Starting phenix.real_space_refine
on Fri Jan 17 11:18:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xv1_38689/01_2025/8xv1_38689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xv1_38689/01_2025/8xv1_38689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xv1_38689/01_2025/8xv1_38689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xv1_38689/01_2025/8xv1_38689.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xv1_38689/01_2025/8xv1_38689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xv1_38689/01_2025/8xv1_38689.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4890 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4254      2.51       5
     N    1084      2.21       5
     O    1277      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-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6652
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1592
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 13, 'TRANS': 184}
    Chain: "D"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "L"
      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: "M"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "N"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      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: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.13, per 1000 atoms: 0.77
  Number of scatterers: 6652
  At special positions: 0
  Unit cell: (102.51, 96.48, 111.555, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1277      8.00
     N    1084      7.00
     C    4254      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 487 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " 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
    ALPHA1-3
      " BMA N   3 " - " MAN N   4 "
    ALPHA1-6
      " BMA N   3 " - " MAN N   5 "
    BETA1-4
      " NAG L   1 " - " NAG L   2 "
      " NAG M   1 " - " NAG M   2 "
      " NAG M   2 " - " BMA M   3 "
      " NAG N   1 " - " NAG N   2 "
      " NAG N   2 " - " BMA N   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG A1302 " - " ASN A 354 "
      " NAG D 701 " - " ASN D 322 "
      " NAG D 702 " - " ASN D 432 "
      " NAG D 703 " - " ASN D  53 "
      " NAG L   1 " - " ASN D 546 "
      " NAG M   1 " - " ASN D  90 "
      " NAG N   1 " - " ASN D 103 "
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 907.9 milliseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 6 sheets defined
      53.4% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.555A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.664A  pdb=" N   GLN D  24 " --> pdb=" O   THR D  20 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 81
    Processing helix  chain 'D' and resid 92 through 104
      removed outlier: 3.697A  pdb=" N   GLN D  96 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY D 104 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 130
    Processing helix  chain 'D' and resid 144 through 155
      removed outlier: 4.276A  pdb=" N   ASN D 149 " --> pdb=" O   GLU D 145 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLU D 150 " --> pdb=" O   PRO D 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 195
      removed outlier: 3.996A  pdb=" N   LYS D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   GLN D 175 " --> pdb=" O   GLU D 171 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
      removed outlier: 4.035A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU D 186 " --> pdb=" O   GLU D 182 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ASN D 194 " --> pdb=" O   MET D 190 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   HIS D 195 " --> pdb=" O   ALA D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 220 through 252
      removed outlier: 4.020A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 279
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 317
    Processing helix  chain 'D' and resid 324 through 331
      removed outlier: 3.701A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.934A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 393
      removed outlier: 3.831A  pdb=" N   ARG D 393 " --> pdb=" O   PHE D 390 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 412
      removed outlier: 3.998A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 422
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.744A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 466
    Processing helix  chain 'D' and resid 472 through 485
    Processing helix  chain 'D' and resid 499 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 3.787A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 559
      removed outlier: 3.686A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 588
      removed outlier: 3.558A  pdb=" N   PHE D 588 " --> pdb=" O   LEU D 584 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.732A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR A 396 " --> pdb=" O   SER A 513 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 376 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.696A  pdb=" N   TYR A 488 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133
    Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.059A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350

    302 hydrogen bonds defined for protein.
