Starting phenix.real_space_refine
on Sat May  2 09:52:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vbd_64920/05_2026/9vbd_64920.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vbd_64920/05_2026/9vbd_64920.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vbd_64920/05_2026/9vbd_64920.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vbd_64920/05_2026/9vbd_64920.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vbd_64920/05_2026/9vbd_64920.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vbd_64920/05_2026/9vbd_64920.map"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.036
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
     Cu      1      5.60       5
     S      15      5.16       5
     C    2708      2.51       5
     N     670      2.21       5
     O     849      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4243
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 521, 4038
          Classifications: {'peptide': 521}
          Link IDs: {'PTRANS': 40, 'TRANS': 480}
    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: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    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: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' CU': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.41, per 1000 atoms: 0.33
  Number of scatterers: 4243
  At special positions: 0
  Unit cell: (55.61, 85.49, 97.11, 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)
     Cu      1     28.99
     S      15     16.00
     O     849      8.00
     N     670      7.00
     C    2708      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 395 " - pdb=" SG  CYS A 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 421 " - pdb=" SG  CYS A 434 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 424 " - pdb=" SG  CYS A 436 " 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 E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
    BETA1-6
      " BMA E   3 " - " BMA E   4 "
    NAG-ASN
      " NAG A1001 " - " ASN A 182 "
      " NAG A1002 " - " ASN A 217 "
      " NAG A1003 " - " ASN A 456 "
      " NAG B   1 " - " ASN A 523 "
      " NAG C   1 " - " ASN A 284 "
      " NAG D   1 " - " ASN A 264 "
      " NAG E   1 " - " ASN A 298 "
      " NAG F   1 " - " ASN A 411 "
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 163.4 milliseconds
  

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  968

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 5 sheets defined
      23.6% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 40
      removed outlier: 3.514A  pdb=" N   TRP A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 131 through 137
      removed outlier: 3.669A  pdb=" N   ILE A 134 " --> pdb=" O   PRO A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 161
    Processing helix  chain 'A' and resid 188 through 192
    Processing helix  chain 'A' and resid 210 through 214
      removed outlier: 3.529A  pdb=" N   PHE A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 241
      removed outlier: 3.505A  pdb=" N   VAL A 241 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 265
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 332 through 336
    Processing helix  chain 'A' and resid 392 through 396
    Processing helix  chain 'A' and resid 402 through 406
      removed outlier: 3.818A  pdb=" N   SER A 406 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 474
    Processing helix  chain 'A' and resid 510 through 523
    Processing helix  chain 'A' and resid 529 through 533
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 6.423A  pdb=" N   THR A  61 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 9.751A  pdb=" N   ILE A  93 " --> pdb=" O   ARG A  66 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL A  68 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   ASP A  95 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ILE A  70 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU A  94 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU A 119 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL A 343 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 176
      removed outlier: 4.253A  pdb=" N   GLY A 176 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232
      removed outlier: 5.484A  pdb=" N   GLY A 232 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 8.265A  pdb=" N   ASP A 257 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   LEU A 254 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   THR A 279 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   GLY A 256 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328
      removed outlier: 3.790A  pdb=" N   GLY A 328 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ILE A 350 " --> pdb=" O   GLU A 373 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   THR A 375 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   GLU A 352 " --> pdb=" O   THR A 375 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR A 377 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU A 354 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 478 through 488
      removed outlier: 6.286A  pdb=" N   VAL A 481 " --> pdb=" O   PHE A 502 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   PHE A 502 " --> pdb=" O   VAL A 481 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   VAL A 483 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   LEU A 500 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   ASN A 485 " --> pdb=" O   ASP A 498 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASP A 498 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)

    101 hydrogen bonds defined for protein.
