Starting phenix.real_space_refine
on Fri Sep 11 18:22:22 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jl1_22369/09_2026/7jl1_22369.cif"
  }
  resolution = 3.9
  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
-------------------------------------------------------------------------------
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=   0.032
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 4056 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: 9
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     Al      1      5.89       5
     P      30      5.49       5
     Mg      1      5.21       5
     S      41      5.16       5
     C    4451      2.51       5
     N    1220      2.21       5
     O    1383      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7132
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 656, 5184
          Classifications: {'peptide': 656}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 25, 'TRANS': 630}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 74
    Chain: "X"
      Number of atoms: 300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 300
          Classifications: {'RNAv2': 14}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 1, 'rna3p': 12}
    Chain: "Y"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 295
          Classifications: {'RNAv2': 14}
          Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 13}
    Chain: "B"
      Number of atoms: 1319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1319
          Classifications: {'peptide': 171}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 7, 'TRANS': 163}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 52
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4362  SG  CYS A 810      69.713  98.163  31.557  1.00 61.48           S
  ATOM   4388  SG  CYS A 813      72.965  99.873  31.865  1.00 62.37           S
  ATOM   4728  SG  CYS A 864      71.899  99.040  28.358  1.00 71.24           S
  ATOM   4767  SG  CYS A 869      72.980  96.306  30.728  1.00 76.60           S

  Time building chain proxies: 1.26, per 1000 atoms: 0.18
  Number of scatterers: 7132
  At special positions: 0
  Unit cell: (96.9088, 121.918, 67.732, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Zn      1     29.99
     S      41     16.00
     P      30     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1383      8.00
     N    1220      7.00
     C    4451      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: 0.67
  Conformation dependent library (CDL) restraints added in 489.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2004 "
        pdb="ZN    ZN A2004 " - pdb=" SG  CYS A 813 "
        pdb="ZN    ZN A2004 " - pdb=" SG  CYS A 869 "
        pdb="ZN    ZN A2004 " - pdb=" SG  CYS A 864 "
        pdb="ZN    ZN A2004 " - pdb=" SG  CYS A 810 "
      Number of angles added : 6


  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      42.1% alpha, 14.8% beta
      9 base pairs and 20 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 250
    Processing helix  chain 'A' and resid 251 through 256
    Processing helix  chain 'A' and resid 269 through 285
      removed outlier: 3.701A  pdb=" N   LYS A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   PHE A 285 " --> pdb=" O   HIS A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 316
      removed outlier: 4.653A  pdb=" N   ARG A 316 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 341
      removed outlier: 3.719A  pdb=" N   GLU A 339 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 4.118A  pdb=" N   LEU A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.583A  pdb=" N   PHE A 366 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 381 through 396
    Processing helix  chain 'A' and resid 419 through 434
      removed outlier: 3.583A  pdb=" N   LEU A 434 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 453
      removed outlier: 3.616A  pdb=" N   GLN A 451 " --> pdb=" O   GLU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 490
      removed outlier: 3.515A  pdb=" N   TYR A 473 " --> pdb=" O   ASP A 469 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   CYS A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 521
      removed outlier: 3.858A  pdb=" N   GLU A 510 " --> pdb=" O   THR A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 558
      removed outlier: 4.239A  pdb=" N   ARG A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ILE A 534 " --> pdb=" O   GLU A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 574
      removed outlier: 3.703A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 592
    Processing helix  chain 'A' and resid 593 through 602
      removed outlier: 3.618A  pdb=" N   ARG A 602 " --> pdb=" O   GLU A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 607
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 649
      removed outlier: 3.669A  pdb=" N   VAL A 640 " --> pdb=" O   THR A 636 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP A 641 " --> pdb=" O   ARG A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 686
      removed outlier: 3.517A  pdb=" N   LYS A 686 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 701
