Starting phenix.real_space_refine
on Tue Feb 11 09:23:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9clp_45728/02_2025/9clp_45728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9clp_45728/02_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_45728/02_2025/9clp_45728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9clp_45728/02_2025/9clp_45728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9clp_45728/02_2025/9clp_45728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9clp_45728/02_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-5592/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: 7.25, per 1000 atoms: 1.44
  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: 1.09
  Conformation dependent library (CDL) restraints added in 972.4 milliseconds
  
  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: 0.58
  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: 1.25

  Time building geometry restraints manager: 1.31 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:             12.680
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.750
  Find NCS groups from input model:        0.050
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.760
-------------------------------------------------------------------------------
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      :  0.002   0.079   5142  Z= 0.172
  Angle     :  0.524   4.302   6973  Z= 0.306
  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 

*********************** 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  : 0.511 
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: 0.1824
  time to fit residues: 18.1194
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  : 0.538 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 16 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   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:    0.3338

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.149948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119769 restraints weight = 7840.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.15
r_work: 0.3269 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    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 = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3336
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5142  Z= 0.170
  Angle     :  0.516   4.624   6973  Z= 0.284
  Chirality :  0.042   0.146    751
  Planarity :  0.004   0.040    914
  Dihedral  :  4.122  18.791    718
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  5.29 %
    Favored  : 93.98 %
  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:  0.46 (0.34), residues: 645
  helix:  0.45 (0.55), residues: 100
  sheet:  1.32 (0.46), residues: 132
  loop : -0.02 (0.32), residues: 413

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   0.015   0.001   PHE A 362 
 TYR   0.016   0.001   TYR A 539 
 ARG   0.004   0.001   ARG A 457 

*********************** 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
  71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: A  303 LEU cc_start: 0.8467 (mt) cc_final: 0.8237 (mt)
REVERT: A  426 ASP cc_start: 0.8696 (t0) cc_final: 0.8239 (t0)
REVERT: A  539 TYR cc_start: 0.7724 (p90) cc_final: 0.7523 (p90)
REVERT: L   32 TYR cc_start: 0.7551 (m-10) cc_final: 0.6931 (m-10)
  outliers start: 4
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1725
  time to fit residues: 15.8254
Evaluate side-chains
  65 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  477 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:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.144442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115070 restraints weight = 7844.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 3.00
r_work: 0.3206 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
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 = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3319
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5142  Z= 0.317
  Angle     :  0.589   4.429   6973  Z= 0.321
  Chirality :  0.045   0.146    751
  Planarity :  0.005   0.049    914
  Dihedral  :  4.712  18.279    718
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  6.75 %
    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:  0.22 (0.33), residues: 645
  helix:  0.60 (0.58), residues: 88
  sheet:  1.08 (0.46), residues: 132
  loop : -0.23 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  96 
 HIS   0.005   0.001   HIS A 341 
 PHE   0.011   0.002   PHE L  62 
 TYR   0.018   0.002   TYR A 548 
 ARG   0.007   0.001   ARG A 286 

*********************** 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
  71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7663 (mm-30)
REVERT: A  426 ASP cc_start: 0.8753 (t0) cc_final: 0.8345 (t0)
REVERT: A  539 TYR cc_start: 0.7871 (p90) cc_final: 0.7629 (p90)
REVERT: H   34 MET cc_start: 0.8226 (mmm) cc_final: 0.7848 (ttm)
  outliers start: 10
  outliers final: 5
  residues processed: 66
  average time/residue: 0.1647
  time to fit residues: 14.4226
Evaluate side-chains
  62 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 THR
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 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:    0.9990
   chunk 42 optimal weight:    0.0970
   chunk 40 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.152553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.123483 restraints weight = 9277.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 3.27
r_work: 0.3254 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.105         |
| 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: 0.7594
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5142  Z= 0.196
  Angle     :  0.506   4.389   6973  Z= 0.276
  Chirality :  0.041   0.143    751
  Planarity :  0.004   0.047    914
  Dihedral  :  4.414  16.536    718
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.58 %
    Favored  : 90.15 %
  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:  0.15 (0.33), residues: 645
  helix:  0.62 (0.58), residues: 89
  sheet:  0.85 (0.44), residues: 138
  loop : -0.24 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   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 

*********************** 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
  72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7685 (mm-30)
REVERT: A  426 ASP cc_start: 0.8773 (t0) cc_final: 0.8349 (t0)
REVERT: A  539 TYR cc_start: 0.7882 (p90) cc_final: 0.7589 (p90)
REVERT: A  559 ASP cc_start: 0.7061 (t70) cc_final: 0.6731 (t70)
  outliers start: 7
  outliers final: 4
  residues processed: 67
  average time/residue: 0.1719
  time to fit residues: 15.3584
Evaluate side-chains
  65 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 4 optimal weight:    0.0470
   chunk 61 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0170
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.5316