    195 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: 0.66

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1324
        1.34 -     1.46: 1010
        1.46 -     1.58: 1986
        1.58 -     1.70: 1
        1.70 -     1.82: 21
  Bond restraints: 4342
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.484 -0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.473 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.70e+00
  bond pdb=" CA  ASP A 359 "
       pdb=" CB  ASP A 359 "
    ideal  model  delta    sigma   weight residual
    1.539  1.640 -0.100 4.88e-02 4.20e+02 4.22e+00
  bond pdb=" C1  BMA E   4 "
       pdb=" C2  BMA E   4 "
    ideal  model  delta    sigma   weight residual
    1.519  1.552 -0.033 2.00e-02 2.50e+03 2.79e+00
  ... (remaining 4337 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 5722
        1.74 -     3.47: 166
        3.47 -     5.21: 20
        5.21 -     6.95: 8
        6.95 -     8.68: 2
  Bond angle restraints: 5918
  Sorted by residual:
  angle pdb=" C   ASN A 411 "
        pdb=" CA  ASN A 411 "
        pdb=" CB  ASN A 411 "
      ideal   model   delta    sigma   weight residual
     110.51  102.10    8.41 1.89e+00 2.80e-01 1.98e+01
  angle pdb=" N   ASN A 411 "
        pdb=" CA  ASN A 411 "
        pdb=" CB  ASN A 411 "
      ideal   model   delta    sigma   weight residual
     110.42  116.81   -6.39 1.52e+00 4.33e-01 1.77e+01
  angle pdb=" CA  ASN A 411 "
        pdb=" CB  ASN A 411 "
        pdb=" CG  ASN A 411 "
      ideal   model   delta    sigma   weight residual
     112.60  115.76   -3.16 1.00e+00 1.00e+00 9.98e+00
  angle pdb=" C   CYS A 421 "
        pdb=" N   SER A 422 "
        pdb=" CA  SER A 422 "
      ideal   model   delta    sigma   weight residual
     120.68  125.45   -4.77 1.52e+00 4.33e-01 9.85e+00
  angle pdb=" C3  NAG F   1 "
        pdb=" C4  NAG F   1 "
        pdb=" O4  NAG F   1 "
      ideal   model   delta    sigma   weight residual
     107.29  115.97   -8.68 3.00e+00 1.11e-01 8.38e+00
  ... (remaining 5913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.42: 2611
       23.42 -    46.85: 148
       46.85 -    70.27: 25
       70.27 -    93.69: 14
       93.69 -   117.12: 11
  Dihedral angle restraints: 2809
    sinusoidal: 1306
      harmonic: 1503
  Sorted by residual:
  dihedral pdb=" CB  CYS A  53 "
           pdb=" SG  CYS A  53 "
           pdb=" SG  CYS A  62 "
           pdb=" CB  CYS A  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.88  -76.88     1      1.00e+01 1.00e-02 7.42e+01
  dihedral pdb=" CA  ASN A 411 "
           pdb=" C   ASN A 411 "
           pdb=" N   THR A 412 "
           pdb=" CA  THR A 412 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.05   42.95     0      5.00e+00 4.00e-02 7.38e+01
  dihedral pdb=" C1  NAG D   1 "
           pdb=" C5  NAG D   1 "
           pdb=" O5  NAG D   1 "
           pdb=" C4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   53.01 -117.12     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 2806 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 649
       0.085 -    0.170: 62
       0.170 -    0.254: 4
       0.254 -    0.339: 3
       0.339 -    0.424: 1
  Chirality restraints: 719
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 523 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.82    0.42 2.00e-01 2.50e+01 4.49e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 298 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" C5  BMA E   4 "
            pdb=" C4  BMA E   4 "
            pdb=" C6  BMA E   4 "
            pdb=" O5  BMA E   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 716 not shown)

  Planarity restraints: 755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 411 "    0.035 2.00e-02 2.50e+03   3.37e-02 1.42e+01
        pdb=" CG  ASN A 411 "   -0.059 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 411 "    0.013 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 411 "   -0.015 2.00e-02 2.50e+03
        pdb=" C1  NAG F   1 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 523 "   -0.029 2.00e-02 2.50e+03   2.74e-02 9.36e+00
        pdb=" CG  ASN A 523 "    0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 523 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 523 "    0.034 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 411 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" CG  ASN A 411 "   -0.051 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 411 "    0.019 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 411 "    0.017 2.00e-02 2.50e+03
