Starting phenix.real_space_refine
on Sun Oct 25 18:20:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dpl_47106/10_2026/9dpl_47106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dpl_47106/10_2026/9dpl_47106.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dpl_47106/10_2026/9dpl_47106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dpl_47106/10_2026/9dpl_47106.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dpl_47106/10_2026/9dpl_47106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dpl_47106/10_2026/9dpl_47106.cif"
  }
  resolution = 2.8
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8237 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     P      79      5.49       5
     Mg      2      5.21       5
     S      62      5.16       5
     Na      2      4.78       5
     C    6424      2.51       5
     N    1809      2.21       5
     O    2177      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.12s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10555
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 4387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4387
          Classifications: {'peptide': 541}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 510}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 507, 4107
          Classifications: {'peptide': 507}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 477}
    Chain: "C"
      Number of atoms: 1665
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 76, 1643
          Unusual residues: {'12A%rna2p': 1}
          Classifications: {'RNA': 72, 'RNAv2': 3, 'undetermined': 1}
          Modifications used: {'rna2p': 6, 'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p': 7, 'rna3p_pur': 27, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 14, 'rna3p': 61}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 7
      Conformer: "B"
        Number of residues, atoms: 76, 1643
          Unusual residues: {'12A%rna2p': 1}
          Classifications: {'RNA': 72, 'RNAv2': 3, 'undetermined': 1}
          Modifications used: {'rna2p': 6, 'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p': 7, 'rna3p_pur': 27, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 14, 'rna3p': 61}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 7
          bond proxies already assigned to first conformer: 1807
    Chain: "D"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 163
          Classifications: {'peptide': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 16}
    Chain: "E"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 163
          Classifications: {'peptide': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 16}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'AMP%rna3p': 1}
          Classifications: {'RNA_mixed': 1}
          Modifications used: {'rna3p': 1}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 1}
          Modifications used: {'rna2p': 1}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 2, ' NA': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A  A C  76 " occ=0.44
      ... (42 atoms not shown)
      pdb=" C4 B  A C  76 " occ=0.56
  Time building chain proxies: 2.74, per 1000 atoms: 0.26
  Number of scatterers: 10555
  At special positions: 0
  Unit cell: (87.74, 100.58, 135.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      62     16.00
     P      79     15.00
     Mg      2     11.99
     Na      2     11.00
     O    2177      8.00
     N    1809      7.00
     C    6424      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.13
  Conformation dependent library (CDL) restraints added in 388.5 milliseconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2046

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      40.1% alpha, 20.1% beta
      20 base pairs and 41 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 41
    Processing helix  chain 'A' and resid 75 through 90
    Processing helix  chain 'A' and resid 104 through 113
    Processing helix  chain 'A' and resid 165 through 176
    Processing helix  chain 'A' and resid 222 through 229
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 238 through 262
      removed outlier: 3.551A  pdb=" N   GLN A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 311
    Processing helix  chain 'A' and resid 346 through 367
      removed outlier: 3.563A  pdb=" N   GLU A 352 " --> pdb=" O   HIS A 348 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A 355 " --> pdb=" O   MET A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 405
    Processing helix  chain 'A' and resid 416 through 430
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 504 through 521
      removed outlier: 3.888A  pdb=" N   ALA A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
      removed outlier: 3.727A  pdb=" N   MET A 527 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 540
      removed outlier: 3.654A  pdb=" N   CYS A 534 " --> pdb=" O   ASP A 530 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 535 " --> pdb=" O   GLU A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'A' and resid 563 through 567
    Processing helix  chain 'B' and resid 72 through 90
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 165 through 174
    Processing helix  chain 'B' and resid 222 through 229
