Starting phenix.real_space_refine
on Wed Sep 17 05:21:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9clp_45728/09_2025/9clp_45728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9clp_45728/09_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_45728/09_2025/9clp_45728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9clp_45728/09_2025/9clp_45728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9clp_45728/09_2025/9clp_45728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9clp_45728/09_2025/9clp_45728.cif"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.04, per 1000 atoms: 0.41
  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: 0.43
  Conformation dependent library (CDL) restraints added in 332.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  
  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: 0.21
  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: 0.65

  Time building geometry restraints manager: 0.60 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:             12.310
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.630
  Find NCS groups from input model:        0.020
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.811   5164  Z= 0.394
  Angle     :  0.527   4.302   7011  Z= 0.307
  Chirality :  0.040   0.132    751
  Planarity :  0.005   0.068    914
  Dihedral  : 12.339  86.297   1855
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG H  66 
 TYR   0.011   0.001   TYR A 239 
 PHE   0.008   0.001   PHE A 273 
 TRP   0.029   0.002   TRP H  96 
 HIS   0.011   0.001   HIS A 347 

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

*********************** 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  : 0.215 
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: 0.0817
  time to fit residues: 8.3199
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  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.144926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.114761 restraints weight = 8234.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 3.16
r_work: 0.3228 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5164  Z= 0.164
  Angle     :  0.567   4.352   7011  Z= 0.310
  Chirality :  0.044   0.149    751
  Planarity :  0.005   0.043    914
  Dihedral  :  4.448  18.568    718
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  5.47 %
    Favored  : 93.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.34), residues: 645
  helix:  0.54 (0.57), residues: 94
  sheet:  1.10 (0.46), residues: 132
  loop : -0.11 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 457 
 TYR   0.018   0.002   TYR A 548 
 PHE   0.015   0.002   PHE A 362 
 TRP   0.022   0.002   TRP H  96 
 HIS   0.005   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 5142)
  covalent geometry    : angle       0.56459 ( 6973)
  SS BOND              : bond        0.00322 (   19)
  SS BOND              : angle       0.85449 (   38)
  hydrogen bonds       : bond        0.04507 (  148)
  hydrogen bonds       : angle       5.27694 (  372)
  metal coordination   : bond        0.01206 (    3)

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

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: A  426 ASP cc_start: 0.8715 (t0) cc_final: 0.8290 (t0)
REVERT: A  467 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7948 (mtt90)
  outliers start: 6
  outliers final: 4
  residues processed: 71
  average time/residue: 0.0773
  time to fit residues: 7.2892
Evaluate side-chains
  64 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0980
   chunk 25 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.152899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.122784 restraints weight = 12967.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.99
r_work: 0.3205 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    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 = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5164  Z= 0.129
  Angle     :  0.515   4.383   7011  Z= 0.281
  Chirality :  0.042   0.143    751
  Planarity :  0.004   0.048    914
  Dihedral  :  4.377  17.114    718
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.30 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.34), residues: 645
  helix:  0.87 (0.59), residues: 89
  sheet:  1.15 (0.45), residues: 137
  loop : -0.19 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 286 
 TYR   0.016   0.001   TYR A 548 
 PHE   0.007   0.001   PHE L  62 
 TRP   0.017   0.001   TRP H  96 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5142)
  covalent geometry    : angle       0.51384 ( 6973)
  SS BOND              : bond        0.00252 (   19)
  SS BOND              : angle       0.71391 (   38)
  hydrogen bonds       : bond        0.03762 (  148)
  hydrogen bonds       : angle       4.95334 (  372)
  metal coordination   : bond        0.00339 (    3)

*********************** 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: 6
    poor density    : 64
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7739 (mm-30)
REVERT: A  426 ASP cc_start: 0.8763 (t0) cc_final: 0.8314 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 66
  average time/residue: 0.0978
  time to fit residues: 8.3664
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  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0000
   chunk 50 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.4384