  ... (remaining 752 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 116
        2.69 -     3.24: 4238
        3.24 -     3.80: 6489
        3.80 -     4.35: 9063
        4.35 -     4.90: 14672
  Nonbonded interactions: 34578
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 108 "
            pdb=" OG  SER A 133 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" ND1 HIS A 222 "
            pdb="CU    CU A1004 "
     model   vdw
     2.164 2.320
  nonbonded pdb=" NE2 HIS A 199 "
            pdb="CU    CU A1004 "
     model   vdw
     2.170 2.320
  nonbonded pdb=" OD2 ASP A  95 "
            pdb=" OG  SER A 522 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OE2 GLU A 429 "
            pdb=" NH1 ARG A 484 "
     model   vdw
     2.206 3.120
  ... (remaining 34573 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'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.140
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.670
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
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   0.100   4361  Z= 0.209
  Angle     :  0.819  16.316   5971  Z= 0.364
  Chirality :  0.055   0.424    719
  Planarity :  0.005   0.039    747
  Dihedral  : 17.289 117.117   1829
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.38), residues: 519
  helix: -1.43 (0.51), residues: 105
  sheet: -2.93 (0.48), residues: 104
  loop : -0.55 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.010   0.001   TYR A 261 
 PHE   0.010   0.001   PHE A 440 
 TRP   0.017   0.001   TRP A 166 
 HIS   0.008   0.002   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 4342)
  covalent geometry    : angle       0.70088 ( 5918)
  SS BOND              : bond        0.00103 (    4)
  SS BOND              : angle       1.05665 (    8)
  hydrogen bonds       : bond        0.18683 (  101)
  hydrogen bonds       : angle       6.42960 (  195)
  link_BETA1-4         : bond        0.01292 (    6)
  link_BETA1-4         : angle       5.79018 (   18)
  link_BETA1-6         : bond        0.00455 (    1)
  link_BETA1-6         : angle       1.53836 (    3)
  link_NAG-ASN         : bond        0.00703 (    8)
  link_NAG-ASN         : angle       4.44503 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  194 GLN cc_start: 0.7562 (mm110) cc_final: 0.7202 (mm-40)
REVERT: A  234 ILE cc_start: 0.6904 (mt) cc_final: 0.6688 (mt)
REVERT: A  349 SER cc_start: 0.7398 (m) cc_final: 0.6979 (t)
REVERT: A  438 TYR cc_start: 0.6924 (m-10) cc_final: 0.6632 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0731
  time to fit residues: 6.1631
Evaluate side-chains
  45 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0470
   chunk 50 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   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 173 GLN
A 386 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.177754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.146675 restraints weight = 4510.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.79
r_work: 0.3450 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4361  Z= 0.136
  Angle     :  0.770  12.539   5971  Z= 0.335
  Chirality :  0.050   0.366    719
  Planarity :  0.005   0.047    747
  Dihedral  : 12.763  82.409    859
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  5.78 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.38), residues: 519
  helix: -1.54 (0.50), residues: 107
  sheet: -3.12 (0.44), residues: 109
  loop : -0.67 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 484 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.018   0.001   PHE A 414 
 TRP   0.013   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4342)
  covalent geometry    : angle       0.68227 ( 5918)
  SS BOND              : bond        0.00153 (    4)
  SS BOND              : angle       1.38192 (    8)
  hydrogen bonds       : bond        0.04186 (  101)
  hydrogen bonds       : angle       5.69285 (  195)
  link_BETA1-4         : bond        0.00995 (    6)
  link_BETA1-4         : angle       4.94522 (   18)
  link_BETA1-6         : bond        0.01142 (    1)
  link_BETA1-6         : angle       3.38374 (    3)
  link_NAG-ASN         : bond        0.00509 (    8)
  link_NAG-ASN         : angle       3.50844 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  194 GLN cc_start: 0.7686 (mm110) cc_final: 0.7050 (mm-40)
REVERT: A  321 MET cc_start: 0.8206 (mpp) cc_final: 0.7802 (mtt)