    867 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: 1.77

  Time building geometry restraints manager: 2.09 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: 2090
        1.34 -     1.46: 1700
        1.46 -     1.58: 2993
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6841
  Sorted by residual:
  bond pdb=" C1  NAG L   1 "
       pdb=" O5  NAG L   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.45e+00
  bond pdb=" C1  NAG D 702 "
       pdb=" O5  NAG D 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C1  NAG L   2 "
       pdb=" O5  NAG L   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.12e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.04e+00
  bond pdb=" C1  NAG M   2 "
       pdb=" O5  NAG M   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.00e+00
  ... (remaining 6836 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 8945
        1.26 -     2.52: 257
        2.52 -     3.78: 63
        3.78 -     5.04: 22
        5.04 -     6.30: 10
  Bond angle restraints: 9297
  Sorted by residual:
  angle pdb=" CA  GLY A 416 "
        pdb=" C   GLY A 416 "
        pdb=" N   ASN A 417 "
      ideal   model   delta    sigma   weight residual
     114.23  117.04   -2.81 8.80e-01 1.29e+00 1.02e+01
  angle pdb=" CA  GLY A 416 "
        pdb=" C   GLY A 416 "
        pdb=" O   GLY A 416 "
      ideal   model   delta    sigma   weight residual
     122.33  120.21    2.12 8.10e-01 1.52e+00 6.86e+00
  angle pdb=" NE  ARG A 466 "
        pdb=" CZ  ARG A 466 "
        pdb=" NH2 ARG A 466 "
      ideal   model   delta    sigma   weight residual
     119.20  121.50   -2.30 9.00e-01 1.23e+00 6.50e+00
  angle pdb=" N   LYS D 234 "
        pdb=" CA  LYS D 234 "
        pdb=" C   LYS D 234 "
      ideal   model   delta    sigma   weight residual
     113.77  116.99   -3.22 1.32e+00 5.74e-01 5.95e+00
  angle pdb=" N   LEU A 517 "
        pdb=" CA  LEU A 517 "
        pdb=" C   LEU A 517 "
      ideal   model   delta    sigma   weight residual
     108.45  111.45   -3.00 1.26e+00 6.30e-01 5.68e+00
  ... (remaining 9292 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.82: 3886
       21.82 -    43.63: 281
       43.63 -    65.45: 34
       65.45 -    87.27: 19
       87.27 -   109.09: 8
  Dihedral angle restraints: 4228
    sinusoidal: 1895
      harmonic: 2333
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 487 "
           pdb=" CB  CYS A 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.83  -72.83     1      1.00e+01 1.00e-02 6.77e+01
  dihedral pdb=" CB  CYS D 530 "
           pdb=" SG  CYS D 530 "
           pdb=" SG  CYS D 542 "
           pdb=" CB  CYS D 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.68   47.68     1      1.00e+01 1.00e-02 3.14e+01
  dihedral pdb=" SG  CYS A 391 "
           pdb=" CB  CYS A 524 "
           pdb=" SG  CYS A 524 "
           pdb=" CA  CYS A 524 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   10.69   68.31     1      2.00e+01 2.50e-03 1.51e+01
  ... (remaining 4225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1000
       0.118 -    0.236: 8
       0.236 -    0.354: 4
       0.354 -    0.472: 0
       0.472 -    0.590: 1
  Chirality restraints: 1013
  Sorted by residual:
  chirality pdb=" C1  NAG N   1 "
            pdb=" ND2 ASN D 103 "
            pdb=" C2  NAG N   1 "
            pdb=" O5  NAG N   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.81   -0.59 2.00e-01 2.50e+01 8.71e+00
  chirality pdb=" C1  NAG D 701 "
            pdb=" ND2 ASN D 322 "
            pdb=" C2  NAG D 701 "
            pdb=" O5  NAG D 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" C5  BMA N   3 "
            pdb=" C4  BMA N   3 "
            pdb=" C6  BMA N   3 "
            pdb=" O5  BMA N   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.29 2.00e-01 2.50e+01 2.06e+00
  ... (remaining 1010 not shown)

  Planarity restraints: 1188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 519 "   -0.026 5.00e-02 4.00e+02   3.99e-02 2.54e+00
        pdb=" N   PRO A 520 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 520 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 520 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 103 "    0.014 2.00e-02 2.50e+03   1.34e-02 2.24e+00
        pdb=" CG  ASN D 103 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 103 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 103 "   -0.019 2.00e-02 2.50e+03
        pdb=" C1  NAG N   1 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 336 "   -0.018 5.00e-02 4.00e+02   2.69e-02 1.15e+00