-------------------------------------------------------------------------------
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 = 0.155232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125712 restraints weight = 11989.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 4.00
r_work: 0.3236 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    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 = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5164  Z= 0.115
  Angle     :  0.493   4.415   7011  Z= 0.267
  Chirality :  0.041   0.141    751
  Planarity :  0.004   0.044    914
  Dihedral  :  4.219  15.471    718
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.94 %
    Favored  : 89.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.33), residues: 645
  helix:  0.92 (0.59), residues: 88
  sheet:  1.03 (0.45), residues: 137
  loop : -0.24 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 286 
 TYR   0.017   0.001   TYR A 539 
 PHE   0.006   0.001   PHE A 273 
 TRP   0.014   0.001   TRP H  96 
 HIS   0.003   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5142)
  covalent geometry    : angle       0.49093 ( 6973)
  SS BOND              : bond        0.00329 (   19)
  SS BOND              : angle       0.72639 (   38)
  hydrogen bonds       : bond        0.03399 (  148)
  hydrogen bonds       : angle       4.76331 (  372)
  metal coordination   : bond        0.00300 (    3)

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

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7909 (tpt) cc_final: 0.7559 (tpp)
REVERT: A  252 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7752 (mm-30)
REVERT: A  426 ASP cc_start: 0.8781 (t0) cc_final: 0.8366 (t0)
REVERT: A  539 TYR cc_start: 0.7865 (p90) cc_final: 0.7665 (p90)
REVERT: L   32 TYR cc_start: 0.7820 (m-10) cc_final: 0.7201 (m-10)
  outliers start: 6
  outliers final: 4
  residues processed: 66
  average time/residue: 0.0890
  time to fit residues: 7.5770
Evaluate side-chains
  64 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 VAL
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 59 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0030
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0040
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0010
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.2608

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.150937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.121894 restraints weight = 9462.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 3.67
r_work: 0.3357 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5164  Z= 0.094
  Angle     :  0.475   4.629   7011  Z= 0.255
  Chirality :  0.040   0.137    751
  Planarity :  0.004   0.050    914
  Dihedral  :  3.985  15.250    718
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.94 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.33), residues: 645
  helix:  1.00 (0.60), residues: 88
  sheet:  1.02 (0.45), residues: 137
  loop : -0.21 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 286 
 TYR   0.016   0.001   TYR A 539 
 PHE   0.006   0.001   PHE A 273 
 TRP   0.013   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 5142)
  covalent geometry    : angle       0.47452 ( 6973)
  SS BOND              : bond        0.00201 (   19)
  SS BOND              : angle       0.58830 (   38)
  hydrogen bonds       : bond        0.03028 (  148)
  hydrogen bonds       : angle       4.59529 (  372)
  metal coordination   : bond        0.00163 (    3)

*********************** 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
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7931 (tpt) cc_final: 0.7575 (tpp)
REVERT: A  252 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: A  426 ASP cc_start: 0.8788 (t0) cc_final: 0.8288 (t0)
REVERT: A  457 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7285 (mtm-85)
REVERT: A  539 TYR cc_start: 0.7903 (p90) cc_final: 0.7633 (p90)
REVERT: L   32 TYR cc_start: 0.7791 (m-10) cc_final: 0.7232 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0936
  time to fit residues: 7.9886
Evaluate side-chains
  70 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
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   75 ILE
Chi-restraints excluded: chain L residue   95 THR
Chi-restraints excluded: chain L residue   96 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0670
   chunk 35 optimal weight:    0.0370
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.2196

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.152202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.124373 restraints weight = 6205.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.68
r_work: 0.3380 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5164  Z= 0.087
  Angle     :  0.462   4.938   7011  Z= 0.246
  Chirality :  0.040   0.138    751
  Planarity :  0.004   0.051    914
  Dihedral  :  3.815  15.497    718
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.94 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.33), residues: 645
  helix:  1.01 (0.60), residues: 88
  sheet:  1.06 (0.45), residues: 137
  loop : -0.17 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 286 
 TYR   0.015   0.001   TYR A 539 
 PHE   0.006   0.001   PHE A 273 
 TRP   0.011   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 5142)
  covalent geometry    : angle       0.46149 ( 6973)
  SS BOND              : bond        0.00193 (   19)
  SS BOND              : angle       0.50516 (   38)
  hydrogen bonds       : bond        0.02903 (  148)
  hydrogen bonds       : angle       4.51508 (  372)
  metal coordination   : bond        0.00133 (    3)

