Starting phenix.real_space_refine
on Thu Jun  5 03:37:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9clp_45728/06_2025/9clp_45728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9clp_45728/06_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_45728/06_2025/9clp_45728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9clp_45728/06_2025/9clp_45728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9clp_45728/06_2025/9clp_45728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9clp_45728/06_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-5710/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: 9.65, per 1000 atoms: 1.92
  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: 1.31
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.64
  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: 1.33

  Time building geometry restraints manager: 1.58 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:             78.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     24.030
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  105.860
-------------------------------------------------------------------------------
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  : 0.600 
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: 0.3308
  time to fit residues: 33.0123
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  : 0.904 
-------------------------------------------------------------------------------
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 = 0.146779 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 = 7816.809|
|-----------------------------------------------------------------------------|
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: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
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  : 0.631 
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: 0.8713 (t0) cc_final: 0.8259 (t0)
REVERT: A  467 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7884 (mtt90)
REVERT: A  539 TYR cc_start: 0.7788 (p90) cc_final: 0.7585 (p90)
  outliers start: 6
  outliers final: 4
  residues processed: 70
  average time/residue: 0.1707
  time to fit residues: 16.0395
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  : 0.538 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.141842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.112590 restraints weight = 7889.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.98
r_work: 0.3252 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    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 = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5164  Z= 0.216
  Angle     :  0.600   4.490   7011  Z= 0.326
  Chirality :  0.045   0.144    751
  Planarity :  0.005   0.051    914
  Dihedral  :  4.820  18.542    718
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  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:  0.13 (0.33), residues: 645
  helix:  0.56 (0.57), residues: 89
  sheet:  0.98 (0.46), residues: 132
  loop : -0.29 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H  96 
 HIS   0.004   0.001   HIS A 341 
 PHE   0.011   0.002   PHE L  62 
 TYR   0.018   0.002   TYR A 548 
 ARG   0.008   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04511 (  148)
  hydrogen bonds       : angle       5.14640 (  372)
  metal coordination   : bond        0.00797 (    3)
  SS BOND              : bond        0.00409 (   19)
  SS BOND              : angle       0.89843 (   38)
  covalent geometry    : bond        0.00523 ( 5142)
  covalent geometry    : angle       0.59797 ( 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  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7657 (mm-30)
REVERT: A  426 ASP cc_start: 0.8739 (t0) cc_final: 0.8341 (t0)
REVERT: A  467 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7898 (mtt90)
REVERT: H   34 MET cc_start: 0.8342 (mmm) cc_final: 0.8004 (ttm)
REVERT: H   95 GLU cc_start: 0.7103 (pt0) cc_final: 0.6902 (pt0)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1892
  time to fit residues: 16.2440
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  : 0.736 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 40 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.151389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.122680 restraints weight = 9282.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 3.55
r_work: 0.3204 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3281
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5164  Z= 0.145
  Angle     :  0.523   4.378   7011  Z= 0.285
  Chirality :  0.042   0.142    751
  Planarity :  0.004   0.046    914
  Dihedral  :  4.563  17.163    718
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.94 %
    Favored  : 89.96 %
  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:  0.03 (0.33), residues: 645
  helix:  0.53 (0.58), residues: 90
  sheet:  0.81 (0.44), residues: 137
  loop : -0.34 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  96 
 HIS   0.004   0.001   HIS A 341 
 PHE   0.007   0.001   PHE L  62 
 TYR   0.019   0.001   TYR L  32 
 ARG   0.011   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  148)
  hydrogen bonds       : angle       4.87728 (  372)
  metal coordination   : bond        0.00436 (    3)
  SS BOND              : bond        0.00319 (   19)
  SS BOND              : angle       0.75115 (   38)
  covalent geometry    : bond        0.00347 ( 5142)
  covalent geometry    : angle       0.52171 ( 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: 6
    poor density    : 63
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: A  426 ASP cc_start: 0.8779 (t0) cc_final: 0.8350 (t0)
REVERT: A  559 ASP cc_start: 0.7159 (t70) cc_final: 0.6831 (t70)
  outliers start: 6
  outliers final: 4
  residues processed: 66
  average time/residue: 0.2705
  time to fit residues: 24.0249
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  : 0.630 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0980
   chunk 63 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.153447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.126393 restraints weight = 8126.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.93
r_work: 0.3294 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2002

