: 0.7892 (tmm)
REVERT: A  479 GLU cc_start: 0.8513 (tp30) cc_final: 0.8220 (tp30)
REVERT: A  557 MET cc_start: 0.8996 (tmm) cc_final: 0.8648 (tmm)
REVERT: E  414 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8961 (tp40)
REVERT: E  417 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7538 (t0)
  outliers start: 27
  outliers final: 18
  residues processed: 101
  average time/residue: 0.1638
  time to fit residues: 23.2361
Evaluate side-chains
  102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 12 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.108470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.089800 restraints weight = 11553.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.093049 restraints weight = 5867.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.095300 restraints weight = 3700.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6695  Z= 0.183
  Angle     :  0.637  24.932   9097  Z= 0.283
  Chirality :  0.044   0.289    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  7.424  69.781   1128
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.05 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.30), residues: 774
  helix:  0.52 (0.29), residues: 360
  sheet: -0.78 (0.72), residues: 49
  loop : -2.52 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.006   0.001   HIS E 339 
 PHE   0.009   0.001   PHE A 327 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 219 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8912 (tmtt) cc_final: 0.8580 (tppt)
REVERT: A   82 MET cc_start: 0.7567 (ttp) cc_final: 0.6531 (tmm)
REVERT: A  101 GLN cc_start: 0.8669 (tt0) cc_final: 0.8439 (tt0)
REVERT: A  156 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8661 (tt)
REVERT: A  201 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7952 (t0)
REVERT: A  249 MET cc_start: 0.8018 (ttp) cc_final: 0.7803 (tmm)
REVERT: A  479 GLU cc_start: 0.8518 (tp30) cc_final: 0.8280 (tp30)
REVERT: A  557 MET cc_start: 0.9000 (tmm) cc_final: 0.8660 (tmm)
REVERT: E  406 GLU cc_start: 0.8752 (tt0) cc_final: 0.8534 (tt0)
  outliers start: 26
  outliers final: 19
  residues processed: 101
  average time/residue: 0.1410
  time to fit residues: 20.8193
Evaluate side-chains
  102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0170
   chunk 41 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.109711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.090960 restraints weight = 11611.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.094220 restraints weight = 5826.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.096432 restraints weight = 3672.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6695  Z= 0.153
  Angle     :  0.604  24.463   9097  Z= 0.275
  Chirality :  0.043   0.298    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  5.943  58.744   1126
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 24.78 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.30), residues: 774
  helix:  0.61 (0.29), residues: 365
  sheet: -0.55 (0.74), residues: 49
  loop : -2.45 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 327 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 219 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8557 (tppt)
REVERT: A   82 MET cc_start: 0.7620 (ttp) cc_final: 0.6589 (tmm)
REVERT: A  156 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8612 (tt)
REVERT: A  201 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7833 (t0)
REVERT: A  479 GLU cc_start: 0.8548 (tp30) cc_final: 0.8243 (tp30)
REVERT: A  557 MET cc_start: 0.9026 (tmm) cc_final: 0.8672 (tmm)
REVERT: E  414 GLN cc_start: 0.9153 (tp40) cc_final: 0.8952 (tp40)
  outliers start: 22
  outliers final: 19
  residues processed: 100
  average time/residue: 0.1426
  time to fit residues: 20.8852
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  406 GLU
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.108980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.090531 restraints weight = 11548.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.093842 restraints weight = 5783.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.096077 restraints weight = 3598.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6695  Z= 0.170
  Angle     :  0.616  23.756   9097  Z= 0.281
  Chirality :  0.044   0.292    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  5.888  58.796   1126
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 24.93 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.30), residues: 774
  helix:  0.66 (0.29), residues: 365
  sheet: -0.46 (0.75), residues: 49
  loop : -2.43 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 417 
 PHE   0.009   0.001   PHE A 327 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 219 

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8532 (tppt)
REVERT: A  156 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8609 (tt)
REVERT: A  201 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7887 (t0)
REVERT: A  479 GLU cc_start: 0.8519 (tp30) cc_final: 0.8298 (tp30)
REVERT: A  557 MET cc_start: 0.9035 (tmm) cc_final: 0.8683 (tmm)
REVERT: E  414 GLN cc_start: 0.9112 (tp40) cc_final: 0.8862 (tp40)
  outliers start: 22
  outliers final: 19
  residues processed: 97
  average time/residue: 0.1423
  time to fit residues: 20.1830
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0770
   chunk 42 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.109795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.091272 restraints weight = 11584.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.094627 restraints weight = 5812.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.096910 restraints weight = 3608.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6695  Z= 0.162
  Angle     :  0.617  23.381   9097  Z= 0.285
  Chirality :  0.043   0.292    986
  Planarity :  0.004   0.053   1161
  Dihedral  :  5.766  58.803   1126
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 25.36 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.30), residues: 774
  helix:  0.75 (0.29), residues: 365
  sheet: -0.40 (0.77), residues: 49
  loop : -2.35 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 417 
 PHE   0.007   0.001   PHE A 327 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 393 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2141.78 seconds
wall clock time: 39 minutes 9.58 seconds (2349.58 seconds total)