*********************** 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: 7
    poor density    : 65
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7850 (tpt) cc_final: 0.7496 (tpp)
REVERT: A  252 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7669 (mm-30)
REVERT: A  426 ASP cc_start: 0.8782 (t0) cc_final: 0.8291 (t0)
REVERT: A  539 TYR cc_start: 0.7907 (p90) cc_final: 0.7587 (p90)
REVERT: L   32 TYR cc_start: 0.7687 (m-10) cc_final: 0.7109 (m-10)
  outliers start: 7
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0992
  time to fit residues: 8.3298
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  : 0.202 
-------------------------------------------------------------------------------
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
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 22 optimal weight:    0.0040
   chunk 58 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0470
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.3290

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.149801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.120830 restraints weight = 12312.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 3.80
r_work: 0.3327 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3342
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3342 r_free = 0.3342    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 = 0.3342 r_free = 0.3342    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3342
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5164  Z= 0.097
  Angle     :  0.476   5.987   7011  Z= 0.250
  Chirality :  0.040   0.142    751
  Planarity :  0.004   0.042    914
  Dihedral  :  3.807  15.177    718
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.12 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.33), residues: 645
  helix:  1.11 (0.59), residues: 88
  sheet:  1.04 (0.45), residues: 137
  loop : -0.18 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 286 
 TYR   0.013   0.001   TYR A 539 
 PHE   0.006   0.001   PHE A 273 
 TRP   0.010   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 5142)
  covalent geometry    : angle       0.47595 ( 6973)
  SS BOND              : bond        0.00205 (   19)
  SS BOND              : angle       0.51975 (   38)
  hydrogen bonds       : bond        0.02990 (  148)
  hydrogen bonds       : angle       4.48883 (  372)
  metal coordination   : bond        0.00250 (    3)

*********************** 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
  69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7904 (tpt) cc_final: 0.7549 (tpp)
REVERT: A  252 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7762 (mm-30)
REVERT: A  426 ASP cc_start: 0.8785 (t0) cc_final: 0.8285 (t0)
REVERT: A  539 TYR cc_start: 0.7906 (p90) cc_final: 0.7585 (p90)
REVERT: H  105 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7869 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0961
  time to fit residues: 7.5880
Evaluate side-chains
  65 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  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 3 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0270
   chunk 59 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.151123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.122320 restraints weight = 7895.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 3.08
r_work: 0.3319 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5164  Z= 0.135
  Angle     :  0.511   5.260   7011  Z= 0.272
  Chirality :  0.041   0.145    751
  Planarity :  0.004   0.040    914
  Dihedral  :  4.061  15.731    718
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.31 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.33), residues: 645
  helix:  0.96 (0.59), residues: 90
  sheet:  0.91 (0.45), residues: 137
  loop : -0.26 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 286 
 TYR   0.013   0.001   TYR H  91 
 PHE   0.007   0.001   PHE A 273 
 TRP   0.013   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5142)
  covalent geometry    : angle       0.51029 ( 6973)
  SS BOND              : bond        0.00288 (   19)
  SS BOND              : angle       0.65935 (   38)
  hydrogen bonds       : bond        0.03458 (  148)
  hydrogen bonds       : angle       4.58326 (  372)
  metal coordination   : bond        0.00486 (    3)

*********************** 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
  71 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7935 (tpt) cc_final: 0.7565 (tpp)
REVERT: A  224 ILE cc_start: 0.7195 (mt) cc_final: 0.6949 (mt)
REVERT: A  252 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7687 (mm-30)
REVERT: A  426 ASP cc_start: 0.8769 (t0) cc_final: 0.8280 (t0)
REVERT: A  539 TYR cc_start: 0.7922 (p90) cc_final: 0.7623 (p90)
REVERT: H  105 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7911 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0869
  time to fit residues: 7.2933
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  : 0.206 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.148873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121774 restraints weight = 6013.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.67
r_work: 0.3331 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5164  Z= 0.154
  Angle     :  0.533   6.136   7011  Z= 0.284
  Chirality :  0.042   0.144    751
  Planarity :  0.004   0.047    914
  Dihedral  :  4.316  16.060    718
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.31 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.33), residues: 645
  helix:  1.07 (0.60), residues: 89
  sheet:  0.72 (0.45), residues: 137
  loop : -0.42 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 286 
 TYR   0.022   0.002   TYR L  32 
 PHE   0.007   0.001   PHE A 273 
 TRP   0.014   0.001   TRP H  96 
 HIS   0.003   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5142)
  covalent geometry    : angle       0.53201 ( 6973)
  SS BOND              : bond        0.00328 (   19)
  SS BOND              : angle       0.72130 (   38)
  hydrogen bonds       : bond        0.03676 (  148)
  hydrogen bonds       : angle       4.68278 (  372)
  metal coordination   : bond        0.00541 (    3)

