Starting phenix.real_space_refine
on Sat May 10 04:32:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9clp_45728/05_2025/9clp_45728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9clp_45728/05_2025/9clp_45728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9clp_45728/05_2025/9clp_45728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9clp_45728/05_2025/9clp_45728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9clp_45728/05_2025/9clp_45728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9clp_45728/05_2025/9clp_45728.cif"
  }
  resolution = 3.43
  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=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     Zn      1      6.06       5
     S      53      5.16       5
     C    3127      2.51       5
     N     864      2.21       5
     O     987      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5035
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3257
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 420, 3249
          Classifications: {'peptide': 420}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 20, 'TRANS': 399}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 20
      Conformer: "B"
        Number of residues, atoms: 420, 3249
          Classifications: {'peptide': 420}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 20, 'TRANS': 399}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 20
          bond proxies already assigned to first conformer: 3310
    Chain: "C"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 35
          Classifications: {'peptide': 7}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'UNK:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
    Chain: "H"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 944
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 795
          Classifications: {'peptide': 110}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 3, ' ZN': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 8.10, per 1000 atoms: 1.61
  Number of scatterers: 5035
  At special positions: 0
  Unit cell: (66.222, 70.75, 126.218, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Ca      3     19.99
     S      53     16.00
     O     987      8.00
     N     864      7.00
     C    3127      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=19, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 352 " - pdb=" SG  CYS A 376 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 354 " - pdb=" SG  CYS A 359 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 408 " - pdb=" SG  CYS A 437 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 421 " - pdb=" SG  CYS A 427 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 431 " - pdb=" SG  CYS A 454 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 445 " - pdb=" SG  CYS A 451 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 450 " - pdb=" SG  CYS A 476 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 463 " - pdb=" SG  CYS A 483 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 495 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 514 " - pdb=" SG  CYS A 567 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 529 " - pdb=" SG  CYS A 578 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 542 " - pdb=" SG  CYS A 555 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 562 " - pdb=" SG  CYS A 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 598 " - pdb=" SG  CYS A 609 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 347 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 341 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 337 "


  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 11 sheets defined
      21.2% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 210 through 217
      removed outlier: 3.764A  pdb=" N   TYR A 217 " --> pdb=" O   MET A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 239
    Processing helix  chain 'A' and resid 240 through 242
      No H-bonds generated for 'chain 'A' and resid 240 through 242'
    Processing helix  chain 'A' and resid 265 through 285
      removed outlier: 5.100A  pdb=" N   LEU A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   ASN A 283 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
    Processing helix  chain 'A' and resid 327 through 343
      removed outlier: 3.646A  pdb=" N   MET A 331 " --> pdb=" O   ILE A 327 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 363
      removed outlier: 4.040A  pdb=" N   GLY A 363 " --> pdb=" O   ILE A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 389
      removed outlier: 3.851A  pdb=" N   TYR A 378 " --> pdb=" O   SER A 374 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   GLN A 380 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 394
      removed outlier: 3.572A  pdb=" N   ILE A 393 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 394 " --> pdb=" O   LYS A 391 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 390 through 394'
    Processing helix  chain 'A' and resid 509 through 518
    Processing helix  chain 'A' and resid 528 through 535
    Processing helix  chain 'A' and resid 559 through 563
      removed outlier: 3.690A  pdb=" N   GLY A 563 " --> pdb=" O   VAL A 560 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.768A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.769A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.715A  pdb=" N   GLU L  83 " --> pdb=" O   ALA L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 253
      removed outlier: 7.870A  pdb=" N   VAL A 207 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LEU A 251 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   VAL A 209 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   PHE A 253 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   HIS A 289 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   GLU A 204 " --> pdb=" O   HIS A 289 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   GLN A 291 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL A 206 " --> pdb=" O   GLN A 291 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   LEU A 293 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL A 208 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 432 through 433
      removed outlier: 3.529A  pdb=" N   ASP A 433 " --> pdb=" O   LYS A 438 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A 438 " --> pdb=" O   ASP A 433 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 464
      removed outlier: 7.123A  pdb=" N   GLU A 474 " --> pdb=" O   CYS A 463 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 495
    Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 524
    Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 605
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.525A  pdb=" N   MET H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   TRP H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.872A  pdb=" N   TRP L  35 " --> pdb=" O   MET L  47 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12
    Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 24

    152 hydrogen bonds defined for protein.
