Starting phenix.real_space_refine
on Fri Dec 27 19:56:26 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y32_38866/12_2024/8y32_38866.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y32_38866/12_2024/8y32_38866.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y32_38866/12_2024/8y32_38866.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y32_38866/12_2024/8y32_38866.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y32_38866/12_2024/8y32_38866.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y32_38866/12_2024/8y32_38866.cif"
  }
  resolution = 4.13
  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=   0.001 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     Cl      1      4.86       5
     C    4207      2.51       5
     N    1084      2.21       5
     O    1241      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6571
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4906
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 571}
    Chain: "B"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1566
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' CL': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    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
  Time building chain proxies: 4.23, per 1000 atoms: 0.64
  Number of scatterers: 6571
  At special positions: 0
  Unit cell: (93.09, 85.6, 126.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      38     16.00
     O    1241      8.00
     N    1084      7.00
     C    4207      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A  53 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 905 " - " ASN A 431 "
      " NAG A 906 " - " ASN A 545 "
      " NAG B 601 " - " ASN B 343 "
      " NAG B 602 " - " ASN B 354 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 935.2 milliseconds
  

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      50.9% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 36
    Processing helix  chain 'A' and resid 37 through 51
      removed outlier: 3.606A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.574A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TRP A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER A  77 " --> pdb=" O   TYR A  73 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ARG A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   MET A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.638A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA A  99 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 115 through 129
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 157 through 165
    Processing helix  chain 'A' and resid 166 through 191
      removed outlier: 4.681A  pdb=" N   GLY A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   LYS A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 3.717A  pdb=" N   VAL A 184 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   MET A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A 191 " --> pdb=" O   ASN A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 197 through 204
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.547A  pdb=" N   LEU A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET A 222 " --> pdb=" O   ARG A 218 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LYS A 223 " --> pdb=" O   ASP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 251
      removed outlier: 3.519A  pdb=" N   HIS A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.564A  pdb=" N   ILE A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 327
    Processing helix  chain 'A' and resid 364 through 384
      removed outlier: 3.911A  pdb=" N   TYR A 384 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 398 through 411
      removed outlier: 3.576A  pdb=" N   ALA A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   MET A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 420
    Processing helix  chain 'A' and resid 430 through 446
      removed outlier: 3.763A  pdb=" N   THR A 444 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.646A  pdb=" N   TRP A 476 " --> pdb=" O   TRP A 472 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU A 482 " --> pdb=" O   GLU A 478 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 483 " --> pdb=" O   MET A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 511 through 532
      removed outlier: 3.974A  pdb=" N   TYR A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   THR A 518 " --> pdb=" O   TYR A 514 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLU A 526 " --> pdb=" O   PHE A 522 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 558
      removed outlier: 3.681A  pdb=" N   MET A 556 " --> pdb=" O   ARG A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 573
      removed outlier: 3.556A  pdb=" N   ALA A 568 " --> pdb=" O   PRO A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 587
      removed outlier: 3.651A  pdb=" N   TYR A 586 " --> pdb=" O   PRO A 582 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 598
      removed outlier: 3.589A  pdb=" N   GLU A 596 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 341
      removed outlier: 4.009A  pdb=" N   GLU B 340 " --> pdb=" O   CYS B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 3.960A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 385 through 389'
    Processing helix  chain 'B' and resid 407 through 411
      removed outlier: 3.613A  pdb=" N   ALA B 411 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.508A  pdb=" N   GLN B 506 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.223A  pdb=" N   LEU A 261 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348
      removed outlier: 3.553A  pdb=" N   LYS A 358 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 356 " --> pdb=" O   TRP A 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 356 through 358
      removed outlier: 4.199A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 392
      removed outlier: 3.512A  pdb=" N   VAL B 524 " --> pdb=" O   PHE B 392 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.618A  pdb=" N   TYR B 473 " --> pdb=" O   TYR B 489 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    240 hydrogen bonds defined for protein.