    Processing helix  chain 'B' and resid 229 through 237
    Processing helix  chain 'B' and resid 238 through 262
      removed outlier: 3.734A  pdb=" N   GLN B 242 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 311
    Processing helix  chain 'B' and resid 346 through 367
      removed outlier: 3.865A  pdb=" N   GLU B 352 " --> pdb=" O   HIS B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 405
    Processing helix  chain 'B' and resid 410 through 414
      removed outlier: 3.934A  pdb=" N   PHE B 414 " --> pdb=" O   THR B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 430
    Processing helix  chain 'B' and resid 439 through 452
    Processing helix  chain 'B' and resid 453 through 456
      removed outlier: 3.556A  pdb=" N   CYS B 456 " --> pdb=" O   GLU B 453 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 453 through 456'
    Processing helix  chain 'B' and resid 466 through 470
    Processing helix  chain 'B' and resid 504 through 521
    Processing helix  chain 'B' and resid 530 through 538
      removed outlier: 3.670A  pdb=" N   CYS B 534 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 560
    Processing helix  chain 'B' and resid 563 through 568
      removed outlier: 3.556A  pdb=" N   LEU B 568 " --> pdb=" O   LYS B 565 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 137
      removed outlier: 3.530A  pdb=" N   ARG A 131 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASP A 146 " --> pdb=" O   HIS A 133 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS A 135 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   PHE A 144 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   ALA A 137 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   LEU A 142 " --> pdb=" O   ALA A 137 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   LYS A 153 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 8.925A  pdb=" N   ILE A 198 " --> pdb=" O   LYS A 153 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   GLN A 155 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   MET A 157 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 9.228A  pdb=" N   GLU A 202 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 10.831A  pdb=" N   ASN A 159 " --> pdb=" O   GLU A 202 " (cutoff:3.500A)
      removed outlier: 13.194A  pdb=" N   THR A 204 " --> pdb=" O   ASN A 159 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   GLN A 185 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   ILE A 203 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   GLY A 183 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   ILE A 181 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265
      removed outlier: 5.922A  pdb=" N   LEU A 264 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   ILE A 318 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ILE A 495 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   GLU A 494 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL A 490 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ARG A 392 " --> pdb=" O   PHE A 461 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   CYS A 463 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ILE A 394 " --> pdb=" O   CYS A 463 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272
    Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373
    Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 137
      removed outlier: 6.267A  pdb=" N   ASP B 146 " --> pdb=" O   HIS B 133 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   LYS B 135 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   PHE B 144 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   ALA B 137 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   LEU B 142 " --> pdb=" O   ALA B 137 " (cutoff:3.500A)
      removed outlier: 8.664A  pdb=" N   LYS B 153 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 8.873A  pdb=" N   ILE B 198 " --> pdb=" O   LYS B 153 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLN B 155 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   MET B 157 " --> pdb=" O   PRO B 200 " (cutoff:3.500A)
      removed outlier: 9.362A  pdb=" N   GLU B 202 " --> pdb=" O   MET B 157 " (cutoff:3.500A)
      removed outlier: 10.543A  pdb=" N   ASN B 159 " --> pdb=" O   GLU B 202 " (cutoff:3.500A)
      removed outlier: 12.744A  pdb=" N   THR B 204 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLN B 185 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   ILE B 203 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLY B 183 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   ILE B 181 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 264 through 265
      removed outlier: 5.894A  pdb=" N   LEU B 264 " --> pdb=" O   TYR B 316 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ILE B 318 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ILE B 495 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU B 488 " --> pdb=" O   ILE B 495 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ASN B 497 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   PHE B 486 " --> pdb=" O   ASN B 497 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 271 through 272
    Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 373

    403 hydrogen bonds defined for protein.