    372 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: 1.38

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1672
        1.35 -     1.46: 1241
        1.46 -     1.58: 2162
        1.58 -     1.70: 0
        1.70 -     1.82: 67
  Bond restraints: 5142
  Sorted by residual:
  bond pdb=" CB  PRO A 390 "
       pdb=" CG  PRO A 390 "
    ideal  model  delta    sigma   weight residual
    1.492  1.571 -0.079 5.00e-02 4.00e+02 2.47e+00
  bond pdb=" N   ASN L  31 "
       pdb=" CA  ASN L  31 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.019 1.29e-02 6.01e+03 2.19e+00
  bond pdb=" C   VAL A 249 "
       pdb=" O   VAL A 249 "
    ideal  model  delta    sigma   weight residual
    1.231  1.243 -0.012 1.02e-02 9.61e+03 1.39e+00
  bond pdb=" CA  MET A 576 "
       pdb=" C   MET A 576 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.009 9.60e-03 1.09e+04 8.63e-01
  bond pdb=" CG  PRO A 390 "
       pdb=" CD  PRO A 390 "
    ideal  model  delta    sigma   weight residual
    1.503  1.532 -0.029 3.40e-02 8.65e+02 7.09e-01
  ... (remaining 5137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.86: 6420
        0.86 -     1.72: 438
        1.72 -     2.58: 79
        2.58 -     3.44: 26
        3.44 -     4.30: 10
  Bond angle restraints: 6973
  Sorted by residual:
  angle pdb=" C   ASP A 586 "
        pdb=" N   GLU A 587 "
        pdb=" CA  GLU A 587 "
      ideal   model   delta    sigma   weight residual
     120.38  124.30   -3.92 1.37e+00 5.33e-01 8.20e+00
  angle pdb=" CA  PRO A 390 "
        pdb=" N   PRO A 390 "
        pdb=" CD  PRO A 390 "
      ideal   model   delta    sigma   weight residual
     112.00  108.21    3.79 1.40e+00 5.10e-01 7.32e+00
  angle pdb=" C   GLU A 462 "
        pdb=" N   CYS A 463 "
        pdb=" CA  CYS A 463 "
      ideal   model   delta    sigma   weight residual
     122.42  118.66    3.76 1.77e+00 3.19e-01 4.51e+00
  angle pdb=" C   TYR A 309 "
        pdb=" CA  TYR A 309 "
        pdb=" CB  TYR A 309 "
      ideal   model   delta    sigma   weight residual
     111.36  108.03    3.33 1.63e+00 3.76e-01 4.17e+00
  angle pdb=" C   VAL A 308 "
        pdb=" N   TYR A 309 "
        pdb=" CA  TYR A 309 "
      ideal   model   delta    sigma   weight residual
     123.05  126.23   -3.18 1.57e+00 4.06e-01 4.11e+00
  ... (remaining 6968 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 2884
       17.26 -    34.52: 180
       34.52 -    51.78: 41
       51.78 -    69.04: 9
       69.04 -    86.30: 8
  Dihedral angle restraints: 3122
    sinusoidal: 1222
      harmonic: 1900
  Sorted by residual:
  dihedral pdb=" CB  CYS A 463 "
           pdb=" SG  CYS A 463 "
           pdb=" SG  CYS A 483 "
           pdb=" CB  CYS A 483 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.90  -85.90     1      1.00e+01 1.00e-02 8.91e+01
  dihedral pdb=" CB  CYS A 431 "
           pdb=" SG  CYS A 431 "
           pdb=" SG  CYS A 454 "
           pdb=" CB  CYS A 454 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.19   72.19     1      1.00e+01 1.00e-02 6.66e+01
  dihedral pdb=" CB  CYS A 354 "
           pdb=" SG  CYS A 354 "
           pdb=" SG  CYS A 359 "
           pdb=" CB  CYS A 359 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.72   64.72     1      1.00e+01 1.00e-02 5.50e+01
  ... (remaining 3119 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 433
       0.026 -    0.053: 195
       0.053 -    0.079: 71
       0.079 -    0.106: 39
       0.106 -    0.132: 13
  Chirality restraints: 751
  Sorted by residual:
  chirality pdb=" CA  ASN L  31 "
            pdb=" N   ASN L  31 "
            pdb=" C   ASN L  31 "
            pdb=" CB  ASN L  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE A 321 "
            pdb=" N   ILE A 321 "
            pdb=" C   ILE A 321 "
            pdb=" CB  ILE A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  ... (remaining 748 not shown)

  Planarity restraints: 914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 389 "   -0.046 5.00e-02 4.00e+02   6.84e-02 7.48e+00
        pdb=" N   PRO A 390 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 390 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 390 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  96 "    0.012 2.00e-02 2.50e+03   1.06e-02 2.82e+00
        pdb=" CG  TRP H  96 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  96 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  96 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  96 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  96 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  96 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  96 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  96 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  96 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 357 "    0.025 5.00e-02 4.00e+02   3.73e-02 2.23e+00