    672 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: 1.61

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2063
        1.34 -     1.46: 1758
        1.46 -     1.58: 2878
        1.58 -     1.71: 0
        1.71 -     1.83: 60
  Bond restraints: 6759
  Sorted by residual:
  bond pdb=" C   TYR A  83 "
       pdb=" N   SER A  84 "
    ideal  model  delta    sigma   weight residual
    1.330  1.450 -0.120 1.31e-02 5.83e+03 8.41e+01
  bond pdb=" C   THR A  82 "
       pdb=" N   TYR A  83 "
    ideal  model  delta    sigma   weight residual
    1.331  1.433 -0.103 1.45e-02 4.76e+03 5.04e+01
  bond pdb=" C   TYR B 489 "
       pdb=" N   PHE B 490 "
    ideal  model  delta    sigma   weight residual
    1.331  1.417 -0.087 1.24e-02 6.50e+03 4.90e+01
  bond pdb=" C   CYS B 488 "
       pdb=" N   TYR B 489 "
    ideal  model  delta    sigma   weight residual
    1.329  1.244  0.085 1.76e-02 3.23e+03 2.35e+01
  bond pdb=" C4  NAG B 602 "
       pdb=" C5  NAG B 602 "
    ideal  model  delta    sigma   weight residual
    1.532  1.499  0.033 2.00e-02 2.50e+03 2.75e+00
  ... (remaining 6754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8988
        2.00 -     4.00: 137
        4.00 -     5.99: 33
        5.99 -     7.99: 12
        7.99 -     9.99: 4
  Bond angle restraints: 9174
  Sorted by residual:
  angle pdb=" CA  TYR B 489 "
        pdb=" C   TYR B 489 "
        pdb=" N   PHE B 490 "
      ideal   model   delta    sigma   weight residual
     115.90  123.10   -7.20 1.21e+00 6.83e-01 3.54e+01
  angle pdb=" O   TYR B 489 "
        pdb=" C   TYR B 489 "
        pdb=" N   PHE B 490 "
      ideal   model   delta    sigma   weight residual
     122.59  115.19    7.40 1.35e+00 5.49e-01 3.01e+01
  angle pdb=" C   TYR B 489 "
        pdb=" N   PHE B 490 "
        pdb=" CA  PHE B 490 "
      ideal   model   delta    sigma   weight residual
     122.65  131.50   -8.85 1.66e+00 3.63e-01 2.84e+01
  angle pdb=" CA  TYR A  83 "
        pdb=" C   TYR A  83 "
        pdb=" N   SER A  84 "
      ideal   model   delta    sigma   weight residual
     116.24  122.20   -5.96 1.34e+00 5.57e-01 1.98e+01
  angle pdb=" O   TYR A  83 "
        pdb=" C   TYR A  83 "
        pdb=" N   SER A  84 "
      ideal   model   delta    sigma   weight residual
     123.01  117.19    5.82 1.33e+00 5.65e-01 1.92e+01
  ... (remaining 9169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.99: 3601
       24.99 -    49.98: 402
       49.98 -    74.97: 43
       74.97 -    99.97: 16
       99.97 -   124.96: 17
  Dihedral angle restraints: 4079
    sinusoidal: 1747
      harmonic: 2332
  Sorted by residual:
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.38   73.62     1      1.00e+01 1.00e-02 6.89e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -15.16  -70.84     1      1.00e+01 1.00e-02 6.45e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.34  -37.34     1      1.00e+01 1.00e-02 1.97e+01
  ... (remaining 4076 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 948
       0.106 -    0.212: 21
       0.212 -    0.318: 0
       0.318 -    0.424: 0
       0.424 -    0.530: 1
  Chirality restraints: 970
  Sorted by residual:
  chirality pdb=" C1  NAG A 902 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG A 902 "
            pdb=" O5  NAG A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 7.02e+00
  chirality pdb=" C1  NAG B 602 "
            pdb=" ND2 ASN B 354 "
            pdb=" C2  NAG B 602 "
            pdb=" O5  NAG B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.60    0.20 2.00e-01 2.50e+01 9.93e-01
  chirality pdb=" CB  ILE A 255 "
            pdb=" CA  ILE A 255 "
            pdb=" CG1 ILE A 255 "
            pdb=" CG2 ILE A 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.68e-01
  ... (remaining 967 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 601 "    0.308 2.00e-02 2.50e+03   2.69e-01 9.06e+02
        pdb=" C7  NAG B 601 "   -0.064 2.00e-02 2.50e+03
        pdb=" C8  NAG B 601 "    0.039 2.00e-02 2.50e+03
        pdb=" N2  NAG B 601 "   -0.475 2.00e-02 2.50e+03
        pdb=" O7  NAG B 601 "    0.192 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 602 "    0.151 2.00e-02 2.50e+03   1.25e-01 1.95e+02
        pdb=" C7  NAG B 602 "   -0.043 2.00e-02 2.50e+03
        pdb=" C8  NAG B 602 "    0.113 2.00e-02 2.50e+03
        pdb=" N2  NAG B 602 "   -0.200 2.00e-02 2.50e+03