REVERT: A  349 SER cc_start: 0.7287 (m) cc_final: 0.6793 (t)
REVERT: A  469 ASP cc_start: 0.8002 (m-30) cc_final: 0.7771 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 45
  average time/residue: 0.0495
  time to fit residues: 3.2530
Evaluate side-chains
  41 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    0.2980
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 23 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.171488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.139822 restraints weight = 4562.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.82
r_work: 0.3466 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4361  Z= 0.127
  Angle     :  0.724  11.463   5971  Z= 0.314
  Chirality :  0.048   0.352    719
  Planarity :  0.004   0.043    747
  Dihedral  :  9.235  48.220    859
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.71 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.38), residues: 519
  helix: -1.49 (0.51), residues: 107
  sheet: -3.25 (0.44), residues: 102
  loop : -0.58 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.023   0.001   PHE A 414 
 TRP   0.013   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4342)
  covalent geometry    : angle       0.63780 ( 5918)
  SS BOND              : bond        0.00071 (    4)
  SS BOND              : angle       1.22008 (    8)
  hydrogen bonds       : bond        0.03803 (  101)
  hydrogen bonds       : angle       5.62486 (  195)
  link_BETA1-4         : bond        0.01058 (    6)
  link_BETA1-4         : angle       4.55185 (   18)
  link_BETA1-6         : bond        0.00407 (    1)
  link_BETA1-6         : angle       3.36802 (    3)
  link_NAG-ASN         : bond        0.00503 (    8)
  link_NAG-ASN         : angle       3.56023 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.7678 (mmm-85) cc_final: 0.7456 (mmm160)
REVERT: A  194 GLN cc_start: 0.7710 (mm110) cc_final: 0.7074 (mm-40)
REVERT: A  349 SER cc_start: 0.7219 (m) cc_final: 0.6727 (t)
REVERT: A  469 ASP cc_start: 0.7923 (m-30) cc_final: 0.7670 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0499
  time to fit residues: 3.3718
Evaluate side-chains
  39 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 38 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0170
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.177249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.146132 restraints weight = 4474.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.80
r_work: 0.3483 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4361  Z= 0.118
  Angle     :  0.695  10.716   5971  Z= 0.302
  Chirality :  0.047   0.348    719
  Planarity :  0.004   0.045    747
  Dihedral  :  7.876  40.361    859
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.99 %
    Favored  : 90.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.39), residues: 519
  helix: -1.37 (0.53), residues: 107
  sheet: -3.32 (0.44), residues: 102
  loop : -0.56 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 447 
 TYR   0.010   0.001   TYR A 445 
 PHE   0.016   0.001   PHE A 414 
 TRP   0.012   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4342)
  covalent geometry    : angle       0.60979 ( 5918)
  SS BOND              : bond        0.00076 (    4)
  SS BOND              : angle       1.08721 (    8)
  hydrogen bonds       : bond        0.03560 (  101)
  hydrogen bonds       : angle       5.48247 (  195)
  link_BETA1-4         : bond        0.01006 (    6)
  link_BETA1-4         : angle       4.26294 (   18)
  link_BETA1-6         : bond        0.00323 (    1)
  link_BETA1-6         : angle       3.19186 (    3)
  link_NAG-ASN         : bond        0.00533 (    8)
  link_NAG-ASN         : angle       3.65211 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7444 (mmm-85)
REVERT: A  194 GLN cc_start: 0.7673 (mm110) cc_final: 0.7042 (mm-40)
REVERT: A  349 SER cc_start: 0.7173 (m) cc_final: 0.6685 (t)
  outliers start: 3
  outliers final: 3
  residues processed: 44
  average time/residue: 0.0437
  time to fit residues: 2.7987
Evaluate side-chains
  41 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  359 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.164065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.133640 restraints weight = 4679.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.70
r_work: 0.3451 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4361  Z= 0.134
  Angle     :  0.690   9.462   5971  Z= 0.303