    Processing helix  chain 'A' and resid 720 through 729
    Processing helix  chain 'A' and resid 744 through 768
      removed outlier: 3.682A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN A 752 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU A 766 " --> pdb=" O   ASN A 762 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 768 " --> pdb=" O   SER A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 771
      No H-bonds generated for 'chain 'A' and resid 769 through 771'
    Processing helix  chain 'A' and resid 774 through 794
    Processing helix  chain 'A' and resid 821 through 823
      No H-bonds generated for 'chain 'A' and resid 821 through 823'
    Processing helix  chain 'A' and resid 835 through 841
    Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 324
      removed outlier: 6.328A  pdb=" N   VAL A 293 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   LEU A 346 " --> pdb=" O   VAL A 293 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   PHE A 295 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   MET A 369 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   LEU A 408 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   PHE A 371 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ILE A 261 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462
      removed outlier: 6.687A  pdb=" N   THR A 630 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ALA A 696 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   LEU A 632 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   GLY A 659 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 667
    Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819
      removed outlier: 7.529A  pdb=" N   LEU A 816 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   CYS A 810 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL A 894 " --> pdb=" O   THR A 903 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR A 903 " --> pdb=" O   VAL A 894 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 874 through 879
    Processing sheet with id=AA6, first strand: chain 'B' and resid 272 through 274
      removed outlier: 3.990A  pdb=" N   ILE B 426 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLU B 316 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   TYR B 390 " --> pdb=" O   GLY B 377 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   TYR B 400 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   SER B 391 " --> pdb=" O   LEU B 398 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   LEU B 398 " --> pdb=" O   SER B 391 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 303
      removed outlier: 4.273A  pdb=" N   TRP B 325 " --> pdb=" O   TRP B 351 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LEU B 357 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS B 361 " --> pdb=" O   LYS B 364 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    840 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      23 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      20 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 0.87 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: 1329
        1.32 -     1.45: 1908
        1.45 -     1.57: 3981
        1.57 -     1.69: 57
        1.69 -     1.81: 60
  Bond restraints: 7335
  Sorted by residual:
  bond pdb=" F2  ALF A2002 "
       pdb="AL   ALF A2002 "
    ideal  model  delta    sigma   weight residual
    1.685  1.799 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" F3  ALF A2002 "
       pdb="AL   ALF A2002 "
    ideal  model  delta    sigma   weight residual
    1.685  1.781 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" F4  ALF A2002 "
       pdb="AL   ALF A2002 "
    ideal  model  delta    sigma   weight residual
    1.686  1.779 -0.093 2.00e-02 2.50e+03 2.17e+01
  bond pdb=" F1  ALF A2002 "
       pdb="AL   ALF A2002 "
    ideal  model  delta    sigma   weight residual
    1.684  1.768 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" N   CYS A 490 "
       pdb=" CA  CYS A 490 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.035 1.33e-02 5.65e+03 7.06e+00
  ... (remaining 7330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.88: 10052
       13.88 -    27.76: 4
       27.76 -    41.64: 0
       41.64 -    55.53: 0
       55.53 -    69.41: 2
  Bond angle restraints: 10058
  Sorted by residual:
  angle pdb=" F1  ALF A2002 "
        pdb="AL   ALF A2002 "
        pdb=" F2  ALF A2002 "
      ideal   model   delta    sigma   weight residual
     108.68  178.09  -69.41 3.00e+00 1.11e-01 5.35e+02
  angle pdb=" F3  ALF A2002 "
        pdb="AL   ALF A2002 "
        pdb=" F4  ALF A2002 "
      ideal   model   delta    sigma   weight residual
     109.63  177.66  -68.03 3.00e+00 1.11e-01 5.14e+02
  angle pdb=" F2  ALF A2002 "
        pdb="AL   ALF A2002 "
        pdb=" F3  ALF A2002 "
      ideal   model   delta    sigma   weight residual
     109.59   88.94   20.65 3.00e+00 1.11e-01 4.74e+01
  angle pdb=" F1  ALF A2002 "
        pdb="AL   ALF A2002 "
        pdb=" F4  ALF A2002 "
      ideal   model   delta    sigma   weight residual
     109.02   88.94   20.08 3.00e+00 1.11e-01 4.48e+01