        pdb=" N   PRO A 358 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 358 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 358 "    0.021 5.00e-02 4.00e+02
  ... (remaining 911 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 143
        2.71 -     3.26: 5003
        3.26 -     3.80: 7490
        3.80 -     4.35: 9600
        4.35 -     4.90: 16839
  Nonbonded interactions: 39075
  Sorted by model distance:
  nonbonded pdb=" CG  HIS A 347 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.160 1.960
  nonbonded pdb=" OG1 THR A 306 "
            pdb=" O   VAL A 318 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD1 ASP A 210 "
            pdb=" N   HIS A 211 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" NH2 ARG L  61 "
            pdb=" O   GLY L  77 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   VAL A 308 "
            pdb=" NH1 ARG A 316 "
     model   vdw
     2.309 3.120
  ... (remaining 39070 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=0.50 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:             15.660
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     22.030
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   41.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
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      :  0.012   0.811   5164  Z= 0.394
  Angle     :  0.527   4.302   7011  Z= 0.307
  Chirality :  0.040   0.132    751
  Planarity :  0.005   0.068    914
  Dihedral  : 12.339  86.297   1855
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.28 (0.33), residues: 645
  helix:  0.48 (0.56), residues: 93
  sheet:  1.05 (0.45), residues: 139
  loop : -0.14 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP H  96 
 HIS   0.011   0.001   HIS A 347 
 PHE   0.008   0.001   PHE A 273 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.006   0.001   ARG H  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21022 (  148)
  hydrogen bonds       : angle       7.08299 (  372)
  metal coordination   : bond        0.46839 (    3)
  SS BOND              : bond        0.00187 (   19)
  SS BOND              : angle       0.89012 (   38)
  covalent geometry    : bond        0.00246 ( 5142)
  covalent geometry    : angle       0.52403 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6870 (mm-30)
REVERT: A  303 LEU cc_start: 0.8716 (mt) cc_final: 0.8502 (mt)
REVERT: A  426 ASP cc_start: 0.8310 (t0) cc_final: 0.8095 (t0)
REVERT: L   32 TYR cc_start: 0.7339 (m-10) cc_final: 0.6916 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1815
  time to fit residues: 18.1777
Evaluate side-chains
  63 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.0770
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 475 HIS
A 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.146780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.116836 restraints weight = 7816.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 3.08
r_work: 0.3229 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5164  Z= 0.138
  Angle     :  0.545   4.436   7011  Z= 0.298
  Chirality :  0.043   0.149    751
  Planarity :  0.004   0.042    914
  Dihedral  :  4.341  18.335    718
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  5.11 %
    Favored  : 93.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.39 (0.34), residues: 645
  helix:  0.58 (0.56), residues: 94
  sheet:  1.16 (0.45), residues: 132
  loop : -0.07 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  96 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.016   0.002   PHE A 362 
 TYR   0.018   0.001   TYR A 548 
 ARG   0.004   0.001   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  148)
  hydrogen bonds       : angle       5.18319 (  372)
  metal coordination   : bond        0.00993 (    3)
  SS BOND              : bond        0.00277 (   19)
  SS BOND              : angle       0.80633 (   38)
  covalent geometry    : bond        0.00328 ( 5142)
  covalent geometry    : angle       0.54307 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7717 (mm-30)
REVERT: A  426 ASP cc_start: 0.8715 (t0) cc_final: 0.8261 (t0)
REVERT: A  467 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7880 (mtt90)
REVERT: A  539 TYR cc_start: 0.7788 (p90) cc_final: 0.7586 (p90)
  outliers start: 6
  outliers final: 4
  residues processed: 70
  average time/residue: 0.1608
  time to fit residues: 15.0211
Evaluate side-chains
  66 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 289 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.144933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115286 restraints weight = 7843.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 3.03
r_work: 0.3299 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5164  Z= 0.160
  Angle     :  0.545   4.358   7011  Z= 0.297
  Chirality :  0.043   0.141    751
  Planarity :  0.005   0.049    914
  Dihedral  :  4.524  17.269    718
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.48 %
