Starting phenix.real_space_refine
on Thu Mar  6 05:32:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9clp_45728/03_2025/9clp_45728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9clp_45728/03_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_45728/03_2025/9clp_45728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9clp_45728/03_2025/9clp_45728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9clp_45728/03_2025/9clp_45728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9clp_45728/03_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-5624/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: 9.19, per 1000 atoms: 1.83
  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: 1.58
  Conformation dependent library (CDL) restraints added in 1.3 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: 1.06
  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: 2.22

  Time building geometry restraints manager: 1.71 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:             85.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     27.800
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  116.870
-------------------------------------------------------------------------------
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  : 0.623 
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: 0.2644
  time to fit residues: 26.9553
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  : 0.587 
-------------------------------------------------------------------------------
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 = 36)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119778 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: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
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  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: A  303 LEU cc_start: 0.8462 (mt) cc_final: 0.8232 (mt)
REVERT: A  426 ASP cc_start: 0.8698 (t0) cc_final: 0.8241 (t0)
REVERT: A  539 TYR cc_start: 0.7725 (p90) cc_final: 0.7523 (p90)
REVERT: L   32 TYR cc_start: 0.7549 (m-10) cc_final: 0.6928 (m-10)
  outliers start: 4
  outliers final: 3
  residues processed: 69
  average time/residue: 0.2010
  time to fit residues: 19.5400
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  : 0.628 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   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:    0.5980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.146275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.116553 restraints weight = 7859.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 3.06
r_work: 0.3296 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    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 = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5142  Z= 0.227
  Angle     :  0.532   4.374   6973  Z= 0.290
  Chirality :  0.043   0.145    751
  Planarity :  0.005   0.049    914
  Dihedral  :  4.365  16.613    718
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  6.57 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.38 (0.34), residues: 645
  helix:  0.73 (0.58), residues: 89
  sheet:  1.22 (0.45), residues: 137
  loop : -0.15 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP H  96 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.016   0.001   TYR A 548 
 ARG   0.009   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
  70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 1.655 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7678 (mm-30)
REVERT: A  426 ASP cc_start: 0.8741 (t0) cc_final: 0.8342 (t0)
REVERT: A  539 TYR cc_start: 0.7855 (p90) cc_final: 0.7572 (p90)
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.2285
  time to fit residues: 19.9818
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  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   73 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:    2.9990
   chunk 42 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.154361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.125171 restraints weight = 9229.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 3.64
r_work: 0.3324 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3236
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1799