    1149 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      53 hydrogen bonds
      94 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      41 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1685
        1.32 -     1.44: 3108
        1.44 -     1.57: 5896
        1.57 -     1.69: 156
        1.69 -     1.81: 106
  Bond restraints: 10951
  Sorted by residual:
  bond pdb=" P   2MU C  54 "
       pdb=" O5' 2MU C  54 "
    ideal  model  delta    sigma   weight residual
    1.731  1.607  0.124 2.00e-02 2.50e+03 3.86e+01
  bond pdb=" C4  AMP A 602 "
       pdb=" C5  AMP A 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.376  0.114 2.00e-02 2.50e+03 3.26e+01
  bond pdb=" C4  AMP B 602 "
       pdb=" C5  AMP B 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.379  0.111 2.00e-02 2.50e+03 3.06e+01
  bond pdb=" C   ASP A 577 "
       pdb=" N   LYS A 578 "
    ideal  model  delta    sigma   weight residual
    1.331  1.273  0.059 1.37e-02 5.33e+03 1.84e+01
  bond pdb=" CA  TYR E   9 "
       pdb=" C   TYR E   9 "
    ideal  model  delta    sigma   weight residual
    1.524  1.470  0.054 1.26e-02 6.30e+03 1.81e+01
  ... (remaining 10946 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 14377
        2.40 -     4.79: 588
        4.79 -     7.19: 161
        7.19 -     9.58: 15
        9.58 -    11.98: 5
  Bond angle restraints: 15146
  Sorted by residual:
  angle pdb=" C3' H2U C  47 "
        pdb=" C2' H2U C  47 "
        pdb=" C1' H2U C  47 "
      ideal   model   delta    sigma   weight residual
     101.30  106.52   -5.22 1.00e+00 1.00e+00 2.72e+01
  angle pdb=" CA  PHE A 218 "
        pdb=" CB  PHE A 218 "
        pdb=" CG  PHE A 218 "
      ideal   model   delta    sigma   weight residual
     113.80  118.70   -4.90 1.00e+00 1.00e+00 2.40e+01
  angle pdb=" C   TYR E   9 "
        pdb=" CA  TYR E   9 "
        pdb=" CB  TYR E   9 "
      ideal   model   delta    sigma   weight residual
     110.90  103.41    7.49 1.58e+00 4.01e-01 2.25e+01
  angle pdb=" C3' H2U C  20 "
        pdb=" C2' H2U C  20 "
        pdb=" C1' H2U C  20 "
      ideal   model   delta    sigma   weight residual
     101.30  105.99   -4.69 1.00e+00 1.00e+00 2.20e+01
  angle pdb=" N   PHE A 218 "
        pdb=" CA  PHE A 218 "
        pdb=" C   PHE A 218 "
      ideal   model   delta    sigma   weight residual
     113.55  107.75    5.80 1.26e+00 6.30e-01 2.12e+01
  ... (remaining 15141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.56: 5968
       21.56 -    43.11: 591
       43.11 -    64.67: 209
       64.67 -    86.22: 54
       86.22 -   107.78: 7
  Dihedral angle restraints: 6829
    sinusoidal: 3650
      harmonic: 3179
  Sorted by residual:
  dihedral pdb=" C5'   U C  60 "
           pdb=" C4'   U C  60 "
           pdb=" C3'   U C  60 "
           pdb=" O3'   U C  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  117.84   29.16     1      8.00e+00 1.56e-02 1.90e+01
  dihedral pdb=" C5'   G C  45 "
           pdb=" C4'   G C  45 "
           pdb=" C3'   G C  45 "
           pdb=" O3'   G C  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  119.49   27.51     1      8.00e+00 1.56e-02 1.70e+01
  dihedral pdb=" C   GLN E   5 "
           pdb=" N   GLN E   5 "
           pdb=" CA  GLN E   5 "
           pdb=" CB  GLN E   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.34  -10.26     0      2.50e+00 1.60e-01 1.68e+01
  ... (remaining 6826 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1485
       0.112 -    0.224: 139
       0.224 -    0.337: 7
       0.337 -    0.449: 48
       0.449 -    0.561: 15
  Chirality restraints: 1694
  Sorted by residual:
  chirality pdb=" P     G C   1 "
            pdb=" OP1   G C   1 "
            pdb=" OP2   G C   1 "
            pdb=" O5'   G C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.97   -0.56 2.00e-01 2.50e+01 7.87e+00
  chirality pdb=" P     G C  45 "
            pdb=" OP1   G C  45 "
            pdb=" OP2   G C  45 "
            pdb=" O5'   G C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.92   -0.51 2.00e-01 2.50e+01 6.48e+00
  chirality pdb=" P     U C  60 "
            pdb=" OP1   U C  60 "
            pdb=" OP2   U C  60 "
            pdb=" O5'   U C  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.92   -0.51 2.00e-01 2.50e+01 6.38e+00
  ... (remaining 1691 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' 70U C  34 "   -0.412 2.00e-02 2.50e+03   2.17e-01 1.06e+03
        pdb=" N1  70U C  34 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2  70U C  34 "    0.071 2.00e-02 2.50e+03