  Chirality :  0.048   0.359    719
  Planarity :  0.004   0.044    747
  Dihedral  :  7.298  40.940    859
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 10.28 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.39), residues: 519
  helix: -1.40 (0.53), residues: 107
  sheet: -3.36 (0.45), residues: 102
  loop : -0.55 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.017   0.001   PHE A 414 
 TRP   0.011   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4342)
  covalent geometry    : angle       0.60998 ( 5918)
  SS BOND              : bond        0.00083 (    4)
  SS BOND              : angle       1.13032 (    8)
  hydrogen bonds       : bond        0.03655 (  101)
  hydrogen bonds       : angle       5.51867 (  195)
  link_BETA1-4         : bond        0.00962 (    6)
  link_BETA1-4         : angle       4.07067 (   18)
  link_BETA1-6         : bond        0.00329 (    1)
  link_BETA1-6         : angle       2.78291 (    3)
  link_NAG-ASN         : bond        0.00432 (    8)
  link_NAG-ASN         : angle       3.57542 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7491 (mmm-85)
REVERT: A  194 GLN cc_start: 0.7781 (mm110) cc_final: 0.7175 (mm-40)
REVERT: A  263 ASN cc_start: 0.7630 (t0) cc_final: 0.7305 (t0)
REVERT: A  349 SER cc_start: 0.7216 (m) cc_final: 0.6732 (t)
  outliers start: 3
  outliers final: 3
  residues processed: 46
  average time/residue: 0.0363
  time to fit residues: 2.5083
Evaluate side-chains
  43 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  359 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.158468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.130390 restraints weight = 4814.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.48
r_work: 0.3421 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4361  Z= 0.139
  Angle     :  0.680   8.794   5971  Z= 0.303
  Chirality :  0.048   0.366    719
  Planarity :  0.004   0.044    747
  Dihedral  :  6.880  41.272    859
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.35 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.39), residues: 519
  helix: -1.58 (0.50), residues: 113
  sheet: -3.38 (0.44), residues: 102
  loop : -0.60 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.018   0.001   PHE A 414 
 TRP   0.011   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4342)
  covalent geometry    : angle       0.60822 ( 5918)
  SS BOND              : bond        0.00086 (    4)
  SS BOND              : angle       1.16562 (    8)
  hydrogen bonds       : bond        0.03761 (  101)
  hydrogen bonds       : angle       5.48834 (  195)
  link_BETA1-4         : bond        0.00913 (    6)
  link_BETA1-4         : angle       4.00878 (   18)
  link_BETA1-6         : bond        0.00344 (    1)
  link_BETA1-6         : angle       2.43840 (    3)
  link_NAG-ASN         : bond        0.00450 (    8)
  link_NAG-ASN         : angle       3.27338 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7656 (mmm-85)
REVERT: A  194 GLN cc_start: 0.7843 (mm110) cc_final: 0.7267 (mm-40)
REVERT: A  263 ASN cc_start: 0.7770 (t0) cc_final: 0.7414 (t0)
REVERT: A  349 SER cc_start: 0.7402 (m) cc_final: 0.6936 (t)
  outliers start: 5
  outliers final: 3
  residues processed: 46
  average time/residue: 0.0363
  time to fit residues: 2.4882
Evaluate side-chains
  43 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  359 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   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 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.157683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128917 restraints weight = 4795.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.53
r_work: 0.3397 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4361  Z= 0.156
  Angle     :  0.703   8.473   5971  Z= 0.316
  Chirality :  0.049   0.381    719
  Planarity :  0.004   0.044    747
  Dihedral  :  6.902  42.016    859
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.35 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.39), residues: 519
  helix: -1.61 (0.50), residues: 112
  sheet: -3.40 (0.44), residues: 102
  loop : -0.63 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 447 
 TYR   0.008   0.001   TYR A 445 
 PHE   0.017   0.001   PHE A 414 
 TRP   0.010   0.001   TRP A 166 
 HIS   0.002   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 4342)
  covalent geometry    : angle       0.63478 ( 5918)
  SS BOND              : bond        0.00084 (    4)