-------------------------------------------------------------------------------
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 = 0.153339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125680 restraints weight = 8120.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.96
r_work: 0.3265 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5142  Z= 0.200
  Angle     :  0.504   4.399   6973  Z= 0.273
  Chirality :  0.041   0.139    751
  Planarity :  0.004   0.053    914
  Dihedral  :  4.279  15.764    718
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.49 %
    Favored  : 89.23 %
  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:  0.12 (0.33), residues: 645
  helix:  0.76 (0.59), residues: 88
  sheet:  0.85 (0.44), residues: 137
  loop : -0.31 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  96 
 HIS   0.003   0.000   HIS A 341 
 PHE   0.007   0.001   PHE A 273 
 TYR   0.014   0.001   TYR A 548 
 ARG   0.012   0.001   ARG A 286 

*********************** 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: 7
    poor density    : 62
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7976 (tpt) cc_final: 0.7771 (tpp)
REVERT: A  252 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7663 (mm-30)
REVERT: A  426 ASP cc_start: 0.8810 (t0) cc_final: 0.8388 (t0)
REVERT: A  467 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7710 (mtt90)
REVERT: A  539 TYR cc_start: 0.7865 (p90) cc_final: 0.7557 (p90)
REVERT: A  559 ASP cc_start: 0.7094 (t70) cc_final: 0.6649 (t70)
REVERT: L   32 TYR cc_start: 0.7871 (m-10) cc_final: 0.7172 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 65
  average time/residue: 0.1964
  time to fit residues: 16.3731
Evaluate side-chains
  67 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
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   75 ILE
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:    0.0870
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4916

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.152499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.123278 restraints weight = 7828.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 3.00
r_work: 0.3346 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5142  Z= 0.187
  Angle     :  0.493   4.631   6973  Z= 0.264
  Chirality :  0.041   0.138    751
  Planarity :  0.004   0.053    914
  Dihedral  :  4.177  15.392    718
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.76 %
    Favored  : 89.60 %
  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:  0.56 (0.58), residues: 94
  sheet:  0.79 (0.44), residues: 137
  loop : -0.35 (0.30), residues: 414

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 A 273 
 TYR   0.013   0.001   TYR A 548 
 ARG   0.012   0.001   ARG A 286 

*********************** 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: 9
    poor density    : 62
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7645 (mm-30)
REVERT: A  426 ASP cc_start: 0.8805 (t0) cc_final: 0.8304 (t0)
REVERT: A  467 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7757 (mtt90)
REVERT: A  539 TYR cc_start: 0.7832 (p90) cc_final: 0.7507 (p90)
REVERT: A  559 ASP cc_start: 0.7023 (t70) cc_final: 0.6813 (t70)
REVERT: H  105 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7885 (pm20)
REVERT: L   45 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7368 (ttpt)
  outliers start: 9
  outliers final: 7
  residues processed: 66
  average time/residue: 0.1838
  time to fit residues: 15.7428
Evaluate side-chains
  68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
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   95 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0070
   chunk 38 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6598

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.151852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.123039 restraints weight = 9904.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 3.66
r_work: 0.3274 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5142  Z= 0.223
  Angle     :  0.515   4.900   6973  Z= 0.276
  Chirality :  0.042   0.139    751
  Planarity :  0.004   0.056    914
  Dihedral  :  4.279  15.973    718
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  8.76 %
    Favored  : 89.23 %
  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:  0.02 (0.33), residues: 645
  helix:  0.94 (0.59), residues: 88
  sheet:  0.74 (0.44), residues: 137
  loop : -0.42 (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   0.008   0.001   PHE L  62 
 TYR   0.021   0.001   TYR L  32 
 ARG   0.013   0.001   ARG A 286 

*********************** 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
  70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7730 (mm-30)
REVERT: A  426 ASP cc_start: 0.8813 (t0) cc_final: 0.8415 (t0)
REVERT: A  539 TYR cc_start: 0.7865 (p90) cc_final: 0.7635 (p90)
REVERT: A  559 ASP cc_start: 0.7169 (t70) cc_final: 0.6931 (t70)
REVERT: H  105 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.7946 (pm20)
  outliers start: 11
  outliers final: 9
  residues processed: 66
  average time/residue: 0.1872
  time to fit residues: 16.1493
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  : 0.615 
-------------------------------------------------------------------------------
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  472 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   30 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
Chi-restraints excluded: chain L residue   96 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 11 optimal weight:    0.3980
   chunk 61 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0040
   chunk 47 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.3792

-------------------------------------------------------------------------------
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 = 0.153206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.124231 restraints weight = 9319.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.32
r_work: 0.3263 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3317
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3317
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5142  Z= 0.165
  Angle     :  0.487   6.047   6973  Z= 0.259
  Chirality :  0.040   0.137    751
  Planarity :  0.004   0.043    914
  Dihedral  :  4.062  15.593    718
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.40 %
    Favored  : 88.32 %
  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:  1.06 (0.60), residues: 88
  sheet:  0.77 (0.44), residues: 138
  loop : -0.38 (0.30), residues: 419