        pdb=" O7  NAG B 602 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 424 "   -0.059 5.00e-02 4.00e+02   8.91e-02 1.27e+01
        pdb=" N   PRO A 425 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A 425 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 425 "   -0.049 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 111
        2.68 -     3.23: 6195
        3.23 -     3.79: 9673
        3.79 -     4.34: 12784
        4.34 -     4.90: 20995
  Nonbonded interactions: 49758
  Sorted by model distance:
  nonbonded pdb=" NE  ARG A 339 "
            pdb=" O7  NAG A 902 "
     model   vdw
     2.120 2.496
  nonbonded pdb=" OD2 ASP A 542 "
            pdb=" OG  SER A 544 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE1 GLN A 238 "
            pdb=" ND2 ASN A 598 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" ND1 HIS B 339 "
            pdb=" OE1 GLU B 340 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   ASP A 366 "
            pdb=" OG1 THR A 370 "
     model   vdw
     2.278 3.040
  ... (remaining 49753 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  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:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.440
  Find NCS groups from input model:        0.070
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   6759  Z= 0.301
  Angle     :  0.699   9.989   9174  Z= 0.365
  Chirality :  0.046   0.530    970
  Planarity :  0.010   0.269   1169
  Dihedral  : 21.050 124.957   2568
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.48 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 33.29 %
    Favored  : 65.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.08 (0.30), residues: 787
  helix:  0.33 (0.29), residues: 346
  sheet:  0.80 (0.89), residues: 36
  loop : -1.87 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 202 
 HIS   0.004   0.001   HIS A 102 
 PHE   0.012   0.001   PHE B 429 
 TYR   0.009   0.001   TYR A 214 
 ARG   0.003   0.000   ARG A  66 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  186 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7368 (tt0)
REVERT: A  254 TYR cc_start: 0.7481 (m-80) cc_final: 0.7182 (m-10)
REVERT: A  381 ASP cc_start: 0.6680 (t0) cc_final: 0.6434 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 117
  average time/residue: 0.1927
  time to fit residues: 30.1976
Evaluate side-chains
  115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0570
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0070
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0030
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.1704

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

Flipped N/Q/H residues before XYZ refinement:
A 299 GLN
A 441 GLN
B 439 ASN
B 474 GLN
B 477 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6862
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6759  Z= 0.162
  Angle     :  0.602  10.285   9174  Z= 0.293
  Chirality :  0.045   0.493    970
  Planarity :  0.005   0.063   1169
  Dihedral  : 10.459 104.392   1017
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.45 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.31), residues: 787
  helix:  0.35 (0.29), residues: 356
  sheet: -0.04 (0.77), residues: 47
  loop : -1.72 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 167 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.022   0.001   PHE A 511 
 TYR   0.018   0.001   TYR A 198 
 ARG   0.004   0.000   ARG A 176 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6427 (tmm) cc_final: 0.6206 (tmm)
REVERT: A  151 MET cc_start: 0.7242 (tpt) cc_final: 0.6811 (tpt)
REVERT: A  164 TRP cc_start: 0.5553 (m100) cc_final: 0.5074 (m100)
REVERT: A  254 TYR cc_start: 0.7433 (m-80) cc_final: 0.7158 (m-10)
REVERT: A  340 LYS cc_start: 0.8495 (mmtm) cc_final: 0.7977 (mptt)
REVERT: A  349 ASP cc_start: 0.6712 (t0) cc_final: 0.6479 (t0)
REVERT: A  507 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6867 (mm-30)
REVERT: B  346 ARG cc_start: 0.7343 (tpt-90) cc_final: 0.7112 (mtp85)
REVERT: B  377 PHE cc_start: 0.8483 (t80) cc_final: 0.8232 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2204
  time to fit residues: 41.6086
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0370
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.9862

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

Flipped N/Q/H residues before XYZ refinement:
** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6759  Z= 0.234
  Angle     :  0.632   9.882   9174  Z= 0.313
  Chirality :  0.048   0.536    970
  Planarity :  0.005   0.053   1169
  Dihedral  :  6.997  57.622   1017
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.72 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.10 (0.31), residues: 787
  helix:  0.23 (0.29), residues: 363
  sheet:  0.09 (0.83), residues: 47
  loop : -1.84 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 167 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.012   0.001   PHE A 437 
 TYR   0.011   0.001   TYR A 216 
 ARG   0.004   0.000   ARG A 305 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6197 (tmm) cc_final: 0.5969 (tmm)
REVERT: A  151 MET cc_start: 0.7507 (tpt) cc_final: 0.6935 (tpt)
REVERT: A  164 TRP cc_start: 0.5630 (m100) cc_final: 0.5133 (m100)
REVERT: A  237 GLU cc_start: 0.7220 (tt0) cc_final: 0.6617 (mt-10)
REVERT: A  254 TYR cc_start: 0.7534 (m-80) cc_final: 0.7326 (m-10)
REVERT: A  269 MET cc_start: 0.5962 (mmm) cc_final: 0.5106 (mmm)
REVERT: A  340 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8316 (mptt)
REVERT: A  349 ASP cc_start: 0.6823 (t0) cc_final: 0.6550 (t0)
REVERT: A  454 MET cc_start: 0.7612 (tpt) cc_final: 0.7189 (tpt)
REVERT: A  479 MET cc_start: 0.7737 (ppp) cc_final: 0.6924 (ppp)
REVERT: A  488 GLU cc_start: 0.5801 (pp20) cc_final: 0.5579 (pp20)
REVERT: A  507 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6819 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2092
  time to fit residues: 36.7388
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 299 GLN
A 598 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6759  Z= 0.202
  Angle     :  0.587   9.201   9174  Z= 0.293
  Chirality :  0.046   0.532    970
  Planarity :  0.004   0.051   1169
  Dihedral  :  6.479  54.383   1017
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.72 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.04 (0.31), residues: 787
  helix:  0.33 (0.29), residues: 363
  sheet:  0.07 (0.82), residues: 47
  loop : -1.86 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 605 
 HIS   0.007   0.001   HIS A 377 
 PHE   0.026   0.001   PHE B 377 
 TYR   0.010   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 552 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6202 (tmm) cc_final: 0.5931 (tmm)
REVERT: A  164 TRP cc_start: 0.5773 (m100) cc_final: 0.5447 (m100)
REVERT: A  269 MET cc_start: 0.6044 (mmm) cc_final: 0.5297 (mmm)
REVERT: A  340 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8166 (mmtm)
REVERT: A  454 MET cc_start: 0.7579 (tpt) cc_final: 0.7020 (tpp)
REVERT: A  479 MET cc_start: 0.7809 (ppp) cc_final: 0.6960 (ppp)
REVERT: B  428 ASP cc_start: 0.8543 (p0) cc_final: 0.8288 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2013
  time to fit residues: 32.7289
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0980
   chunk 64 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 67 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6759  Z= 0.172
  Angle     :  0.579  10.388   9174  Z= 0.285
  Chirality :  0.045   0.507    970
  Planarity :  0.004   0.047   1169
  Dihedral  :  6.096  48.299   1017
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.34 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.31), residues: 787
  helix:  0.40 (0.29), residues: 365
  sheet:  0.01 (0.82), residues: 45
  loop : -1.76 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 605 
 HIS   0.004   0.001   HIS A 377 
 PHE   0.019   0.001   PHE B 377 
 TYR   0.009   0.001   TYR B 495 
 ARG   0.004   0.000   ARG A 160 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6221 (tmm) cc_final: 0.5975 (tmm)
REVERT: A  152 GLU cc_start: 0.6154 (mt-10) cc_final: 0.5910 (mt-10)
REVERT: A  269 MET cc_start: 0.5816 (mmm) cc_final: 0.5593 (mmm)
REVERT: A  297 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7143 (mt-10)
REVERT: A  300 SER cc_start: 0.8741 (m) cc_final: 0.8509 (p)
REVERT: A  340 LYS cc_start: 0.8719 (mmtm) cc_final: 0.8163 (mmtm)
REVERT: A  526 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6505 (tt0)
REVERT: B  481 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6965 (tmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2151
  time to fit residues: 35.7252
Evaluate side-chains
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0370