  SS BOND              : angle       1.27560 (    8)
  hydrogen bonds       : bond        0.03925 (  101)
  hydrogen bonds       : angle       5.63482 (  195)
  link_BETA1-4         : bond        0.00916 (    6)
  link_BETA1-4         : angle       3.94255 (   18)
  link_BETA1-6         : bond        0.00332 (    1)
  link_BETA1-6         : angle       2.17784 (    3)
  link_NAG-ASN         : bond        0.00395 (    8)
  link_NAG-ASN         : angle       3.26036 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7621 (mmm-85)
REVERT: A  194 GLN cc_start: 0.7881 (mm110) cc_final: 0.7328 (mm-40)
REVERT: A  263 ASN cc_start: 0.7774 (t0) cc_final: 0.7385 (t0)
REVERT: A  349 SER cc_start: 0.7428 (m) cc_final: 0.6943 (t)
  outliers start: 4
  outliers final: 4
  residues processed: 43
  average time/residue: 0.0298
  time to fit residues: 1.8975
Evaluate side-chains
  44 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  410 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0670
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0060
   chunk 10 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.4534

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.161270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.133703 restraints weight = 4636.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.35
r_work: 0.3469 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4361  Z= 0.118
  Angle     :  0.663   8.443   5971  Z= 0.298
  Chirality :  0.046   0.341    719
  Planarity :  0.004   0.046    747
  Dihedral  :  6.577  41.124    859
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.56 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.39), residues: 519
  helix: -1.42 (0.52), residues: 106
  sheet: -3.36 (0.45), residues: 102
  loop : -0.49 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.020   0.001   PHE A 414 
 TRP   0.012   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4342)
  covalent geometry    : angle       0.59581 ( 5918)
  SS BOND              : bond        0.00080 (    4)
  SS BOND              : angle       1.01927 (    8)
  hydrogen bonds       : bond        0.03677 (  101)
  hydrogen bonds       : angle       5.50699 (  195)
  link_BETA1-4         : bond        0.00954 (    6)
  link_BETA1-4         : angle       3.77696 (   18)
  link_BETA1-6         : bond        0.00375 (    1)
  link_BETA1-6         : angle       2.01927 (    3)
  link_NAG-ASN         : bond        0.00443 (    8)
  link_NAG-ASN         : angle       3.19094 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7776 (mmm-85)
REVERT: A  194 GLN cc_start: 0.7988 (mm110) cc_final: 0.7461 (mm-40)
REVERT: A  263 ASN cc_start: 0.7879 (t0) cc_final: 0.7444 (t0)
REVERT: A  349 SER cc_start: 0.7503 (m) cc_final: 0.7043 (t)
REVERT: A  389 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7842 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0294
  time to fit residues: 2.0413
Evaluate side-chains
  47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  410 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 36 optimal weight:    0.0770
   chunk 45 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0170
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.183734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.154154 restraints weight = 4447.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.52
r_work: 0.3474 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4361  Z= 0.119
  Angle     :  0.652   8.324   5971  Z= 0.293
  Chirality :  0.046   0.333    719
  Planarity :  0.004   0.046    747
  Dihedral  :  6.382  40.712    859
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.78 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.39), residues: 519
  helix: -1.41 (0.52), residues: 106
  sheet: -3.35 (0.45), residues: 102
  loop : -0.46 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.019   0.001   PHE A 414 
 TRP   0.011   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4342)
  covalent geometry    : angle       0.58641 ( 5918)
  SS BOND              : bond        0.00100 (    4)
  SS BOND              : angle       1.01929 (    8)
  hydrogen bonds       : bond        0.03626 (  101)
  hydrogen bonds       : angle       5.47771 (  195)
  link_BETA1-4         : bond        0.00934 (    6)
  link_BETA1-4         : angle       3.71369 (   18)
  link_BETA1-6         : bond        0.00354 (    1)
  link_BETA1-6         : angle       1.86914 (    3)
  link_NAG-ASN         : bond        0.00411 (    8)