        pdb=" N   PRO A 337 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1185 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1305
        2.78 -     3.31: 6166
        3.31 -     3.84: 10592
        3.84 -     4.37: 11790
        4.37 -     4.90: 21126
  Nonbonded interactions: 50979
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 217 "
            pdb=" OD2 ASP D 225 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OG1 THR D  55 "
            pdb=" ND2 ASN D  58 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" O   ASP D 499 "
            pdb=" OG  SER D 502 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ILE D 151 "
            pdb=" OG  SER D 155 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG1 THR A 499 "
            pdb=" OH  TYR D  41 "
     model   vdw
     2.281 3.040
  ... (remaining 50974 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 individual isotropic
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:             3.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  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:                     18.940
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6331
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      :  0.003   0.037   6841  Z= 0.196
  Angle     :  0.571   6.297   9297  Z= 0.279
  Chirality :  0.048   0.590   1013
  Planarity :  0.003   0.040   1180
  Dihedral  : 15.767 109.087   2709
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.32), residues: 790
  helix:  2.27 (0.27), residues: 389
  sheet:  0.99 (0.87), residues: 44
  loop : -1.11 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 566 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.011   0.001   PHE D 369 
 TYR   0.007   0.001   TYR D 183 
 ARG   0.001   0.000   ARG D 169 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.6951 (tppp) cc_final: 0.6666 (mmmt)
REVERT: A  380 TYR cc_start: 0.8020 (m-80) cc_final: 0.7601 (m-80)
REVERT: A  383 SER cc_start: 0.7511 (m) cc_final: 0.7191 (p)
REVERT: A  444 LYS cc_start: 0.7176 (mtmt) cc_final: 0.6940 (mtpt)
REVERT: A  467 ASP cc_start: 0.7779 (t0) cc_final: 0.7530 (t0)
REVERT: D  197 GLU cc_start: 0.7506 (mp0) cc_final: 0.6728 (mp0)
REVERT: D  329 GLU cc_start: 0.6533 (tp30) cc_final: 0.6294 (mt-10)
REVERT: D  341 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7203 (mtpp)
REVERT: D  435 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5844 (pt0)
REVERT: D  474 MET cc_start: 0.6375 (mmp) cc_final: 0.5727 (mmp)
REVERT: D  596 LYS cc_start: 0.6949 (mtmt) cc_final: 0.6622 (mtmm)
REVERT: D  597 ASP cc_start: 0.7716 (t0) cc_final: 0.7453 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2103
  time to fit residues: 44.3217
Evaluate side-chains
  100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  33 ASN
D  58 ASN
** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.151282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122211 restraints weight = 8653.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.54
r_work: 0.3289 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6841  Z= 0.178
  Angle     :  0.557  11.644   9297  Z= 0.284
  Chirality :  0.045   0.341   1013
  Planarity :  0.004   0.036   1180
  Dihedral  : 10.661  79.942   1168
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.94 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  8.31 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.32), residues: 790
  helix:  2.24 (0.28), residues: 394
  sheet:  0.66 (0.81), residues: 44
  loop : -1.22 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D 374 
 PHE   0.013   0.001   PHE A 392 
 TYR   0.014   0.001   TYR A 494 
 ARG   0.003   0.000   ARG D 177 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: D  197 GLU cc_start: 0.7857 (mp0) cc_final: 0.7411 (mp0)
REVERT: D  201 ASP cc_start: 0.8598 (t0) cc_final: 0.8392 (t0)
REVERT: D  287 GLN cc_start: 0.7867 (mp10) cc_final: 0.7660 (mp10)
REVERT: D  341 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7861 (mtpp)
REVERT: D  416 LYS cc_start: 0.7269 (ttmm) cc_final: 0.7067 (ttpp)
REVERT: D  435 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7007 (pt0)
REVERT: D  597 ASP cc_start: 0.8452 (t0) cc_final: 0.8247 (t70)
  outliers start: 11
  outliers final: 7
  residues processed: 110
  average time/residue: 0.1883
  time to fit residues: 27.7360
Evaluate side-chains
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.148858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.120336 restraints weight = 8649.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.46