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

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 ILE cc_start: 0.7139 (mt) cc_final: 0.6889 (mt)
REVERT: A  252 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7630 (mm-30)
REVERT: A  391 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7969 (mtpp)
REVERT: A  426 ASP cc_start: 0.8802 (t0) cc_final: 0.8415 (t0)
REVERT: A  539 TYR cc_start: 0.7924 (p90) cc_final: 0.7635 (p90)
REVERT: A  559 ASP cc_start: 0.7264 (t70) cc_final: 0.6790 (t0)
REVERT: H  105 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7935 (pm20)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.0841
  time to fit residues: 7.3904
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  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   45 LYS
Chi-restraints excluded: chain L residue   95 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0060
   chunk 6 optimal weight:    0.3980
   chunk 14 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.150992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.122570 restraints weight = 9688.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 3.75
r_work: 0.3256 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
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      :  0.003   0.035   5164  Z= 0.116
  Angle     :  0.500   5.957   7011  Z= 0.266
  Chirality :  0.041   0.139    751
  Planarity :  0.004   0.047    914
  Dihedral  :  4.138  15.747    718
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.12 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.33), residues: 645
  helix:  1.09 (0.59), residues: 89
  sheet:  0.67 (0.45), residues: 138
  loop : -0.38 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 286 
 TYR   0.032   0.001   TYR L  32 
 PHE   0.007   0.001   PHE A 273 
 TRP   0.013   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5142)
  covalent geometry    : angle       0.49918 ( 6973)
  SS BOND              : bond        0.00254 (   19)
  SS BOND              : angle       0.63321 (   38)
  hydrogen bonds       : bond        0.03302 (  148)
  hydrogen bonds       : angle       4.58883 (  372)
  metal coordination   : bond        0.00332 (    3)

********************** 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
  74 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7734 (mm-30)
REVERT: A  426 ASP cc_start: 0.8827 (t0) cc_final: 0.8398 (t0)
REVERT: A  539 TYR cc_start: 0.7915 (p90) cc_final: 0.7598 (p90)
REVERT: A  559 ASP cc_start: 0.7164 (t70) cc_final: 0.6737 (t0)
REVERT: H  105 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.7963 (pm20)
  outliers start: 11
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0785
  time to fit residues: 6.7086
Evaluate side-chains
  72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   45 LYS
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 45 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 48 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.149997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121293 restraints weight = 8022.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.11
r_work: 0.3267 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5164  Z= 0.133
  Angle     :  0.517   5.828   7011  Z= 0.275
  Chirality :  0.041   0.140    751
  Planarity :  0.004   0.046    914
  Dihedral  :  4.169  15.715    718
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  9.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.33), residues: 645
  helix:  1.54 (0.60), residues: 83
  sheet:  0.63 (0.45), residues: 138
  loop : -0.38 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 286 
 TYR   0.023   0.001   TYR L  32 
 PHE   0.007   0.001   PHE A 273 
 TRP   0.013   0.001   TRP H  96 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5142)
  covalent geometry    : angle       0.51555 ( 6973)
  SS BOND              : bond        0.00286 (   19)
  SS BOND              : angle       0.67503 (   38)
  hydrogen bonds       : bond        0.03447 (  148)
  hydrogen bonds       : angle       4.64105 (  372)
  metal coordination   : bond        0.00443 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1791.62 seconds
wall clock time: 31 minutes 26.65 seconds (1886.65 seconds total)