  link_NAG-ASN         : angle       3.15781 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7758 (mmm-85)
REVERT: A  194 GLN cc_start: 0.7990 (mm110) cc_final: 0.7465 (mm-40)
REVERT: A  263 ASN cc_start: 0.7881 (t0) cc_final: 0.7499 (t0)
REVERT: A  349 SER cc_start: 0.7507 (m) cc_final: 0.7042 (t)
REVERT: A  389 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7833 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.0290
  time to fit residues: 1.8393
Evaluate side-chains
  44 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  410 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 41 optimal weight:    0.0050
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.182382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152716 restraints weight = 4394.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.53
r_work: 0.3472 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4361  Z= 0.136
  Angle     :  0.669   8.303   5971  Z= 0.301
  Chirality :  0.047   0.348    719
  Planarity :  0.004   0.046    747
  Dihedral  :  6.404  41.217    859
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.56 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.39), residues: 519
  helix: -1.62 (0.49), residues: 112
  sheet: -3.35 (0.45), residues: 102
  loop : -0.57 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.019   0.001   PHE A 414 
 TRP   0.009   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4342)
  covalent geometry    : angle       0.60482 ( 5918)
  SS BOND              : bond        0.00085 (    4)
  SS BOND              : angle       1.08051 (    8)
  hydrogen bonds       : bond        0.03782 (  101)
  hydrogen bonds       : angle       5.48548 (  195)
  link_BETA1-4         : bond        0.00928 (    6)
  link_BETA1-4         : angle       3.72824 (   18)
  link_BETA1-6         : bond        0.00384 (    1)
  link_BETA1-6         : angle       1.78444 (    3)
  link_NAG-ASN         : bond        0.00361 (    8)
  link_NAG-ASN         : angle       3.16497 (   24)

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

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

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1038 Ramachandran restraints generated.
    519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7723 (mmm-85)
REVERT: A  194 GLN cc_start: 0.7999 (mm110) cc_final: 0.7461 (mm-40)
REVERT: A  349 SER cc_start: 0.7526 (m) cc_final: 0.7050 (t)
REVERT: A  389 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7800 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 44
  average time/residue: 0.0271
  time to fit residues: 1.7593
Evaluate side-chains
  44 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  410 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 42 optimal weight:    0.0470
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0060
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4694

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN
A 510 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.167440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136060 restraints weight = 4612.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.81
r_work: 0.3457 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4361  Z= 0.120
  Angle     :  0.648   8.378   5971  Z= 0.292
  Chirality :  0.046   0.327    719
  Planarity :  0.004   0.046    747
  Dihedral  :  6.260  40.691    859
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.35 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.39), residues: 519
  helix: -1.58 (0.50), residues: 112
  sheet: -3.38 (0.45), residues: 103
  loop : -0.50 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.019   0.001   PHE A 414 
 TRP   0.011   0.001   TRP A 166 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4342)
  covalent geometry    : angle       0.58354 ( 5918)
  SS BOND              : bond        0.00089 (    4)
  SS BOND              : angle       0.99583 (    8)
  hydrogen bonds       : bond        0.03630 (  101)
  hydrogen bonds       : angle       5.45265 (  195)
  link_BETA1-4         : bond        0.00945 (    6)
  link_BETA1-4         : angle       3.64755 (   18)
  link_BETA1-6         : bond        0.00419 (    1)
  link_BETA1-6         : angle       1.73338 (    3)
  link_NAG-ASN         : bond        0.00386 (    8)
  link_NAG-ASN         : angle       3.11425 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 955.18 seconds
wall clock time: 17 minutes 11.53 seconds (1031.53 seconds total)