r_work: 0.3293 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6841  Z= 0.176
  Angle     :  0.515   7.270   9297  Z= 0.263
  Chirality :  0.045   0.318   1013
  Planarity :  0.004   0.036   1180
  Dihedral  :  8.609  70.222   1168
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.06 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.32 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.31), residues: 790
  helix:  2.19 (0.28), residues: 395
  sheet:  0.59 (0.79), residues: 44
  loop : -1.31 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D 374 
 PHE   0.012   0.001   PHE D 369 
 TYR   0.014   0.001   TYR D 183 
 ARG   0.003   0.000   ARG A 357 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7881 (ttm-80)
REVERT: A  420 ASP cc_start: 0.8772 (p0) cc_final: 0.8402 (p0)
REVERT: D   87 GLU cc_start: 0.7537 (mp0) cc_final: 0.7239 (pm20)
REVERT: D  118 THR cc_start: 0.7832 (m) cc_final: 0.7512 (p)
REVERT: D  201 ASP cc_start: 0.8804 (t0) cc_final: 0.8555 (t0)
REVERT: D  341 LYS cc_start: 0.8413 (mtmt) cc_final: 0.7964 (mtpp)
REVERT: D  383 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8021 (mtp)
REVERT: D  597 ASP cc_start: 0.8573 (t0) cc_final: 0.8360 (t70)
  outliers start: 15
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1928
  time to fit residues: 25.4422
Evaluate side-chains
  97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0970
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.147408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.119512 restraints weight = 8737.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.41
r_work: 0.3283 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6841  Z= 0.173
  Angle     :  0.506   8.325   9297  Z= 0.259
  Chirality :  0.044   0.313   1013
  Planarity :  0.004   0.038   1180
  Dihedral  :  7.642  63.909   1168
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.06 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.32 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.31), residues: 790
  helix:  2.06 (0.28), residues: 400
  sheet:  0.55 (0.77), residues: 44
  loop : -1.19 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.005   0.001   HIS D 374 
 PHE   0.012   0.001   PHE D 369 
 TYR   0.015   0.001   TYR D 183 
 ARG   0.002   0.000   ARG D 177 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8734 (p0) cc_final: 0.8317 (p0)
REVERT: D   87 GLU cc_start: 0.7556 (mp0) cc_final: 0.7235 (pm20)
REVERT: D  215 TYR cc_start: 0.7856 (m-80) cc_final: 0.7612 (m-80)
REVERT: D  341 LYS cc_start: 0.8383 (mtmt) cc_final: 0.7902 (mtpp)
REVERT: D  383 MET cc_start: 0.8530 (mtp) cc_final: 0.8051 (mtp)
REVERT: D  597 ASP cc_start: 0.8568 (t0) cc_final: 0.8351 (t70)
  outliers start: 15
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1850
  time to fit residues: 24.6265
Evaluate side-chains
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 68 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.148982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.121011 restraints weight = 8749.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.42
r_work: 0.3270 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6841  Z= 0.182
  Angle     :  0.509   8.060   9297  Z= 0.262
  Chirality :  0.044   0.306   1013
  Planarity :  0.004   0.042   1180
  Dihedral  :  7.199  58.065   1168
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.44 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.18 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.31), residues: 790
  helix:  2.02 (0.28), residues: 401
  sheet:  0.75 (0.80), residues: 42
  loop : -1.23 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.005   0.001   HIS D 374 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.016   0.001   TYR D 183 
 ARG   0.008   0.000   ARG A 357 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8716 (p0) cc_final: 0.8317 (p0)
REVERT: A  481 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7094 (tptp)
REVERT: D  118 THR cc_start: 0.7914 (m) cc_final: 0.7601 (p)
REVERT: D  215 TYR cc_start: 0.7954 (m-80) cc_final: 0.7362 (m-10)
REVERT: D  341 LYS cc_start: 0.8406 (mtmt) cc_final: 0.7880 (mtpp)
REVERT: D  383 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8132 (mtp)
REVERT: D  597 ASP cc_start: 0.8564 (t0) cc_final: 0.8344 (t70)
  outliers start: 14
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1894
  time to fit residues: 24.5989
Evaluate side-chains
  98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.145253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.117349 restraints weight = 8747.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.41