        pdb=" N3  70U C  34 "    0.044 2.00e-02 2.50e+03
        pdb=" C4  70U C  34 "   -0.031 2.00e-02 2.50e+03
        pdb=" O4  70U C  34 "   -0.320 2.00e-02 2.50e+03
        pdb=" C5  70U C  34 "    0.240 2.00e-02 2.50e+03
        pdb=" C6  70U C  34 "    0.237 2.00e-02 2.50e+03
        pdb=" S2  70U C  34 "    0.173 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' H2U C  16 "   -0.278 2.00e-02 2.50e+03   3.39e-01 8.42e+02
        pdb=" N1  H2U C  16 "    0.157 2.00e-02 2.50e+03
        pdb=" C2  H2U C  16 "    0.032 2.00e-02 2.50e+03
        pdb=" O2  H2U C  16 "    0.196 2.00e-02 2.50e+03
        pdb=" N3  H2U C  16 "   -0.279 2.00e-02 2.50e+03
        pdb=" C6  H2U C  16 "    0.686 4.00e-02 6.25e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' H2U C  20 "    0.224 2.00e-02 2.50e+03   2.62e-01 5.29e+02
        pdb=" N1  H2U C  20 "   -0.128 2.00e-02 2.50e+03
        pdb=" C2  H2U C  20 "   -0.034 2.00e-02 2.50e+03
        pdb=" O2  H2U C  20 "   -0.159 2.00e-02 2.50e+03
        pdb=" N3  H2U C  20 "    0.227 2.00e-02 2.50e+03
        pdb=" C6  H2U C  20 "   -0.518 4.00e-02 6.25e+02
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 827
        2.73 -     3.27: 9938
        3.27 -     3.82: 18665
        3.82 -     4.36: 23512
        4.36 -     4.90: 37867
  Nonbonded interactions: 90809
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 418 "
            pdb=" OE1 GLU B 418 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" N   GLN B 381 "
            pdb=" OE1 GLN B 381 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   ILE A 109 "
            pdb=" OG  SER A 113 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" NH2 ARG A 178 "
            pdb=" O   LEU A 213 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OD1 ASP A 233 "
            pdb=" ND2 ASN A 237 "
     model   vdw
     2.268 3.120
  ... (remaining 90804 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 71 through 578 or resid 602))
  selection = (chain 'B' and (resid 71 through 577 or (resid 601 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 
 602))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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=0.44 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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.140
  Find NCS groups from input model:        0.180
  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:8.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2940
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      :  0.008   0.124  10951  Z= 0.495
  Angle     :  1.128  11.981  15146  Z= 0.643
  Chirality :  0.103   0.561   1694
  Planarity :  0.015   0.339   1668
  Dihedral  : 19.536 107.776   4783
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.65 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole: -0.01 (0.26), residues: 1080
  helix:  1.19 (0.27), residues: 391
  sheet: -0.12 (0.36), residues: 224
  loop : -0.93 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  25 
 TYR   0.016   0.001   TYR B 499 
 PHE   0.025   0.002   PHE A 340 
 TRP   0.017   0.003   TRP B 547 
 HIS   0.009   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00768 /  0.49 (10951)
  covalent geometry    : angle       1.12762 /  0.64 (15146)
  hydrogen bonds       : bond        0.13503 /  8.40 (  456)
  hydrogen bonds       : angle       7.23333 /  4.85 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 9
  residues processed: 107
  average time/residue: 0.5980
  time to fit residues: 68.6057
Evaluate side-chains
  91 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  407 LYS
Chi-restraints excluded: chain B residue  478 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100]
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.092147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.071307 restraints weight = 23853.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 2.47
r_work: 0.2864 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10951  Z= 0.186
  Angle     :  0.643   8.950  15146  Z= 0.322
  Chirality :  0.041   0.197   1694
  Planarity :  0.004   0.044   1668
  Dihedral  : 19.232 101.629   2503
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.79 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.48 (0.26), residues: 1080
  helix:  1.61 (0.26), residues: 397
  sheet: -0.02 (0.36), residues: 223
  loop : -0.60 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 393 
 TYR   0.018   0.001   TYR B 499 
 PHE   0.032   0.002   PHE B 340 
 TRP   0.014   0.003   TRP A 547 