    Favored  : 91.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.27 (0.34), residues: 645
  helix:  0.70 (0.58), residues: 89
  sheet:  1.07 (0.45), residues: 137
  loop : -0.22 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP H  96 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.016   0.002   TYR A 548 
 ARG   0.007   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04062 (  148)
  hydrogen bonds       : angle       4.99086 (  372)
  metal coordination   : bond        0.00555 (    3)
  SS BOND              : bond        0.00316 (   19)
  SS BOND              : angle       0.77370 (   38)
  covalent geometry    : bond        0.00383 ( 5142)
  covalent geometry    : angle       0.54326 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7669 (mm-30)
REVERT: A  426 ASP cc_start: 0.8748 (t0) cc_final: 0.8350 (t0)
REVERT: A  467 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7897 (mtt90)
REVERT: A  539 TYR cc_start: 0.7854 (p90) cc_final: 0.7603 (p90)
REVERT: H   34 MET cc_start: 0.8330 (mmm) cc_final: 0.7919 (ttm)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1654
  time to fit residues: 14.3203
Evaluate side-chains
  62 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.123818 restraints weight = 9279.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 3.59
r_work: 0.3205 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5164  Z= 0.139
  Angle     :  0.515   4.392   7011  Z= 0.280
  Chirality :  0.042   0.142    751
  Planarity :  0.004   0.046    914
  Dihedral  :  4.412  16.694    718
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.94 %
    Favored  : 89.78 %
  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:  0.14 (0.33), residues: 645
  helix:  0.70 (0.58), residues: 89
  sheet:  0.91 (0.44), residues: 137
  loop : -0.30 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H  96 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.007   0.001   PHE L  62 
 TYR   0.015   0.001   TYR A 548 
 ARG   0.010   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  148)
  hydrogen bonds       : angle       4.81663 (  372)
  metal coordination   : bond        0.00432 (    3)
  SS BOND              : bond        0.00326 (   19)
  SS BOND              : angle       0.69901 (   38)
  covalent geometry    : bond        0.00332 ( 5142)
  covalent geometry    : angle       0.51394 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7709 (mm-30)
REVERT: A  426 ASP cc_start: 0.8792 (t0) cc_final: 0.8365 (t0)
REVERT: A  539 TYR cc_start: 0.7882 (p90) cc_final: 0.7601 (p90)
REVERT: A  559 ASP cc_start: 0.7116 (t70) cc_final: 0.6760 (t70)
REVERT: L   32 TYR cc_start: 0.7860 (m-10) cc_final: 0.7195 (m-10)
  outliers start: 7
  outliers final: 4
  residues processed: 66
  average time/residue: 0.1646
  time to fit residues: 14.5168
Evaluate side-chains
  63 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.148354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120943 restraints weight = 8196.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.94
r_work: 0.3238 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5164  Z= 0.203
  Angle     :  0.580   4.545   7011  Z= 0.313
  Chirality :  0.044   0.143    751
  Planarity :  0.005   0.052    914
  Dihedral  :  4.752  17.760    718
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.31 %
    Favored  : 88.69 %
  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: -0.21 (0.32), residues: 645
  helix:  0.51 (0.58), residues: 89
  sheet:  0.55 (0.44), residues: 136
  loop : -0.50 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H  96 
 HIS   0.004   0.001   HIS A 341 
 PHE   0.010   0.002   PHE L  62 
 TYR   0.016   0.002   TYR H  91 
 ARG   0.011   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  148)
  hydrogen bonds       : angle       4.96607 (  372)
  metal coordination   : bond        0.00740 (    3)
  SS BOND              : bond        0.00405 (   19)
  SS BOND              : angle       0.88564 (   38)
  covalent geometry    : bond        0.00491 ( 5142)
  covalent geometry    : angle       0.57744 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7919 (tpt) cc_final: 0.7553 (tpp)
REVERT: A  252 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7653 (mm-30)
REVERT: A  426 ASP cc_start: 0.8764 (t0) cc_final: 0.8359 (t0)
REVERT: A  539 TYR cc_start: 0.7913 (p90) cc_final: 0.7666 (p90)
REVERT: A  559 ASP cc_start: 0.7353 (t70) cc_final: 0.6953 (t70)
REVERT: H  105 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.7897 (pm20)
  outliers start: 11
  outliers final: 7
  residues processed: 65
  average time/residue: 0.1927
  time to fit residues: 16.4616
Evaluate side-chains
  65 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.151122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.122409 restraints weight = 7812.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.95