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= 0.112
  Angle     :  0.497   4.395   7011  Z= 0.268
  Chirality :  0.041   0.139    751
  Planarity :  0.004   0.051    914
  Dihedral  :  4.292  15.746    718
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.49 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.33), residues: 645
  helix:  0.54 (0.58), residues: 94
  sheet:  0.74 (0.44), residues: 137
  loop : -0.40 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  96 
 HIS   0.003   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.018   0.001   TYR L  32 
 ARG   0.011   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03342 (  148)
  hydrogen bonds       : angle       4.71634 (  372)
  metal coordination   : bond        0.00303 (    3)
  SS BOND              : bond        0.00266 (   19)
  SS BOND              : angle       0.65580 (   38)
  covalent geometry    : bond        0.00265 ( 5142)
  covalent geometry    : angle       0.49600 ( 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
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7915 (tpt) cc_final: 0.7569 (tpp)
REVERT: A  252 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7679 (mm-30)
REVERT: A  426 ASP cc_start: 0.8791 (t0) cc_final: 0.8322 (t0)
REVERT: A  559 ASP cc_start: 0.7072 (t70) cc_final: 0.6623 (t70)
REVERT: H  105 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.7899 (pm20)
REVERT: L   32 TYR cc_start: 0.7853 (m-10) cc_final: 0.7264 (m-10)
  outliers start: 9
  outliers final: 6
  residues processed: 65
  average time/residue: 0.1984
  time to fit residues: 16.5977
Evaluate side-chains
  65 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0970
   chunk 8 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.151679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.122693 restraints weight = 7839.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.98
r_work: 0.3278 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5164  Z= 0.134
  Angle     :  0.510   4.503   7011  Z= 0.273
  Chirality :  0.041   0.140    751
  Planarity :  0.004   0.055    914
  Dihedral  :  4.303  15.785    718
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.67 %
    Favored  : 88.50 %
  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: -0.04 (0.33), residues: 645
  helix:  0.96 (0.59), residues: 88
  sheet:  0.63 (0.44), residues: 137
  loop : -0.45 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   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   0.013   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03450 (  148)
  hydrogen bonds       : angle       4.70251 (  372)
  metal coordination   : bond        0.00445 (    3)
  SS BOND              : bond        0.00294 (   19)
  SS BOND              : angle       0.66000 (   38)
  covalent geometry    : bond        0.00321 ( 5142)
  covalent geometry    : angle       0.50858 ( 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
  71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7875 (tpt) cc_final: 0.7523 (tpp)
REVERT: A  252 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7719 (mm-30)
REVERT: A  426 ASP cc_start: 0.8818 (t0) cc_final: 0.8340 (t0)
REVERT: A  559 ASP cc_start: 0.7105 (t70) cc_final: 0.6901 (t70)
REVERT: H  105 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7924 (pm20)
REVERT: L   32 TYR cc_start: 0.7841 (m-10) cc_final: 0.7217 (m-10)
REVERT: L   45 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7355 (ttpt)
  outliers start: 10
  outliers final: 7
  residues processed: 66
  average time/residue: 0.1938
  time to fit residues: 16.4079
Evaluate side-chains
  67 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
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  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   45 LYS
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:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0470
   chunk 38 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 48 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.146643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117953 restraints weight = 10054.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 3.61
r_work: 0.3189 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    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 = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5164  Z= 0.126
  Angle     :  0.505   4.914   7011  Z= 0.270
  Chirality :  0.041   0.139    751
  Planarity :  0.004   0.055    914
  Dihedral  :  4.263  15.437    718
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.04 %
    Favored  : 87.23 %
  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: -0.03 (0.33), residues: 645
  helix:  1.00 (0.59), residues: 88
  sheet:  0.63 (0.44), residues: 137
  loop : -0.46 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  96 
 HIS   0.003   0.000   HIS A 341 
 PHE   0.006   0.001   PHE L  62 
 TYR   0.013   0.001   TYR A 548 
 ARG   0.013   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  148)
  hydrogen bonds       : angle       4.61383 (  372)
  metal coordination   : bond        0.00411 (    3)
  SS BOND              : bond        0.00272 (   19)
  SS BOND              : angle       0.64952 (   38)
  covalent geometry    : bond        0.00301 ( 5142)
  covalent geometry    : angle       0.50420 ( 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
  75 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7895 (tpt) cc_final: 0.7546 (tpp)
REVERT: A  252 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7755 (mm-30)
REVERT: A  426 ASP cc_start: 0.8830 (t0) cc_final: 0.8337 (t0)
REVERT: A  559 ASP cc_start: 0.7110 (t70) cc_final: 0.6860 (t70)
REVERT: H  105 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7948 (pm20)
REVERT: L   32 TYR cc_start: 0.7904 (m-10) cc_final: 0.7218 (m-10)
  outliers start: 15
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1807
  time to fit residues: 16.3490
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  : 0.542 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 49 optimal weight:    0.3980
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.151110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.122756 restraints weight = 9362.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 3.25
r_work: 0.3224 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    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 = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5164  Z= 0.139
  Angle     :  0.521   5.847   7011  Z= 0.277
  Chirality :  0.041   0.141    751
  Planarity :  0.004   0.045    914
  Dihedral  :  4.301  15.970    718
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.40 %
    Favored  : 87.41 %
  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: -0.04 (0.33), residues: 645
  helix:  0.99 (0.59), residues: 88
  sheet:  0.60 (0.45), residues: 136
  loop : -0.45 (0.30), residues: 421