 HIS   0.005   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.19 (10951)
  covalent geometry    : angle       0.64335 /  0.32 (15146)
  hydrogen bonds       : bond        0.04773 /  3.09 (  456)
  hydrogen bonds       : angle       5.01537 /  3.43 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9494 (mmt90) cc_final: 0.9281 (mpp-170)
REVERT: A  165 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8438 (p)
REVERT: A  351 MET cc_start: 0.8851 (mtp) cc_final: 0.8538 (mtm)
REVERT: A  525 GLU cc_start: 0.8996 (pm20) cc_final: 0.8633 (mm-30)
REVERT: E    5 GLN cc_start: 0.8733 (mt0) cc_final: 0.8158 (tt0)
  outliers start: 16
  outliers final: 9
  residues processed: 97
  average time/residue: 0.6248
  time to fit residues: 64.9436
Evaluate side-chains
  91 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  445 ASP
Chi-restraints excluded: chain E residue    1 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [16, 3, 30, 17, 78, 63, 26, 71, 70, 110, 84]
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0040
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    0.2980
   chunk 110 optimal weight:   10.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.0396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.092745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.072273 restraints weight = 21004.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.33
r_work: 0.2892 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10951  Z= 0.143
  Angle     :  0.582   8.859  15146  Z= 0.287
  Chirality :  0.039   0.223   1694
  Planarity :  0.004   0.043   1668
  Dihedral  : 19.429 176.391   2494
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 20.62 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.72 (0.26), residues: 1080
  helix:  1.87 (0.26), residues: 398
  sheet:  0.06 (0.36), residues: 218
  loop : -0.50 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 393 
 TYR   0.017   0.001   TYR A 499 
 PHE   0.029   0.002   PHE B 340 
 TRP   0.014   0.003   TRP B 547 
 HIS   0.003   0.001   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 (10951)
  covalent geometry    : angle       0.58221 /  0.29 (15146)
  hydrogen bonds       : bond        0.04046 /  2.57 (  456)
  hydrogen bonds       : angle       4.69917 /  3.23 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9470 (mmt90) cc_final: 0.9107 (mmp80)
REVERT: A  165 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8329 (p)
REVERT: A  351 MET cc_start: 0.8767 (mtp) cc_final: 0.8430 (mtm)
REVERT: A  525 GLU cc_start: 0.8960 (pm20) cc_final: 0.8642 (mm-30)
REVERT: E    5 GLN cc_start: 0.8727 (mt0) cc_final: 0.8144 (tt0)
  outliers start: 14
  outliers final: 5
  residues processed: 97
  average time/residue: 0.6420
  time to fit residues: 66.8189
Evaluate side-chains
  87 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  317 GLU
Chi-restraints excluded: chain B residue  357 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [98, 63, 70, 83, 4, 46, 99, 82, 67, 47, 56]
   chunk 98 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.092241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.071775 restraints weight = 21006.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.33
r_work: 0.2888 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10951  Z= 0.147
  Angle     :  0.578   9.177  15146  Z= 0.282
  Chirality :  0.039   0.168   1694
  Planarity :  0.004   0.042   1668
  Dihedral  : 18.898  92.588   2492
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 21.14 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.81 (0.26), residues: 1080
  helix:  1.94 (0.26), residues: 398
  sheet:  0.06 (0.36), residues: 218
  loop : -0.41 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  80 
 TYR   0.018   0.001   TYR A 499 
 PHE   0.030   0.002   PHE A 340 
 TRP   0.015   0.002   TRP B 547 
 HIS   0.004   0.001   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 (10951)
  covalent geometry    : angle       0.57786 /  0.28 (15146)
  hydrogen bonds       : bond        0.03941 /  2.51 (  456)
  hydrogen bonds       : angle       4.60685 /  3.18 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9487 (mmt90) cc_final: 0.9232 (mpp-170)
REVERT: A  164 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8564 (ptmm)
REVERT: A  165 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8182 (p)
REVERT: A  351 MET cc_start: 0.8792 (mtp) cc_final: 0.8477 (mtm)
REVERT: A  525 GLU cc_start: 0.8942 (pm20) cc_final: 0.8497 (mt-10)
REVERT: B  407 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9096 (mmmm)