   chunk 75 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0370
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 72 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6759  Z= 0.159
  Angle     :  0.567   9.841   9174  Z= 0.278
  Chirality :  0.044   0.476    970
  Planarity :  0.004   0.045   1169
  Dihedral  :  5.690  41.971   1017
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.08 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.31), residues: 787
  helix:  0.53 (0.29), residues: 356
  sheet:  0.15 (0.81), residues: 47
  loop : -1.76 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 377 
 PHE   0.014   0.001   PHE B 377 
 TYR   0.010   0.001   TYR B 380 
 ARG   0.003   0.000   ARG A  66 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6316 (tmm) cc_final: 0.6036 (tmm)
REVERT: A  164 TRP cc_start: 0.5632 (m100) cc_final: 0.5353 (m100)
REVERT: A  297 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7088 (mt-10)
REVERT: A  300 SER cc_start: 0.8764 (m) cc_final: 0.8402 (p)
REVERT: A  340 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8134 (mmtm)
REVERT: A  349 ASP cc_start: 0.6819 (t0) cc_final: 0.6611 (t0)
REVERT: A  507 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6828 (mm-30)
REVERT: B  481 LYS cc_start: 0.7403 (mmtp) cc_final: 0.6950 (tmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1800
  time to fit residues: 28.4849
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6759  Z= 0.195
  Angle     :  0.603  11.177   9174  Z= 0.297
  Chirality :  0.046   0.499    970
  Planarity :  0.004   0.038   1169
  Dihedral  :  5.803  41.239   1017
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.59 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.31), residues: 787
  helix:  0.52 (0.29), residues: 349
  sheet:  0.20 (0.83), residues: 45
  loop : -1.73 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 167 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.013   0.001   PHE B 377 
 TYR   0.009   0.001   TYR B 495 
 ARG   0.003   0.000   ARG A  66 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6306 (tmm) cc_final: 0.6056 (tmm)
REVERT: A  152 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5696 (mt-10)
REVERT: A  164 TRP cc_start: 0.5711 (m100) cc_final: 0.4009 (m100)
REVERT: A  237 GLU cc_start: 0.7071 (tt0) cc_final: 0.6813 (mt-10)
REVERT: A  269 MET cc_start: 0.5951 (mmm) cc_final: 0.5588 (mtm)
REVERT: A  297 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7245 (mt-10)
REVERT: A  340 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8166 (mmtm)
REVERT: A  349 ASP cc_start: 0.6847 (t0) cc_final: 0.6448 (t0)
REVERT: A  507 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6800 (mm-30)
REVERT: A  526 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6469 (tt0)
REVERT: B  481 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6997 (tmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1916
  time to fit residues: 29.0101
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6759  Z= 0.210
  Angle     :  0.619  11.498   9174  Z= 0.304
  Chirality :  0.047   0.524    970
  Planarity :  0.004   0.045   1169
  Dihedral  :  5.988  43.093   1017
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.34 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.02 (0.31), residues: 787
  helix:  0.36 (0.29), residues: 356
  sheet:  0.03 (0.82), residues: 46
  loop : -1.81 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 167 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.012   0.001   PHE A 591 
 TYR   0.009   0.001   TYR B 380 
 ARG   0.003   0.000   ARG A  66 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6319 (tmm) cc_final: 0.6088 (tmm)
REVERT: A  237 GLU cc_start: 0.7122 (tt0) cc_final: 0.6804 (mt-10)
REVERT: A  340 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8140 (mmtm)
REVERT: A  507 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6916 (mm-30)
REVERT: A  526 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6497 (tt0)
REVERT: B  428 ASP cc_start: 0.8637 (p0) cc_final: 0.8404 (p0)
REVERT: B  481 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7011 (tmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2045
  time to fit residues: 33.5874
Evaluate side-chains
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0770
   chunk 63 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0770