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   0.015   0.001   TYR L  32 
 ARG   0.012   0.001   ARG A 286 

*********************** 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
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7734 (mm-30)
REVERT: A  426 ASP cc_start: 0.8852 (t0) cc_final: 0.8378 (t0)
REVERT: A  539 TYR cc_start: 0.7792 (p90) cc_final: 0.7452 (p90)
REVERT: A  559 ASP cc_start: 0.6901 (t70) cc_final: 0.6608 (t70)
REVERT: H  105 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7947 (pm20)
REVERT: L   32 TYR cc_start: 0.7804 (m-10) cc_final: 0.7131 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1988
  time to fit residues: 16.6726
Evaluate side-chains
  66 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
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   30 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 2 optimal weight:    0.0670
   chunk 7 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 29 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0770
   chunk 12 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0570
   overall best weight:    0.2594

-------------------------------------------------------------------------------
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 = 0.3824 r_free = 0.3824 target = 0.154301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.125296 restraints weight = 12318.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 4.08
r_work: 0.3275 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5142  Z= 0.147
  Angle     :  0.477   5.617   6973  Z= 0.252
  Chirality :  0.040   0.137    751
  Planarity :  0.004   0.043    914
  Dihedral  :  3.889  15.251    718
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.85 %
    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:  0.08 (0.33), residues: 645
  helix:  0.75 (0.59), residues: 94
  sheet:  0.81 (0.44), residues: 138
  loop : -0.35 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 347 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.013   0.001   TYR L  32 
 ARG   0.010   0.001   ARG A 286 

*********************** 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
  75 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7793 (mm-30)
REVERT: A  426 ASP cc_start: 0.8818 (t0) cc_final: 0.8394 (t0)
REVERT: A  539 TYR cc_start: 0.7821 (p90) cc_final: 0.7466 (p90)
REVERT: A  559 ASP cc_start: 0.6896 (t70) cc_final: 0.6564 (t70)
REVERT: H  105 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7958 (pm20)
REVERT: L   32 TYR cc_start: 0.7756 (m-10) cc_final: 0.7126 (m-10)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1777
  time to fit residues: 15.9781
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  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 GLU
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   30 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
Chi-restraints excluded: chain L residue   96 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0570
   chunk 25 optimal weight:    0.0970
   chunk 43 optimal weight:    0.0770
   chunk 6 optimal weight:    0.3980
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.2454

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.154611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.126367 restraints weight = 9375.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 3.77
r_work: 0.3325 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5142  Z= 0.146
  Angle     :  0.476   5.620   6973  Z= 0.251
  Chirality :  0.040   0.138    751
  Planarity :  0.004   0.040    914
  Dihedral  :  3.827  15.082    718
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.95 %
    Favored  : 87.59 %
  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:  0.25 (0.33), residues: 645
  helix:  1.25 (0.60), residues: 88
  sheet:  0.80 (0.44), residues: 138
  loop : -0.27 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  96 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.012   0.001   TYR L  32 
 ARG   0.010   0.001   ARG A 286 

********************** 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
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7778 (mm-30)
REVERT: A  426 ASP cc_start: 0.8805 (t0) cc_final: 0.8391 (t0)
REVERT: A  539 TYR cc_start: 0.7814 (p90) cc_final: 0.7457 (p90)
REVERT: A  559 ASP cc_start: 0.6900 (t70) cc_final: 0.6563 (t70)
REVERT: H  105 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7952 (pm20)
REVERT: L   32 TYR cc_start: 0.7714 (m-10) cc_final: 0.7086 (m-10)
  outliers start: 8
  outliers final: 7
  residues processed: 66
  average time/residue: 0.2089
  time to fit residues: 17.5727
Evaluate side-chains
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 GLU
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   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   95 THR
Chi-restraints excluded: chain L residue   96 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.0170
   chunk 23 optimal weight:    4.9990
   chunk 59 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0270
   chunk 52 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.3676

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.153674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123682 restraints weight = 12582.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 4.64
r_work: 0.3264 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3251
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3251
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5142  Z= 0.162
  Angle     :  0.482   5.517   6973  Z= 0.254
  Chirality :  0.040   0.141    751
  Planarity :  0.004   0.040    914
  Dihedral  :  3.858  15.121    718
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.22 %
    Favored  : 87.77 %
  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 (0.33), residues: 645
  helix:  1.25 (0.59), residues: 88
  sheet:  0.72 (0.44), residues: 138
  loop : -0.28 (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   0.009   0.001   ARG A 286 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3374.39 seconds
wall clock time: 60 minutes 39.72 seconds (3639.72 seconds total)