r_work: 0.3269 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5164  Z= 0.132
  Angle     :  0.513   4.502   7011  Z= 0.276
  Chirality :  0.041   0.138    751
  Planarity :  0.004   0.053    914
  Dihedral  :  4.440  16.166    718
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.04 %
    Favored  : 88.14 %
  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: -0.17 (0.32), residues: 645
  helix:  0.89 (0.58), residues: 88
  sheet:  0.50 (0.44), residues: 136
  loop : -0.54 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  96 
 HIS   0.003   0.000   HIS A 341 
 PHE   0.007   0.001   PHE L  62 
 TYR   0.013   0.001   TYR A 548 
 ARG   0.012   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  148)
  hydrogen bonds       : angle       4.77061 (  372)
  metal coordination   : bond        0.00416 (    3)
  SS BOND              : bond        0.00291 (   19)
  SS BOND              : angle       0.69268 (   38)
  covalent geometry    : bond        0.00317 ( 5142)
  covalent geometry    : angle       0.51214 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7943 (tpt) cc_final: 0.7601 (tpp)
REVERT: A  252 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7677 (mm-30)
REVERT: A  426 ASP cc_start: 0.8816 (t0) cc_final: 0.8431 (t0)
REVERT: A  539 TYR cc_start: 0.7888 (p90) cc_final: 0.7615 (p90)
REVERT: H  105 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.7914 (pm20)
  outliers start: 10
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1820
  time to fit residues: 15.3174
Evaluate side-chains
  66 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.146811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117962 restraints weight = 9937.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 3.69
r_work: 0.3181 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5164  Z= 0.226
  Angle     :  0.601   5.676   7011  Z= 0.322
  Chirality :  0.044   0.142    751
  Planarity :  0.005   0.042    914
  Dihedral  :  4.753  17.104    718
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.58 %
    Favored  : 86.86 %
  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: -0.41 (0.32), residues: 645
  helix:  0.67 (0.57), residues: 89
  sheet:  0.31 (0.44), residues: 136
  loop : -0.69 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  96 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.010   0.002   PHE L  98 
 TYR   0.020   0.002   TYR L  32 
 ARG   0.011   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04298 (  148)
  hydrogen bonds       : angle       4.97827 (  372)
  metal coordination   : bond        0.00904 (    3)
  SS BOND              : bond        0.00455 (   19)
  SS BOND              : angle       0.91294 (   38)
  covalent geometry    : bond        0.00546 ( 5142)
  covalent geometry    : angle       0.59845 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7773 (mm-30)
REVERT: A  426 ASP cc_start: 0.8820 (t0) cc_final: 0.8419 (t0)
REVERT: A  539 TYR cc_start: 0.7917 (p90) cc_final: 0.7621 (p90)
REVERT: H  105 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.7914 (pm20)
REVERT: L   45 LYS cc_start: 0.7568 (ttpt) cc_final: 0.7358 (ttpt)
  outliers start: 14
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1682
  time to fit residues: 15.1030
Evaluate side-chains
  68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.142280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.114157 restraints weight = 9472.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 3.20
r_work: 0.3257 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5164  Z= 0.156
  Angle     :  0.542   5.324   7011  Z= 0.291
  Chirality :  0.042   0.139    751
  Planarity :  0.004   0.038    914
  Dihedral  :  4.558  16.442    718
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 10.95 %
    Favored  : 86.68 %
  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: -0.33 (0.32), residues: 645
  helix:  0.80 (0.58), residues: 89
  sheet:  0.32 (0.45), residues: 131
  loop : -0.62 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  96 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.008   0.001   PHE L  62 
 TYR   0.030   0.002   TYR L  32 
 ARG   0.009   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  148)
  hydrogen bonds       : angle       4.83954 (  372)
  metal coordination   : bond        0.00554 (    3)
  SS BOND              : bond        0.00334 (   19)
  SS BOND              : angle       0.77665 (   38)
  covalent geometry    : bond        0.00375 ( 5142)
  covalent geometry    : angle       0.54044 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.8824 (t0) cc_final: 0.8460 (t0)
REVERT: A  539 TYR cc_start: 0.7882 (p90) cc_final: 0.7587 (p90)
REVERT: H  105 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.7910 (pm20)
REVERT: L   45 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7386 (ttpt)
  outliers start: 13
  outliers final: 10
  residues processed: 66
  average time/residue: 0.1706