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= 0.207
  Angle     :  0.506   4.439   6973  Z= 0.275
  Chirality :  0.042   0.141    751
  Planarity :  0.004   0.046    914
  Dihedral  :  4.289  16.013    718
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.21 %
    Favored  : 90.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.33), residues: 645
  helix:  0.76 (0.59), residues: 88
  sheet:  1.07 (0.45), residues: 137
  loop : -0.22 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   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   0.011   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  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: A  426 ASP cc_start: 0.8769 (t0) cc_final: 0.8352 (t0)
REVERT: A  539 TYR cc_start: 0.7894 (p90) cc_final: 0.7557 (p90)
REVERT: A  559 ASP cc_start: 0.7086 (t70) cc_final: 0.6706 (t70)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 0.3021
  time to fit residues: 26.6040
Evaluate side-chains
  67 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain L residue   96 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 61 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0870
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.152417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124749 restraints weight = 8164.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.98
r_work: 0.3255 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5142  Z= 0.235
  Angle     :  0.520   4.430   6973  Z= 0.281
  Chirality :  0.042   0.141    751
  Planarity :  0.004   0.052    914
  Dihedral  :  4.336  16.238    718
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  8.94 %
    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:  0.01 (0.33), residues: 645
  helix:  0.46 (0.58), residues: 94
  sheet:  0.90 (0.44), residues: 137
  loop : -0.39 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  96 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.008   0.001   PHE L  62 
 TYR   0.014   0.001   TYR A 548 
 ARG   0.011   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
  72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: A  426 ASP cc_start: 0.8794 (t0) cc_final: 0.8368 (t0)
REVERT: A  539 TYR cc_start: 0.7905 (p90) cc_final: 0.7594 (p90)
REVERT: A  559 ASP cc_start: 0.7159 (t70) cc_final: 0.6689 (t70)
REVERT: L   32 TYR cc_start: 0.7856 (m-10) cc_final: 0.7161 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 68
  average time/residue: 0.3030
  time to fit residues: 27.0855
Evaluate side-chains
  66 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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 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:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 64 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.148582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.119367 restraints weight = 7934.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 3.03
r_work: 0.3318 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5142  Z= 0.178
  Angle     :  0.492   4.702   6973  Z= 0.263
  Chirality :  0.041   0.137    751
  Planarity :  0.004   0.052    914
  Dihedral  :  4.158  15.327    718
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.21 %
    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:  0.03 (0.33), residues: 645
  helix:  0.52 (0.58), residues: 94
  sheet:  0.83 (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   0.013   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
  72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7681 (mm-30)
REVERT: A  426 ASP cc_start: 0.8798 (t0) cc_final: 0.8296 (t0)
REVERT: A  539 TYR cc_start: 0.7866 (p90) cc_final: 0.7528 (p90)
REVERT: A  559 ASP cc_start: 0.7032 (t70) cc_final: 0.6788 (t70)
REVERT: H  105 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7916 (pm20)
REVERT: L   45 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7412 (ttpt)
  outliers start: 9
  outliers final: 7
  residues processed: 65
  average time/residue: 0.2693
  time to fit residues: 23.5968
Evaluate side-chains
  72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
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 H residue  105 GLN
Chi-restraints excluded: chain L residue   45 LYS
Chi-restraints excluded: chain L residue   95 THR
Chi-restraints excluded: chain L residue   96 VAL
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:    1.9990
   chunk 40 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.151845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.122881 restraints weight = 9908.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 3.68
r_work: 0.3234 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5142  Z= 0.232
  Angle     :  0.519   5.601   6973  Z= 0.277
  Chirality :  0.042   0.140    751
  Planarity :  0.004   0.043    914
  Dihedral  :  4.279  16.014    718
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.94 %
    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: -0.06 (0.33), residues: 645
  helix:  0.45 (0.58), residues: 94
  sheet:  0.78 (0.44), residues: 137
  loop : -0.42 (0.30), residues: 414

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   0.008   0.001   PHE L  62 
 TYR   0.013   0.001   TYR A 548 
 ARG   0.011   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
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: A  426 ASP cc_start: 0.8805 (t0) cc_final: 0.8398 (t0)
REVERT: A  539 TYR cc_start: 0.7872 (p90) cc_final: 0.7534 (p90)
REVERT: A  559 ASP cc_start: 0.7138 (t70) cc_final: 0.6864 (t70)
REVERT: H  105 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7940 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 68
  average time/residue: 0.2027
  time to fit residues: 17.9460
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  : 0.575 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.1980
   chunk 55 optimal weight:    0.4980
   chunk 47 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.153745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.125434 restraints weight = 9291.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 3.21
r_work: 0.3281 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5142  Z= 0.177
  Angle     :  0.491   5.359   6973  Z= 0.262
  Chirality :  0.041   0.137    751
  Planarity :  0.004   0.037    914
  Dihedral  :  4.105  15.800    718
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.67 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.33), residues: 645
  helix:  0.56 (0.58), residues: 94
  sheet:  0.81 (0.44), residues: 137
  loop : -0.39 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  96 
 HIS   0.003   0.000   HIS A 341 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.022   0.001   TYR L  32 
 ARG   0.009   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
  70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7668 (mm-30)
REVERT: A  426 ASP cc_start: 0.8799 (t0) cc_final: 0.8340 (t0)
REVERT: A  539 TYR cc_start: 0.7872 (p90) cc_final: 0.7537 (p90)
REVERT: A  559 ASP cc_start: 0.7090 (t70) cc_final: 0.6786 (t70)
  outliers start: 9
  outliers final: 8
  residues processed: 62
  average time/residue: 0.2236
  time to fit residues: 19.3190
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  : 0.626 
-------------------------------------------------------------------------------
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   75 ILE
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:    0.2980
   chunk 7 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0770
   chunk 12 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.3938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.151950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.123250 restraints weight = 12290.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 3.95
r_work: 0.3280 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    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 = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2239