REVERT: E    5 GLN cc_start: 0.8715 (mt0) cc_final: 0.8129 (tt0)
  outliers start: 14
  outliers final: 4
  residues processed: 97
  average time/residue: 0.6453
  time to fit residues: 66.8861
Evaluate side-chains
  87 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  164 LYS
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  317 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [114, 12, 16, 90, 0, 67, 45, 50, 113, 61, 82]
   chunk 114 optimal weight:    0.0970
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.6978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.093380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.072975 restraints weight = 21381.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.34
r_work: 0.2914 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10951  Z= 0.114
  Angle     :  0.552   8.310  15146  Z= 0.269
  Chirality :  0.038   0.163   1694
  Planarity :  0.004   0.042   1668
  Dihedral  : 19.120 178.808   2491
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 21.55 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.87 (0.26), residues: 1080
  helix:  2.00 (0.26), residues: 399
  sheet:  0.04 (0.36), residues: 213
  loop : -0.36 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 161 
 TYR   0.017   0.001   TYR A 499 
 PHE   0.026   0.001   PHE A 340 
 TRP   0.013   0.002   TRP B 547 
 HIS   0.003   0.000   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 (10951)
  covalent geometry    : angle       0.55214 /  0.27 (15146)
  hydrogen bonds       : bond        0.03656 /  2.29 (  456)
  hydrogen bonds       : angle       4.51108 /  3.12 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9488 (mmt90) cc_final: 0.9226 (mpp-170)
REVERT: A  157 MET cc_start: 0.9264 (ttp) cc_final: 0.8967 (ptt)
REVERT: A  164 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8546 (ptmm)
REVERT: A  525 GLU cc_start: 0.8955 (pm20) cc_final: 0.8437 (mt-10)
REVERT: B  407 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9152 (mmmm)
REVERT: E    5 GLN cc_start: 0.8730 (mt0) cc_final: 0.8176 (tt0)
  outliers start: 11
  outliers final: 5
  residues processed: 93
  average time/residue: 0.6518
  time to fit residues: 64.8029
Evaluate side-chains
  87 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  164 LYS
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [88, 113, 12, 36, 70, 85, 48, 55, 91, 105, 25]
   chunk 88 optimal weight:    0.9980
   chunk 113 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.092984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.072630 restraints weight = 21260.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.33
r_work: 0.2901 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10951  Z= 0.134
  Angle     :  0.562   8.478  15146  Z= 0.274
  Chirality :  0.038   0.162   1694
  Planarity :  0.004   0.043   1668
  Dihedral  : 18.677  90.423   2491
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 21.97 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.88 (0.26), residues: 1080
  helix:  1.98 (0.26), residues: 399
  sheet:  0.07 (0.36), residues: 213
  loop : -0.33 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 161 
 TYR   0.016   0.001   TYR A 499 
 PHE   0.026   0.001   PHE B 340 
 TRP   0.015   0.002   TRP B 547 
 HIS   0.005   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (10951)
  covalent geometry    : angle       0.56224 /  0.27 (15146)
  hydrogen bonds       : bond        0.03736 /  2.34 (  456)
  hydrogen bonds       : angle       4.49485 /  3.11 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9493 (mmt90) cc_final: 0.9111 (mmp80)
REVERT: A  351 MET cc_start: 0.8696 (mtp) cc_final: 0.8316 (mtm)
REVERT: A  525 GLU cc_start: 0.8945 (pm20) cc_final: 0.8438 (mt-10)
REVERT: B  407 LYS cc_start: 0.9384 (mtpp) cc_final: 0.9145 (mmmm)
REVERT: E    5 GLN cc_start: 0.8742 (mt0) cc_final: 0.8217 (tt0)
  outliers start: 10
  outliers final: 5
  residues processed: 93
  average time/residue: 0.7246
  time to fit residues: 71.7181
Evaluate side-chains
  88 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [45, 113, 100, 34, 90, 104, 28, 56, 14, 67, 80]
   chunk 45 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.092250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.071800 restraints weight = 21437.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.34
r_work: 0.2884 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10951  Z= 0.159
  Angle     :  0.583   8.546  15146  Z= 0.284
  Chirality :  0.039   0.161   1694
  Planarity :  0.004   0.044   1668