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.2696

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6759  Z= 0.145
  Angle     :  0.559  10.739   9174  Z= 0.274
  Chirality :  0.043   0.439    970
  Planarity :  0.004   0.041   1169
  Dihedral  :  5.349  34.660   1017
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.21 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.58 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.31), residues: 787
  helix:  0.49 (0.29), residues: 361
  sheet:  0.51 (0.84), residues: 43
  loop : -1.64 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 167 
 HIS   0.005   0.001   HIS A 377 
 PHE   0.009   0.001   PHE B 377 
 TYR   0.011   0.001   TYR B 380 
 ARG   0.004   0.000   ARG A  66 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6407 (tmm) cc_final: 0.6176 (tmm)
REVERT: A  164 TRP cc_start: 0.5430 (m100) cc_final: 0.4550 (m100)
REVERT: A  340 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8078 (mmtm)
REVERT: A  356 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8031 (mtt-85)
REVERT: A  507 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6795 (mm-30)
REVERT: A  509 TYR cc_start: 0.7224 (m-80) cc_final: 0.6970 (m-80)
REVERT: A  526 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6469 (tt0)
REVERT: B  481 LYS cc_start: 0.7327 (mmtp) cc_final: 0.6899 (tmmt)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2089
  time to fit residues: 33.8827
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 6 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0370
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
A 441 GLN
A 600 ASN
B 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6759  Z= 0.161
  Angle     :  0.567  10.496   9174  Z= 0.280
  Chirality :  0.044   0.433    970
  Planarity :  0.004   0.043   1169
  Dihedral  :  5.185  31.056   1017
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.46 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.29 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.31), residues: 787
  helix:  0.62 (0.29), residues: 353
  sheet:  0.16 (0.81), residues: 48
  loop : -1.60 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 164 
 HIS   0.004   0.001   HIS A 373 
 PHE   0.024   0.001   PHE A 437 
 TYR   0.008   0.001   TYR B 495 
 ARG   0.004   0.000   ARG A  66 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6460 (tmm) cc_final: 0.6253 (tmm)
REVERT: A  151 MET cc_start: 0.7628 (tpt) cc_final: 0.7149 (tpt)
REVERT: A  152 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6076 (mt-10)
REVERT: A  340 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8033 (mmtm)
REVERT: A  507 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6863 (mm-30)
REVERT: A  509 TYR cc_start: 0.7403 (m-80) cc_final: 0.7173 (m-80)
REVERT: A  526 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6441 (tt0)
REVERT: B  481 LYS cc_start: 0.7423 (mmtp) cc_final: 0.7009 (tmmt)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1881
  time to fit residues: 30.6746
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0470
   chunk 3 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
A 379 GLN
A 600 ASN
B 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.123228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.123072 restraints weight = 10032.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 82)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.119990 restraints weight = 20191.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.120020 restraints weight = 19218.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6759  Z= 0.165
  Angle     :  0.563  10.395   9174  Z= 0.279
  Chirality :  0.044   0.424    970
  Planarity :  0.004   0.042   1169
  Dihedral  :  5.111  29.293   1017
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.34 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.58 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.31), residues: 787
  helix:  0.64 (0.29), residues: 354
  sheet:  0.23 (0.82), residues: 46
  loop : -1.55 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 164 
 HIS   0.005   0.001   HIS A 377 
 PHE   0.019   0.001   PHE A 437 
 TYR   0.007   0.001   TYR B 495 
 ARG   0.004   0.000   ARG A  66 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1704.90 seconds
wall clock time: 31 minutes 37.06 seconds (1897.06 seconds total)