  angle pdb=" F2  ALF A2002 "
        pdb="AL   ALF A2002 "
        pdb=" F4  ALF A2002 "
      ideal   model   delta    sigma   weight residual
     110.21   91.34   18.87 3.00e+00 1.11e-01 3.96e+01
  ... (remaining 10053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.43: 4220
       35.43 -    70.85: 108
       70.85 -   106.28: 3
      106.28 -   141.70: 2
      141.70 -   177.12: 3
  Dihedral angle restraints: 4336
    sinusoidal: 1917
      harmonic: 2419
  Sorted by residual:
  dihedral pdb=" C4'   A X   2 "
           pdb=" C3'   A X   2 "
           pdb=" C2'   A X   2 "
           pdb=" C1'   A X   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -31.62   67.96     1      3.10e+00 1.04e-01 6.24e+02
  dihedral pdb=" O4'   A X   2 "
           pdb=" C4'   A X   2 "
           pdb=" C3'   A X   2 "
           pdb=" C2'   A X   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.15   21.08  -56.23     1      4.00e+00 6.25e-02 2.66e+02
  dihedral pdb=" O4'   A X   2 "
           pdb=" C2'   A X   2 "
           pdb=" C1'   A X   2 "
           pdb=" C3'   A X   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.59  -32.17   57.77     3      3.80e+00 6.93e-02 1.47e+02
  ... (remaining 4333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 954
       0.074 -    0.147: 173
       0.147 -    0.220: 25
       0.220 -    0.294: 9
       0.294 -    0.367: 3
  Chirality restraints: 1164
  Sorted by residual:
  chirality pdb=" C2'   A X   2 "
            pdb=" C3'   A X   2 "
            pdb=" O2'   A X   2 "
            pdb=" C1'   A X   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.42   -0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" C3'   G Y   4 "
            pdb=" C4'   G Y   4 "
            pdb=" O3'   G Y   4 "
            pdb=" C2'   G Y   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.17   -0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" P     G X   1 "
            pdb=" OP1   G X   1 "
            pdb=" OP2   G X   1 "
            pdb=" O5'   G X   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.47   -0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1161 not shown)

  Planarity restraints: 1158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A X   2 "    0.042 2.00e-02 2.50e+03   1.85e-02 9.43e+00
        pdb=" N9    A X   2 "   -0.041 2.00e-02 2.50e+03
        pdb=" C8    A X   2 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7    A X   2 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A X   2 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A X   2 "    0.007 2.00e-02 2.50e+03
        pdb=" N6    A X   2 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    A X   2 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    A X   2 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    A X   2 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A X   2 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 313 "    0.015 2.00e-02 2.50e+03   1.72e-02 4.46e+00
        pdb=" CG  HIS B 313 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 313 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 313 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 313 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 313 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 411 "   -0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO B 412 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 412 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 412 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1155 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.36: 14
        2.36 -     3.00: 3988
        3.00 -     3.63: 9937
        3.63 -     4.27: 14913
        4.27 -     4.90: 25060
  Nonbonded interactions: 53912
  Sorted by model distance:
  nonbonded pdb=" F1  ALF A2002 "
            pdb="MG    MG A2003 "
     model   vdw
     1.727 2.120
  nonbonded pdb=" O1B ADP A2001 "
            pdb="MG    MG A2003 "
     model   vdw
     1.793 2.170
  nonbonded pdb=" F4  ALF A2002 "
            pdb="MG    MG A2003 "
     model   vdw
     1.813 2.120
  nonbonded pdb=" O1B ADP A2001 "
            pdb=" F4  ALF A2002 "
     model   vdw
     2.014 2.990
  nonbonded pdb=" O2B ADP A2001 "
            pdb=" F2  ALF A2002 "
     model   vdw
     2.064 2.990
  ... (remaining 53907 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
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      :  0.011   0.114   7339  Z= 0.474
  Angle     :  1.404  69.407  10064  Z= 0.598
  Chirality :  0.063   0.367   1164
  Planarity :  0.005   0.050   1158
  Dihedral  : 16.153 177.125   2760
  Min Nonbonded Distance : 1.727

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.44 %
    Favored  : 93.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.42 (0.29), residues: 805
  helix:  1.22 (0.30), residues: 302
  sheet:  0.06 (0.45), residues: 144
  loop : -0.35 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 296 
 TYR   0.031   0.003   TYR A 303 
 PHE   0.019   0.003   PHE A 295 
 TRP   0.013   0.002   TRP B 315 
 HIS   0.020   0.002   HIS B 313 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01075 /  0.47 ( 7335)