  Dihedral  : 18.943 176.240   2491
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 22.07 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.85 (0.26), residues: 1080
  helix:  1.95 (0.26), residues: 399
  sheet: -0.04 (0.36), residues: 221
  loop : -0.30 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 161 
 TYR   0.016   0.001   TYR B 499 
 PHE   0.028   0.002   PHE B 340 
 TRP   0.016   0.003   TRP B 547 
 HIS   0.007   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 (10951)
  covalent geometry    : angle       0.58266 /  0.28 (15146)
  hydrogen bonds       : bond        0.03875 /  2.45 (  456)
  hydrogen bonds       : angle       4.51209 /  3.13 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9500 (mmt90) cc_final: 0.9121 (mmp80)
REVERT: A  351 MET cc_start: 0.8784 (mtp) cc_final: 0.8472 (mtm)
REVERT: B  329 LEU cc_start: 0.8187 (mt) cc_final: 0.7698 (pt)
REVERT: B  407 LYS cc_start: 0.9387 (mtpp) cc_final: 0.9161 (mmmm)
  outliers start: 12
  outliers final: 8
  residues processed: 96
  average time/residue: 0.6771
  time to fit residues: 69.5136
Evaluate side-chains
  92 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  164 LYS
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  371 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [5, 40, 70, 108, 22, 12, 94, 38, 61, 96, 64]
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.091339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.070902 restraints weight = 20961.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.31
r_work: 0.2867 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2885
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2885
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10951  Z= 0.199
  Angle     :  0.615   8.726  15146  Z= 0.302
  Chirality :  0.040   0.164   1694
  Planarity :  0.004   0.046   1668
  Dihedral  : 18.569  90.600   2491
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 22.49 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.81 (0.26), residues: 1080
  helix:  1.87 (0.26), residues: 399
  sheet: -0.03 (0.36), residues: 221
  loop : -0.29 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.019   0.002   TYR B 499 
 PHE   0.029   0.002   PHE A 340 
 TRP   0.016   0.003   TRP B 547 
 HIS   0.004   0.001   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.20 (10951)
  covalent geometry    : angle       0.61550 /  0.30 (15146)
  hydrogen bonds       : bond        0.04177 /  2.66 (  456)
  hydrogen bonds       : angle       4.60041 /  3.18 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9515 (mmt90) cc_final: 0.9115 (mmp80)
REVERT: A  157 MET cc_start: 0.9231 (ttp) cc_final: 0.8925 (ptt)
REVERT: A  351 MET cc_start: 0.8811 (mtp) cc_final: 0.8501 (mtm)
REVERT: A  525 GLU cc_start: 0.9017 (pm20) cc_final: 0.8659 (mt-10)
REVERT: B  202 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8673 (tt0)
REVERT: B  329 LEU cc_start: 0.8222 (mt) cc_final: 0.7728 (pt)
REVERT: B  407 LYS cc_start: 0.9397 (mtpp) cc_final: 0.9176 (mmmm)
  outliers start: 10
  outliers final: 5
  residues processed: 91
  average time/residue: 0.7113
  time to fit residues: 69.2347
Evaluate side-chains
  87 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  371 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [114, 52, 24, 82, 70, 92, 71, 76, 35, 38, 27]
   chunk 114 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   chunk 35 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.092927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.072648 restraints weight = 20664.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 2.30
r_work: 0.2901 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10951  Z= 0.122
  Angle     :  0.587   9.017  15146  Z= 0.286
  Chirality :  0.038   0.167   1694
  Planarity :  0.004   0.043   1668
  Dihedral  : 18.881 177.701   2491
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 22.18 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.86 (0.26), residues: 1080
  helix:  1.90 (0.26), residues: 399
  sheet: -0.03 (0.36), residues: 221
  loop : -0.24 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 161 
 TYR   0.016   0.001   TYR A 499 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.013   0.002   TRP A 547 
 HIS   0.009   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 (10951)
  covalent geometry    : angle       0.58727 /  0.29 (15146)
  hydrogen bonds       : bond        0.03673 /  2.31 (  456)
  hydrogen bonds       : angle       4.49705 /  3.12 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9502 (mmt90) cc_final: 0.9121 (mmp80)