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   0.007   0.001   PHE L  62 
 TYR   0.013   0.001   TYR A 548 
 ARG   0.011   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  148)
  hydrogen bonds       : angle       4.63808 (  372)
  metal coordination   : bond        0.00495 (    3)
  SS BOND              : bond        0.00291 (   19)
  SS BOND              : angle       0.68414 (   38)
  covalent geometry    : bond        0.00333 ( 5142)
  covalent geometry    : angle       0.51997 ( 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
  74 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7892 (tpt) cc_final: 0.7548 (tpp)
REVERT: A  252 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7744 (mm-30)
REVERT: A  426 ASP cc_start: 0.8841 (t0) cc_final: 0.8364 (t0)
REVERT: A  559 ASP cc_start: 0.7130 (t70) cc_final: 0.6866 (t70)
REVERT: H  105 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7973 (pm20)
REVERT: L   32 TYR cc_start: 0.7934 (m-10) cc_final: 0.7224 (m-10)
  outliers start: 12
  outliers final: 11
  residues processed: 68
  average time/residue: 0.2044
  time to fit residues: 17.9703
Evaluate side-chains
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0020
   overall best weight:    0.4388

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.153270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.124630 restraints weight = 12121.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 3.80
r_work: 0.3297 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2308

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= 0.110
  Angle     :  0.498   5.664   7011  Z= 0.264
  Chirality :  0.041   0.138    751
  Planarity :  0.004   0.042    914
  Dihedral  :  4.143  15.699    718
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  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:  0.01 (0.33), residues: 645
  helix:  1.12 (0.60), residues: 88
  sheet:  0.57 (0.45), residues: 138
  loop : -0.42 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.012   0.001   TYR A 548 
 ARG   0.010   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (  148)
  hydrogen bonds       : angle       4.53539 (  372)
  metal coordination   : bond        0.00331 (    3)
  SS BOND              : bond        0.00230 (   19)
  SS BOND              : angle       0.58960 (   38)
  covalent geometry    : bond        0.00261 ( 5142)
  covalent geometry    : angle       0.49704 ( 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
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7978 (tpt) cc_final: 0.7636 (tpp)
REVERT: A  252 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7733 (mm-30)
REVERT: A  338 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6886 (mm-30)
REVERT: A  426 ASP cc_start: 0.8859 (t0) cc_final: 0.8431 (t0)
REVERT: A  559 ASP cc_start: 0.7091 (t70) cc_final: 0.6797 (t70)
REVERT: H   34 MET cc_start: 0.8318 (mmm) cc_final: 0.8112 (ttm)
REVERT: H  105 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8010 (pm20)
REVERT: L   32 TYR cc_start: 0.7988 (m-10) cc_final: 0.7296 (m-10)
  outliers start: 11
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1973
  time to fit residues: 17.1819
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  : 0.783 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0970
   chunk 55 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.151740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123724 restraints weight = 9387.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 3.67
r_work: 0.3262 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5164  Z= 0.101
  Angle     :  0.495   5.610   7011  Z= 0.262
  Chirality :  0.040   0.138    751
  Planarity :  0.004   0.040    914
  Dihedral  :  4.016  15.526    718
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.31 %
    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:  0.05 (0.33), residues: 645
  helix:  1.19 (0.60), residues: 88
  sheet:  0.59 (0.44), residues: 138
  loop : -0.39 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.011   0.001   TYR A 548 
 ARG   0.010   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03062 (  148)
  hydrogen bonds       : angle       4.49288 (  372)
  metal coordination   : bond        0.00260 (    3)
  SS BOND              : bond        0.00208 (   19)
  SS BOND              : angle       0.56840 (   38)
  covalent geometry    : bond        0.00240 ( 5142)
  covalent geometry    : angle       0.49428 ( 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
  71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7944 (tpt) cc_final: 0.7603 (tpp)
REVERT: A  252 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7736 (mm-30)
REVERT: A  338 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6898 (mm-30)
REVERT: A  426 ASP cc_start: 0.8848 (t0) cc_final: 0.8436 (t0)
REVERT: A  559 ASP cc_start: 0.7022 (t70) cc_final: 0.6703 (t70)
REVERT: H  105 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8012 (pm20)
REVERT: L   32 TYR cc_start: 0.7942 (m-10) cc_final: 0.7249 (m-10)
  outliers start: 9
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1824
  time to fit residues: 15.3761
Evaluate side-chains
  70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 59 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 35 optimal weight:    0.2980
   chunk 52 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.149959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121569 restraints weight = 12597.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 3.91
r_work: 0.3227 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5164  Z= 0.124
  Angle     :  0.511   5.489   7011  Z= 0.271
  Chirality :  0.041   0.141    751
  Planarity :  0.004   0.041    914
  Dihedral  :  4.109  15.679    718
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  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: -0.04 (0.33), residues: 645
  helix:  1.13 (0.60), residues: 88
  sheet:  0.51 (0.44), residues: 138
  loop : -0.45 (0.31), residues: 419

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   0.012   0.001   TYR A 548 
 ARG   0.009   0.001   ARG A 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03296 (  148)
  hydrogen bonds       : angle       4.54594 (  372)
  metal coordination   : bond        0.00433 (    3)
  SS BOND              : bond        0.00259 (   19)
  SS BOND              : angle       0.63379 (   38)
  covalent geometry    : bond        0.00299 ( 5142)
  covalent geometry    : angle       0.51046 ( 6973)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5286.95 seconds
wall clock time: 95 minutes 12.45 seconds (5712.45 seconds total)