  covalent geometry    : angle       1.40130 /  0.60 (10058)
  hydrogen bonds       : bond        0.15475 / 10.10 (  319)
  hydrogen bonds       : angle       6.65900 /  4.74 (  886)
  metal coordination   : bond        0.00757 /  0.37 (    4)
  metal coordination   : angle       3.76063 /  2.10 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8412 (tppt) cc_final: 0.8197 (ttpt)
REVERT: A  387 MET cc_start: 0.8925 (mmp) cc_final: 0.8701 (mmt)
REVERT: A  435 ASP cc_start: 0.8639 (t0) cc_final: 0.7757 (t0)
REVERT: A  492 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7656 (p0)
REVERT: A  610 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7415 (mtpp)
REVERT: A  690 ASP cc_start: 0.8452 (p0) cc_final: 0.8165 (p0)
REVERT: A  692 ASN cc_start: 0.8152 (m-40) cc_final: 0.7544 (t0)
REVERT: A  756 TYR cc_start: 0.7623 (t80) cc_final: 0.7403 (t80)
REVERT: A  761 MET cc_start: 0.7522 (ttp) cc_final: 0.7241 (ttp)
REVERT: A  859 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7319 (tpp80)
REVERT: B  321 ASN cc_start: 0.8208 (t0) cc_final: 0.7864 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0860
  time to fit residues: 19.6385
Evaluate side-chains
  131 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 376 ASN
A 573 ASN
A 782 HIS
A 876 HIS
** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.160058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.126472 restraints weight = 8190.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.125745 restraints weight = 7419.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.127574 restraints weight = 7726.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.128323 restraints weight = 5100.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.128384 restraints weight = 5200.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7339  Z= 0.174
  Angle     :  0.695   7.192  10064  Z= 0.333
  Chirality :  0.050   0.350   1164
  Planarity :  0.004   0.039   1158
  Dihedral  : 13.133 172.671   1218
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.45 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.30), residues: 805
  helix:  1.52 (0.29), residues: 304
  sheet:  0.11 (0.46), residues: 154
  loop : -0.12 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 637 
 TYR   0.021   0.002   TYR A 541 
 PHE   0.016   0.001   PHE A 913 
 TRP   0.013   0.001   TRP B 257 
 HIS   0.007   0.001   HIS A 782 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.17 ( 7335)
  covalent geometry    : angle       0.68632 /  0.33 (10058)
  hydrogen bonds       : bond        0.05645 /  3.80 (  319)
  hydrogen bonds       : angle       4.87990 /  3.51 (  886)
  metal coordination   : bond        0.00319 /  0.16 (    4)
  metal coordination   : angle       4.65580 /  2.42 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  241 PHE cc_start: 0.7969 (m-80) cc_final: 0.7752 (m-80)
REVERT: A  283 LYS cc_start: 0.8526 (tppt) cc_final: 0.8042 (tttp)
REVERT: A  387 MET cc_start: 0.9040 (mmp) cc_final: 0.8774 (mmt)
REVERT: A  481 ASP cc_start: 0.8083 (m-30) cc_final: 0.7797 (m-30)
REVERT: A  610 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7410 (mttm)
REVERT: A  692 ASN cc_start: 0.8287 (m-40) cc_final: 0.7769 (t0)
REVERT: A  756 TYR cc_start: 0.7516 (t80) cc_final: 0.7288 (t80)
REVERT: A  761 MET cc_start: 0.7398 (ttp) cc_final: 0.7127 (ttp)
REVERT: A  792 ASP cc_start: 0.8420 (m-30) cc_final: 0.8059 (m-30)
REVERT: A  822 ASP cc_start: 0.8444 (m-30) cc_final: 0.7775 (t0)
REVERT: B  321 ASN cc_start: 0.8063 (t0) cc_final: 0.7809 (t0)
REVERT: B  362 MET cc_start: 0.7626 (mmm) cc_final: 0.7019 (mtp)
  outliers start: 16
  outliers final: 10
  residues processed: 147
  average time/residue: 0.0812
  time to fit residues: 16.0612
Evaluate side-chains
  137 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  916 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 26 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0770
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 1 optimal weight:    0.1980
   overall best weight:    0.7540

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 678 GLN
A 876 HIS
B 313 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.165244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.132570 restraints weight = 7991.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.131481 restraints weight = 7995.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.134285 restraints weight = 7744.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.134178 restraints weight = 5277.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.134846 restraints weight = 5477.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7339  Z= 0.107
  Angle     :  0.587   5.968  10064  Z= 0.280
  Chirality :  0.047   0.322   1164
  Planarity :  0.003   0.041   1158
  Dihedral  : 12.677 171.416   1216
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.31 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.30), residues: 805
  helix:  1.85 (0.29), residues: 304
  sheet:  0.34 (0.46), residues: 148
  loop : -0.14 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 244 
 TYR   0.015   0.001   TYR A 454 
 PHE   0.014   0.001   PHE A 913 