REVERT: A  157 MET cc_start: 0.9215 (ttp) cc_final: 0.8954 (ptt)
REVERT: A  164 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8617 (ptmm)
REVERT: A  351 MET cc_start: 0.8757 (mtp) cc_final: 0.8445 (mtm)
REVERT: A  525 GLU cc_start: 0.9026 (pm20) cc_final: 0.8639 (mt-10)
REVERT: B  202 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8704 (tt0)
REVERT: B  329 LEU cc_start: 0.8173 (mt) cc_final: 0.7676 (pt)
REVERT: B  407 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9178 (mmmm)
  outliers start: 9
  outliers final: 4
  residues processed: 92
  average time/residue: 0.6714
  time to fit residues: 66.1084
Evaluate side-chains
  87 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  164 LYS
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  202 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [107, 0, 20, 109, 44, 31, 72, 78, 111, 61, 38]
   chunk 107 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 109 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.090941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.070540 restraints weight = 21078.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.31
r_work: 0.2860 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10951  Z= 0.233
  Angle     :  0.646   9.342  15146  Z= 0.316
  Chirality :  0.041   0.174   1694
  Planarity :  0.005   0.047   1668
  Dihedral  : 18.518  90.079   2491
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 21.97 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.72 (0.26), residues: 1080
  helix:  1.74 (0.26), residues: 399
  sheet: -0.03 (0.35), residues: 226
  loop : -0.32 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 161 
 TYR   0.021   0.002   TYR B 499 
 PHE   0.031   0.002   PHE B 340 
 TRP   0.018   0.003   TRP B 547 
 HIS   0.007   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00546 /  0.23 (10951)
  covalent geometry    : angle       0.64639 /  0.32 (15146)
  hydrogen bonds       : bond        0.04267 /  2.72 (  456)
  hydrogen bonds       : angle       4.63368 /  3.21 ( 1243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.9502 (mmt90) cc_final: 0.9115 (mmp80)
REVERT: A  157 MET cc_start: 0.9268 (ttp) cc_final: 0.8943 (ptt)
REVERT: A  164 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8685 (ptmm)
REVERT: A  361 MET cc_start: 0.9093 (ttm) cc_final: 0.8842 (ttp)
REVERT: A  525 GLU cc_start: 0.9027 (pm20) cc_final: 0.8626 (mt-10)
REVERT: B  202 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8648 (tt0)
REVERT: B  329 LEU cc_start: 0.8215 (mt) cc_final: 0.7718 (pt)
REVERT: B  407 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9186 (mmmm)
REVERT: B  513 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7515 (mp0)
  outliers start: 8
  outliers final: 5
  residues processed: 90
  average time/residue: 0.7279
  time to fit residues: 69.8407
Evaluate side-chains
  91 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  164 LYS
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  513 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks: [110, 65, 92, 93, 71, 60, 38, 82, 108, 53, 61]
   chunk 110 optimal weight:   10.9990
   chunk 65 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0170
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.1824

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.092061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.071673 restraints weight = 20921.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.31
r_work: 0.2880 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10951  Z= 0.152
  Angle     :  0.604   8.453  15146  Z= 0.295
  Chirality :  0.039   0.160   1694
  Planarity :  0.004   0.045   1668
  Dihedral  : 18.863 179.067   2491
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 22.28 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 are not related in a simple way.
  whole:  0.76 (0.26), residues: 1080
  helix:  1.76 (0.26), residues: 399
  sheet: -0.04 (0.36), residues: 221
  loop : -0.25 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 161 
 TYR   0.016   0.001   TYR A 499 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.014   0.002   TRP A 547 
 HIS   0.008   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (10951)
  covalent geometry    : angle       0.60351 /  0.29 (15146)
  hydrogen bonds       : bond        0.03907 /  2.47 (  456)
  hydrogen bonds       : angle       4.57399 /  3.17 ( 1243)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3284.09 seconds
wall clock time: 56 minutes 42.40 seconds (3402.40 seconds total)