  time to fit residues: 14.7244
Evaluate side-chains
  71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   45 LYS
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.4158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.150287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121848 restraints weight = 12189.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 3.75
r_work: 0.3237 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5164  Z= 0.107
  Angle     :  0.496   5.340   7011  Z= 0.265
  Chirality :  0.040   0.137    751
  Planarity :  0.004   0.037    914
  Dihedral  :  4.227  15.505    718
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.95 %
    Favored  : 87.04 %
  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: -0.18 (0.33), residues: 645
  helix:  1.04 (0.59), residues: 88
  sheet:  0.38 (0.44), residues: 137
  loop : -0.54 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.023   0.001   TYR L  32 
 ARG   0.009   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03205 (  148)
  hydrogen bonds       : angle       4.61949 (  372)
  metal coordination   : bond        0.00294 (    3)
  SS BOND              : bond        0.00233 (   19)
  SS BOND              : angle       0.61729 (   38)
  covalent geometry    : bond        0.00253 ( 5142)
  covalent geometry    : angle       0.49531 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.8861 (t0) cc_final: 0.8442 (t0)
REVERT: A  539 TYR cc_start: 0.7878 (p90) cc_final: 0.7574 (p90)
REVERT: H  105 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.7966 (pm20)
REVERT: L   32 TYR cc_start: 0.7817 (m-10) cc_final: 0.7235 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 68
  average time/residue: 0.1684
  time to fit residues: 15.0451
Evaluate side-chains
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0000
   chunk 6 optimal weight:    0.0870
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.4762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.152155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123695 restraints weight = 9238.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.25
r_work: 0.3227 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5164  Z= 0.116
  Angle     :  0.510   6.195   7011  Z= 0.270
  Chirality :  0.041   0.139    751
  Planarity :  0.004   0.049    914
  Dihedral  :  4.186  15.530    718
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.13 %
    Favored  : 87.04 %
  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: -0.19 (0.33), residues: 645
  helix:  0.73 (0.59), residues: 94
  sheet:  0.49 (0.45), residues: 138
  loop : -0.53 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.021   0.001   TYR L  32 
 ARG   0.013   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03293 (  148)
  hydrogen bonds       : angle       4.60575 (  372)
  metal coordination   : bond        0.00353 (    3)
  SS BOND              : bond        0.00247 (   19)
  SS BOND              : angle       0.63468 (   38)
  covalent geometry    : bond        0.00276 ( 5142)
  covalent geometry    : angle       0.50875 ( 6973)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.8870 (t0) cc_final: 0.8457 (t0)
REVERT: A  539 TYR cc_start: 0.7859 (p90) cc_final: 0.7560 (p90)
REVERT: H  105 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7980 (pm20)
REVERT: L   32 TYR cc_start: 0.7821 (m-10) cc_final: 0.7162 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 0.1692
  time to fit residues: 14.1609
Evaluate side-chains
  68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 23 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0980
   chunk 52 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.150111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.120305 restraints weight = 12511.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 4.47
r_work: 0.3237 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5164  Z= 0.118
  Angle     :  0.512   5.980   7011  Z= 0.272
  Chirality :  0.041   0.139    751
  Planarity :  0.004   0.051    914
  Dihedral  :  4.154  15.447    718
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.31 %
    Favored  : 86.86 %
  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: -0.10 (0.33), residues: 645
  helix:  1.08 (0.60), residues: 89
  sheet:  0.44 (0.45), residues: 138
  loop : -0.48 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.021   0.001   TYR L  32 
 ARG   0.012   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03277 (  148)
  hydrogen bonds       : angle       4.56939 (  372)
  metal coordination   : bond        0.00385 (    3)
  SS BOND              : bond        0.00247 (   19)
  SS BOND              : angle       0.63195 (   38)
  covalent geometry    : bond        0.00282 ( 5142)
  covalent geometry    : angle       0.51135 ( 6973)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3392.51 seconds
wall clock time: 60 minutes 26.18 seconds (3626.18 seconds total)