 TRP   0.015   0.001   TRP B 257 
 HIS   0.014   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.11 ( 7335)
  covalent geometry    : angle       0.58036 /  0.28 (10058)
  hydrogen bonds       : bond        0.04264 /  2.88 (  319)
  hydrogen bonds       : angle       4.28671 /  3.06 (  886)
  metal coordination   : bond        0.00171 /  0.09 (    4)
  metal coordination   : angle       3.54107 /  1.84 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8493 (tppt) cc_final: 0.7984 (tttp)
REVERT: A  387 MET cc_start: 0.8863 (mmp) cc_final: 0.8540 (mmt)
REVERT: A  610 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7231 (mttt)
REVERT: A  692 ASN cc_start: 0.8257 (m-40) cc_final: 0.7681 (t0)
REVERT: A  715 TYR cc_start: 0.8903 (t80) cc_final: 0.8257 (t80)
REVERT: A  756 TYR cc_start: 0.7517 (t80) cc_final: 0.7222 (t80)
REVERT: A  822 ASP cc_start: 0.8447 (m-30) cc_final: 0.7743 (t0)
REVERT: B  335 SER cc_start: 0.8794 (t) cc_final: 0.8112 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 140
  average time/residue: 0.0817
  time to fit residues: 15.4834
Evaluate side-chains
  144 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 66 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0970
   chunk 48 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0020
   chunk 55 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 876 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.162584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.129481 restraints weight = 8094.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.128538 restraints weight = 8023.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.130750 restraints weight = 7832.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.131098 restraints weight = 5339.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.131276 restraints weight = 5649.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7339  Z= 0.131
  Angle     :  0.588   6.767  10064  Z= 0.280
  Chirality :  0.047   0.328   1164
  Planarity :  0.003   0.041   1158
  Dihedral  : 12.569 172.518   1216
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.31 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.30), residues: 805
  helix:  1.87 (0.29), residues: 304
  sheet:  0.35 (0.45), residues: 148
  loop : -0.24 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 637 
 TYR   0.014   0.001   TYR A 303 
 PHE   0.012   0.001   PHE B 414 
 TRP   0.013   0.001   TRP B 257 
 HIS   0.005   0.001   HIS B 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 7335)
  covalent geometry    : angle       0.57971 /  0.28 (10058)
  hydrogen bonds       : bond        0.04414 /  2.98 (  319)
  hydrogen bonds       : angle       4.21041 /  3.00 (  886)
  metal coordination   : bond        0.00230 /  0.11 (    4)
  metal coordination   : angle       4.12837 /  2.06 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8553 (tppt) cc_final: 0.7959 (tttp)
REVERT: A  387 MET cc_start: 0.8933 (mmp) cc_final: 0.8623 (mmt)
REVERT: A  435 ASP cc_start: 0.8555 (t0) cc_final: 0.8016 (t0)
REVERT: A  554 ILE cc_start: 0.8897 (mm) cc_final: 0.8489 (mt)
REVERT: A  657 LYS cc_start: 0.8709 (tptm) cc_final: 0.8146 (tppt)
REVERT: A  690 ASP cc_start: 0.8276 (p0) cc_final: 0.7985 (p0)
REVERT: A  692 ASN cc_start: 0.8386 (m-40) cc_final: 0.7550 (t0)
REVERT: A  756 TYR cc_start: 0.7540 (t80) cc_final: 0.7189 (t80)
REVERT: A  822 ASP cc_start: 0.8338 (m-30) cc_final: 0.7621 (t0)
REVERT: B  362 MET cc_start: 0.7848 (mtp) cc_final: 0.7424 (ttm)
  outliers start: 28
  outliers final: 21
  residues processed: 150
  average time/residue: 0.0790
  time to fit residues: 16.0884
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  829 CYS
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  296 ARG
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 72 optimal weight:    8.9990
   chunk 76 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0270
   chunk 57 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.7044

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 619 GLN
A 678 GLN
A 876 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.162128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.129221 restraints weight = 8122.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.129361 restraints weight = 7306.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.130818 restraints weight = 7188.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.131295 restraints weight = 5475.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.131636 restraints weight = 4804.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7339  Z= 0.124
  Angle     :  0.581   6.685  10064  Z= 0.276
  Chirality :  0.046   0.322   1164
  Planarity :  0.003   0.042   1158
  Dihedral  : 12.532 172.895   1216
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.03 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.30), residues: 805
  helix:  1.92 (0.29), residues: 304
  sheet:  0.29 (0.45), residues: 148
  loop : -0.30 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 637 
 TYR   0.013   0.001   TYR A 303 
 PHE   0.009   0.001   PHE A 911 
 TRP   0.013   0.001   TRP B 257 
 HIS   0.005   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 7335)