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= 0.173
  Angle     :  0.494   6.006   6973  Z= 0.262
  Chirality :  0.040   0.138    751
  Planarity :  0.004   0.047    914
  Dihedral  :  4.041  15.675    718
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.49 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.33), residues: 645
  helix:  1.07 (0.60), residues: 88
  sheet:  0.79 (0.45), residues: 137
  loop : -0.32 (0.30), residues: 420

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   0.019   0.001   TYR L  32 
 ARG   0.012   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
  76 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7764 (mm-30)
REVERT: A  426 ASP cc_start: 0.8833 (t0) cc_final: 0.8379 (t0)
REVERT: A  539 TYR cc_start: 0.7843 (p90) cc_final: 0.7489 (p90)
REVERT: A  559 ASP cc_start: 0.6964 (t70) cc_final: 0.6621 (t70)
REVERT: H  105 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7976 (pm20)
  outliers start: 10
  outliers final: 9
  residues processed: 68
  average time/residue: 0.1959
  time to fit residues: 17.0898
Evaluate side-chains
  75 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
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    5 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   45 LYS
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 56 optimal weight:    0.1980
   chunk 26 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0170
   chunk 10 optimal weight:    0.0010
   overall best weight:    0.3224

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.153479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.124941 restraints weight = 9370.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 3.73
r_work: 0.3291 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3319
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2274

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= 0.157
  Angle     :  0.485   5.886   6973  Z= 0.256
  Chirality :  0.040   0.138    751
  Planarity :  0.004   0.047    914
  Dihedral  :  3.914  15.405    718
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.85 %
    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:  0.23 (0.34), residues: 645
  helix:  1.18 (0.60), residues: 88
  sheet:  0.81 (0.45), residues: 137
  loop : -0.28 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 337 
 PHE   0.006   0.001   PHE A 273 
 TYR   0.017   0.001   TYR L  32 
 ARG   0.011   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: 9
    poor density    : 64
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7752 (mm-30)
REVERT: A  426 ASP cc_start: 0.8807 (t0) cc_final: 0.8382 (t0)
REVERT: A  539 TYR cc_start: 0.7829 (p90) cc_final: 0.7469 (p90)
REVERT: H  105 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.7966 (pm20)
REVERT: L   32 TYR cc_start: 0.7754 (m-10) cc_final: 0.7085 (m-10)
  outliers start: 9
  outliers final: 7
  residues processed: 66
  average time/residue: 0.3181
  time to fit residues: 26.8494
Evaluate side-chains
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.0370
   chunk 23 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0060
   chunk 38 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0020
   chunk 52 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.2282

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.154734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.124284 restraints weight = 12554.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 4.74
r_work: 0.3245 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5142  Z= 0.147
  Angle     :  0.480   5.871   6973  Z= 0.252
  Chirality :  0.039   0.137    751
  Planarity :  0.004   0.044    914
  Dihedral  :  3.779  15.030    718
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.04 %
    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:  0.27 (0.34), residues: 645
  helix:  1.26 (0.61), residues: 88
  sheet:  0.81 (0.45), residues: 137
  loop : -0.24 (0.31), residues: 420

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   0.005   0.001   PHE A 273 
 TYR   0.016   0.001   TYR L  32 
 ARG   0.011   0.001   ARG A 286 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4231.96 seconds
wall clock time: 78 minutes 19.74 seconds (4699.74 seconds total)