r_work: 0.3219 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6841  Z= 0.261
  Angle     :  0.572   9.360   9297  Z= 0.295
  Chirality :  0.046   0.303   1013
  Planarity :  0.004   0.047   1180
  Dihedral  :  7.273  56.205   1168
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.32 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.04 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.31), residues: 790
  helix:  1.98 (0.28), residues: 392
  sheet:  0.68 (0.81), residues: 42
  loop : -1.47 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 436 
 HIS   0.008   0.002   HIS D 374 
 PHE   0.015   0.002   PHE D 369 
 TYR   0.021   0.002   TYR D 381 
 ARG   0.008   0.001   ARG A 357 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8767 (p0) cc_final: 0.8340 (p0)
REVERT: A  481 LYS cc_start: 0.7647 (ttmt) cc_final: 0.7099 (tptp)
REVERT: D  110 GLU cc_start: 0.6289 (pm20) cc_final: 0.6080 (tt0)
REVERT: D  224 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7271 (mt-10)
REVERT: D  255 TYR cc_start: 0.7845 (m-80) cc_final: 0.7544 (m-10)
REVERT: D  341 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7892 (mtpp)
REVERT: D  597 ASP cc_start: 0.8577 (t0) cc_final: 0.8360 (t70)
  outliers start: 14
  outliers final: 13
  residues processed: 97
  average time/residue: 0.1980
  time to fit residues: 25.3414
Evaluate side-chains
  98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0060
   chunk 45 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0980
   chunk 23 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.149801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.121240 restraints weight = 8703.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.43
r_work: 0.3310 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6841  Z= 0.149
  Angle     :  0.501   8.285   9297  Z= 0.253
  Chirality :  0.043   0.305   1013
  Planarity :  0.004   0.046   1180
  Dihedral  :  6.678  55.383   1168
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.94 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.47 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.31), residues: 790
  helix:  2.00 (0.28), residues: 400
  sheet:  0.75 (0.80), residues: 42
  loop : -1.29 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 566 
 HIS   0.003   0.001   HIS D 401 
 PHE   0.011   0.001   PHE D 369 
 TYR   0.014   0.001   TYR D 183 
 ARG   0.004   0.000   ARG A 357 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8684 (p0) cc_final: 0.8280 (p0)
REVERT: A  481 LYS cc_start: 0.7555 (ttmt) cc_final: 0.7019 (tptp)
REVERT: D  118 THR cc_start: 0.7860 (m) cc_final: 0.7501 (p)
REVERT: D  255 TYR cc_start: 0.7800 (m-80) cc_final: 0.7478 (m-10)
REVERT: D  341 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7874 (mtpp)
REVERT: D  383 MET cc_start: 0.8559 (mtp) cc_final: 0.8180 (mtp)
REVERT: D  597 ASP cc_start: 0.8573 (t0) cc_final: 0.8364 (t70)
  outliers start: 13
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1909
  time to fit residues: 25.2558
Evaluate side-chains
  100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0170
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0270
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.5076

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.149635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121197 restraints weight = 8766.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.42
r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6841  Z= 0.154
  Angle     :  0.493   7.669   9297  Z= 0.252
  Chirality :  0.043   0.304   1013
  Planarity :  0.004   0.047   1180
  Dihedral  :  6.329  55.464   1168
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.06 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.61 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.31), residues: 790
  helix:  2.02 (0.28), residues: 401
  sheet:  0.67 (0.79), residues: 42
  loop : -1.22 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D 374 
 PHE   0.012   0.001   PHE D 369 
 TYR   0.016   0.001   TYR D 183 
 ARG   0.001   0.000   ARG D 177 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8683 (p0) cc_final: 0.8374 (p0)
REVERT: A  481 LYS cc_start: 0.7583 (ttmt) cc_final: 0.7047 (tptp)
REVERT: D  118 THR cc_start: 0.8012 (m) cc_final: 0.7664 (p)
REVERT: D  255 TYR cc_start: 0.7812 (m-80) cc_final: 0.7534 (m-10)
REVERT: D  341 LYS cc_start: 0.8385 (mtmt) cc_final: 0.7884 (mtpp)
REVERT: D  383 MET cc_start: 0.8531 (mtp) cc_final: 0.8143 (mtp)