  covalent geometry    : angle       0.57283 /  0.28 (10058)
  hydrogen bonds       : bond        0.04292 /  2.91 (  319)
  hydrogen bonds       : angle       4.13574 /  2.95 (  886)
  metal coordination   : bond        0.00197 /  0.10 (    4)
  metal coordination   : angle       3.90196 /  1.89 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8577 (tppt) cc_final: 0.7945 (tttp)
REVERT: A  387 MET cc_start: 0.8948 (mmp) cc_final: 0.8647 (mmt)
REVERT: A  435 ASP cc_start: 0.8525 (t0) cc_final: 0.7996 (t0)
REVERT: A  657 LYS cc_start: 0.8677 (tptm) cc_final: 0.8126 (tppt)
REVERT: A  690 ASP cc_start: 0.8301 (p0) cc_final: 0.7976 (p0)
REVERT: A  692 ASN cc_start: 0.8419 (m-40) cc_final: 0.7555 (t0)
REVERT: A  705 ASP cc_start: 0.8056 (t0) cc_final: 0.7838 (t0)
REVERT: A  756 TYR cc_start: 0.7528 (t80) cc_final: 0.7161 (t80)
REVERT: A  822 ASP cc_start: 0.8277 (m-30) cc_final: 0.7515 (t0)
REVERT: B  362 MET cc_start: 0.7857 (mtp) cc_final: 0.7425 (tpp)
  outliers start: 26
  outliers final: 24
  residues processed: 152
  average time/residue: 0.0777
  time to fit residues: 15.9704
Evaluate side-chains
  151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  829 CYS
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  296 ARG
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    4.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 341 ASN
A 678 GLN
A 782 HIS
A 876 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.156458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.122453 restraints weight = 8252.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.123042 restraints weight = 7680.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.124101 restraints weight = 6950.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.124800 restraints weight = 5245.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.124989 restraints weight = 4829.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   7339  Z= 0.242
  Angle     :  0.696   8.960  10064  Z= 0.333
  Chirality :  0.050   0.381   1164
  Planarity :  0.004   0.042   1158
  Dihedral  : 12.537 171.516   1216
  Min Nonbonded Distance : 1.699

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 20.74 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.29), residues: 805
  helix:  1.58 (0.28), residues: 303
  sheet: -0.10 (0.44), residues: 153
  loop : -0.41 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 637 
 TYR   0.021   0.002   TYR A 303 
 PHE   0.013   0.002   PHE A 911 
 TRP   0.010   0.001   TRP B 379 
 HIS   0.011   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00566 /  0.24 ( 7335)
  covalent geometry    : angle       0.68536 /  0.33 (10058)
  hydrogen bonds       : bond        0.05598 /  3.79 (  319)
  hydrogen bonds       : angle       4.55449 /  3.25 (  886)
  metal coordination   : bond        0.00323 /  0.15 (    4)
  metal coordination   : angle       5.01636 /  2.39 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8678 (tppt) cc_final: 0.8162 (ttpp)
REVERT: A  387 MET cc_start: 0.9111 (mmp) cc_final: 0.8843 (mmt)
REVERT: A  435 ASP cc_start: 0.8658 (t0) cc_final: 0.7930 (t0)
REVERT: A  554 ILE cc_start: 0.8956 (mm) cc_final: 0.8701 (mt)
REVERT: A  612 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7754 (tm-30)
REVERT: A  657 LYS cc_start: 0.8672 (tptm) cc_final: 0.8205 (tppt)
REVERT: A  690 ASP cc_start: 0.8419 (p0) cc_final: 0.8199 (p0)
REVERT: A  705 ASP cc_start: 0.8076 (t0) cc_final: 0.7870 (t0)
REVERT: A  756 TYR cc_start: 0.7499 (t80) cc_final: 0.7136 (t80)
REVERT: A  822 ASP cc_start: 0.8392 (m-30) cc_final: 0.7562 (t0)
REVERT: B  362 MET cc_start: 0.8000 (mtp) cc_final: 0.7632 (tpp)
  outliers start: 32
  outliers final: 26
  residues processed: 150
  average time/residue: 0.0772
  time to fit residues: 15.6931
Evaluate side-chains
  144 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  829 CYS
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 678 GLN
A 782 HIS
A 876 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.159796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.126102 restraints weight = 8062.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.127536 restraints weight = 7210.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.129054 restraints weight = 6269.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.129163 restraints weight = 4469.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.129256 restraints weight = 4227.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7339  Z= 0.144
  Angle     :  0.617   7.974  10064  Z= 0.292
  Chirality :  0.048   0.333   1164
  Planarity :  0.003   0.041   1158
  Dihedral  : 12.554 171.809   1216
  Min Nonbonded Distance : 1.781

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.32 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.29), residues: 805
  helix:  1.74 (0.29), residues: 303
  sheet:  0.04 (0.43), residues: 157
  loop : -0.40 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 296 
 TYR   0.026   0.002   TYR A 541 
 PHE   0.011   0.001   PHE A 911 
 TRP   0.011   0.001   TRP B 257 
 HIS   0.008   0.001   HIS A 782 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 7335)
  covalent geometry    : angle       0.60867 /  0.29 (10058)
  hydrogen bonds       : bond        0.04698 /  3.21 (  319)
  hydrogen bonds       : angle       4.28428 /  3.07 (  886)
  metal coordination   : bond        0.00206 /  0.10 (    4)
  metal coordination   : angle       4.26716 /  2.02 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8595 (tppt) cc_final: 0.7945 (tttp)
REVERT: A  387 MET cc_start: 0.9016 (mmp) cc_final: 0.8721 (mmt)
REVERT: A  612 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7761 (tm-30)
REVERT: A  657 LYS cc_start: 0.8642 (tptm) cc_final: 0.8119 (tppt)
REVERT: A  756 TYR cc_start: 0.7530 (t80) cc_final: 0.7138 (t80)
REVERT: A  822 ASP cc_start: 0.8331 (m-30) cc_final: 0.7458 (t0)
REVERT: B  340 LEU cc_start: 0.8502 (tt) cc_final: 0.8283 (tt)
REVERT: B  362 MET cc_start: 0.7960 (mtp) cc_final: 0.7612 (tpp)
  outliers start: 22
  outliers final: 22
  residues processed: 139
  average time/residue: 0.0743
  time to fit residues: 14.0719
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  762 ASN
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  829 CYS
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 63 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    3.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 678 GLN
A 876 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.157011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.122844 restraints weight = 8308.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.123315 restraints weight = 7614.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.124522 restraints weight = 7052.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.124759 restraints weight = 5166.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.124993 restraints weight = 4848.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7339  Z= 0.216
  Angle     :  0.678   9.127  10064  Z= 0.322
  Chirality :  0.049   0.370   1164
  Planarity :  0.003   0.041   1158
  Dihedral  : 12.527 171.088   1216
  Min Nonbonded Distance : 1.675

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.46 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.29), residues: 805
  helix:  1.54 (0.29), residues: 303
  sheet: -0.18 (0.43), residues: 157
  loop : -0.51 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 296 
 TYR   0.025   0.002   TYR A 541 
 PHE   0.013   0.002   PHE B 414 
 TRP   0.009   0.001   TRP B 379 
 HIS   0.005   0.001   HIS B 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00505 /  0.22 ( 7335)
  covalent geometry    : angle       0.66787 /  0.32 (10058)
  hydrogen bonds       : bond        0.05333 /  3.62 (  319)
  hydrogen bonds       : angle       4.45447 /  3.18 (  886)
  metal coordination   : bond        0.00315 /  0.15 (    4)
  metal coordination   : angle       4.92921 /  2.30 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8641 (tppt) cc_final: 0.8106 (ttpp)
REVERT: A  387 MET cc_start: 0.9094 (mmp) cc_final: 0.8829 (mmt)
REVERT: A  435 ASP cc_start: 0.8656 (t0) cc_final: 0.7941 (t0)
REVERT: A  612 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7762 (tm-30)
REVERT: A  657 LYS cc_start: 0.8596 (tptm) cc_final: 0.8107 (tppt)
REVERT: A  690 ASP cc_start: 0.8441 (p0) cc_final: 0.8181 (p0)
REVERT: A  705 ASP cc_start: 0.8085 (t0) cc_final: 0.7855 (t0)
REVERT: A  756 TYR cc_start: 0.7543 (t80) cc_final: 0.7206 (t80)
REVERT: A  822 ASP cc_start: 0.8394 (m-30) cc_final: 0.7484 (t0)
  outliers start: 25
  outliers final: 21
  residues processed: 148
  average time/residue: 0.0813
  time to fit residues: 16.6069
Evaluate side-chains
  146 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  829 CYS
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 74 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:   20.0000
   overall best weight:    2.0386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 678 GLN
A 876 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.159665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.126059 restraints weight = 8032.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.127586 restraints weight = 7421.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.129650 restraints weight = 5934.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.129281 restraints weight = 4315.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.129464 restraints weight = 4305.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7339  Z= 0.140
  Angle     :  0.623   8.879  10064  Z= 0.294
  Chirality :  0.047   0.330   1164
  Planarity :  0.003   0.041   1158
  Dihedral  : 12.524 171.365   1216
  Min Nonbonded Distance : 1.752

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 23.18 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.29), residues: 805
  helix:  1.73 (0.29), residues: 303
  sheet: -0.05 (0.43), residues: 155
  loop : -0.51 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 296 
 TYR   0.028   0.002   TYR A 541 
 PHE   0.012   0.001   PHE A 911 
 TRP   0.009   0.001   TRP B 257 
 HIS   0.004   0.001   HIS B 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 7335)
  covalent geometry    : angle       0.61547 /  0.29 (10058)