REVERT: D  536 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7610 (mt-10)
REVERT: D  597 ASP cc_start: 0.8540 (t0) cc_final: 0.8339 (t70)
  outliers start: 15
  outliers final: 13
  residues processed: 93
  average time/residue: 0.1862
  time to fit residues: 23.5297
Evaluate side-chains
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  507 SER
Chi-restraints excluded: chain D residue  536 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0570
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.120498 restraints weight = 8828.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.44
r_work: 0.3299 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6841  Z= 0.170
  Angle     :  0.501   7.898   9297  Z= 0.256
  Chirality :  0.043   0.294   1013
  Planarity :  0.004   0.047   1180
  Dihedral  :  6.143  58.771   1168
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.32 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.76 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.31), residues: 790
  helix:  2.00 (0.28), residues: 401
  sheet:  0.69 (0.80), residues: 42
  loop : -1.24 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D 374 
 PHE   0.012   0.001   PHE D 369 
 TYR   0.016   0.001   TYR D 183 
 ARG   0.002   0.000   ARG D 177 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8686 (p0) cc_final: 0.8383 (p0)
REVERT: A  481 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7025 (tptp)
REVERT: D  118 THR cc_start: 0.7925 (m) cc_final: 0.7595 (p)
REVERT: D  255 TYR cc_start: 0.7835 (m-80) cc_final: 0.7538 (m-10)
REVERT: D  341 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7911 (mtpp)
REVERT: D  383 MET cc_start: 0.8578 (mtp) cc_final: 0.8203 (mtp)
REVERT: D  597 ASP cc_start: 0.8528 (t0) cc_final: 0.8048 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1916
  time to fit residues: 24.4369
Evaluate side-chains
  97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.118185 restraints weight = 8912.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.43
r_work: 0.3267 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6841  Z= 0.224
  Angle     :  0.558   9.201   9297  Z= 0.284
  Chirality :  0.044   0.293   1013
  Planarity :  0.004   0.048   1180
  Dihedral  :  6.237  59.104   1168
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.94 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.90 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.31), residues: 790
  helix:  1.98 (0.28), residues: 400
  sheet:  0.68 (0.80), residues: 42
  loop : -1.33 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 477 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.013   0.002   PHE D 369 
 TYR   0.018   0.002   TYR D 183 
 ARG   0.003   0.000   ARG D 177 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8734 (p0) cc_final: 0.8347 (p0)
REVERT: A  441 LEU cc_start: 0.7838 (mp) cc_final: 0.7452 (mt)
REVERT: A  481 LYS cc_start: 0.7551 (ttmt) cc_final: 0.7039 (tptp)
REVERT: D  118 THR cc_start: 0.7928 (m) cc_final: 0.7596 (p)
REVERT: D  255 TYR cc_start: 0.7857 (m-80) cc_final: 0.7552 (m-10)
REVERT: D  341 LYS cc_start: 0.8410 (mtmt) cc_final: 0.7931 (mtpp)
REVERT: D  383 MET cc_start: 0.8673 (mtp) cc_final: 0.8266 (mtp)
REVERT: D  597 ASP cc_start: 0.8567 (t0) cc_final: 0.8355 (t70)
  outliers start: 13
  outliers final: 12
  residues processed: 93
  average time/residue: 0.2001
  time to fit residues: 24.9155
Evaluate side-chains
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  507 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 52 optimal weight:    0.3980
   chunk 54 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.146210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.117726 restraints weight = 8862.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.43
r_work: 0.3260 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6841  Z= 0.218
  Angle     :  0.557   8.658   9297  Z= 0.283
  Chirality :  0.044   0.284   1013
  Planarity :  0.004   0.048   1180
  Dihedral  :  6.252  57.566   1168
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.32 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.19 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.31), residues: 790
  helix:  2.05 (0.28), residues: 392
  sheet:  0.60 (0.80), residues: 42
  loop : -1.43 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 566 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.017   0.002   TYR D 183 
 ARG   0.002   0.000   ARG D 177 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3826.00 seconds
wall clock time: 68 minutes 42.95 seconds (4122.95 seconds total)