  hydrogen bonds       : bond        0.04581 /  3.12 (  319)
  hydrogen bonds       : angle       4.22074 /  3.03 (  886)
  metal coordination   : bond        0.00219 /  0.11 (    4)
  metal coordination   : angle       4.04014 /  1.89 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8597 (tppt) cc_final: 0.7909 (tttp)
REVERT: A  387 MET cc_start: 0.9024 (mmp) cc_final: 0.8746 (mmt)
REVERT: A  612 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7723 (tm-30)
REVERT: A  756 TYR cc_start: 0.7521 (t80) cc_final: 0.7128 (t80)
REVERT: A  822 ASP cc_start: 0.8269 (m-30) cc_final: 0.7475 (t0)
  outliers start: 22
  outliers final: 21
  residues processed: 141
  average time/residue: 0.0822
  time to fit residues: 15.9782
Evaluate side-chains
  145 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  762 ASN
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  829 CYS
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0070
   chunk 20 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.1804

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 678 GLN
A 876 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.159996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.125742 restraints weight = 8184.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.126903 restraints weight = 7462.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.128900 restraints weight = 6242.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.128655 restraints weight = 4506.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.128784 restraints weight = 4395.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7339  Z= 0.146
  Angle     :  0.623   8.489  10064  Z= 0.294
  Chirality :  0.047   0.334   1164
  Planarity :  0.003   0.041   1158
  Dihedral  : 12.485 171.493   1216
  Min Nonbonded Distance : 1.740

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.75 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.29), residues: 805
  helix:  1.74 (0.29), residues: 303
  sheet:  0.02 (0.44), residues: 155
  loop : -0.52 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 296 
 TYR   0.029   0.002   TYR A 541 
 PHE   0.014   0.001   PHE B 414 
 TRP   0.008   0.001   TRP B 315 
 HIS   0.005   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 7335)
  covalent geometry    : angle       0.61435 /  0.29 (10058)
  hydrogen bonds       : bond        0.04560 /  3.10 (  319)
  hydrogen bonds       : angle       4.20561 /  3.02 (  886)
  metal coordination   : bond        0.00233 /  0.12 (    4)
  metal coordination   : angle       4.16015 /  1.90 (    6)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8601 (tppt) cc_final: 0.7908 (tttp)
REVERT: A  387 MET cc_start: 0.9009 (mmp) cc_final: 0.8722 (mmt)
REVERT: A  612 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: A  756 TYR cc_start: 0.7518 (t80) cc_final: 0.7127 (t80)
REVERT: A  822 ASP cc_start: 0.8284 (m-30) cc_final: 0.7475 (t0)
  outliers start: 21
  outliers final: 21
  residues processed: 131
  average time/residue: 0.0836
  time to fit residues: 15.1897
Evaluate side-chains
  141 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  605 SER
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  829 CYS
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  382 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    0.1980
   chunk 60 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0270
   chunk 25 optimal weight:    0.0050
   overall best weight:    0.3652

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 678 GLN
A 876 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.164667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.131373 restraints weight = 8027.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.132124 restraints weight = 7344.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.133627 restraints weight = 6726.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.134180 restraints weight = 4698.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.134480 restraints weight = 4471.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7339  Z= 0.098
  Angle     :  0.579   9.309  10064  Z= 0.273
  Chirality :  0.046   0.315   1164
  Planarity :  0.003   0.040   1158
  Dihedral  : 12.467 172.621   1216
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 24.89 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.29), residues: 805
  helix:  1.96 (0.29), residues: 304
  sheet:  0.29 (0.45), residues: 145
  loop : -0.53 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 559 
 TYR   0.029   0.001   TYR A 541 
 PHE   0.009   0.001   PHE A 590 
 TRP   0.014   0.001   TRP B 257 
 HIS   0.005   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00197 /  0.10 ( 7335)
  covalent geometry    : angle       0.57462 /  0.27 (10058)
  hydrogen bonds       : bond        0.03668 /  2.49 (  319)
  hydrogen bonds       : angle       3.92503 /  2.81 (  886)
  metal coordination   : bond        0.00231 /  0.12 (    4)
  metal coordination   : angle       2.90651 /  1.38 (    6)

===============================================================================
Job complete
usr+sys time: 1125.58 seconds
wall clock time: 20 minutes 13.50 seconds (1213.50 seconds total)