Starting phenix.real_space_refine
on Thu Jul  2 08:34:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m33_63597/07_2026/9m33_63597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m33_63597/07_2026/9m33_63597.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m33_63597/07_2026/9m33_63597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m33_63597/07_2026/9m33_63597.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m33_63597/07_2026/9m33_63597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m33_63597/07_2026/9m33_63597.map"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      67      5.49       5
     Mg      1      5.21       5
     S      21      5.16       5
     C    4673      2.51       5
     N    1309      2.21       5
     O    1610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7681
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6236
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 750, 6226
          Classifications: {'peptide': 750}
          Link IDs: {'PTRANS': 19, 'TRANS': 730}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 750, 6226
          Classifications: {'peptide': 750}
          Link IDs: {'PTRANS': 19, 'TRANS': 730}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 6351
    Chain: "B"
      Number of atoms: 1042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 1042
          Classifications: {'RNA': 49}
          Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 23, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 8, 'rna3p': 40}
    Chain: "C"
      Number of atoms: 402
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 402
          Classifications: {'RNA': 19}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 1, 'rna3p': 17}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A 575 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 575 " occ=0.50
  Time building chain proxies: 2.49, per 1000 atoms: 0.32
  Number of scatterers: 7681
  At special positions: 0
  Unit cell: (86.48, 97.52, 115.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     P      67     15.00
     Mg      1     11.99
     O    1610      8.00
     N    1309      7.00
     C    4673      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: 0.73
  Conformation dependent library (CDL) restraints added in 410.0 milliseconds
  

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1456

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 1 sheets defined
      71.6% alpha, 0.3% beta
      9 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 96 through 105
    Processing helix  chain 'A' and resid 113 through 143
      removed outlier: 3.572A  pdb=" N   LEU A 117 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLN A 120 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU A 125 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LYS A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 3.905A  pdb=" N   LEU A 169 " --> pdb=" O   ASP A 165 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ARG A 170 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY A 171 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   THR A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 183
    Processing helix  chain 'A' and resid 187 through 191
      removed outlier: 3.581A  pdb=" N   TYR A 190 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 222
    Processing helix  chain 'A' and resid 249 through 270
      removed outlier: 3.947A  pdb=" N   THR A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   SER A 255 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU A 263 " --> pdb=" O   GLU A 259 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG A 264 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP A 266 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER A 267 " --> pdb=" O   GLU A 263 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU A 270 " --> pdb=" O   ASP A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 284
      removed outlier: 3.819A  pdb=" N   ILE A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 301
      removed outlier: 3.557A  pdb=" N   ILE A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL A 293 " --> pdb=" O   LYS A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 321
    Processing helix  chain 'A' and resid 330 through 336
      removed outlier: 3.504A  pdb=" N   SER A 335 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 356
      removed outlier: 4.546A  pdb=" N   LEU A 343 " --> pdb=" O   LYS A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
    Processing helix  chain 'A' and resid 371 through 399
      removed outlier: 6.532A  pdb=" N   ALA A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ASP A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 412
    Processing helix  chain 'A' and resid 431 through 442
      removed outlier: 3.761A  pdb=" N   LEU A 436 " --> pdb=" O   TYR A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 473
      removed outlier: 3.504A  pdb=" N   ASN A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 504
      removed outlier: 3.538A  pdb=" N   LEU A 496 " --> pdb=" O   CYS A 492 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU A 497 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A 499 " --> pdb=" O   THR A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 3.910A  pdb=" N   ARG A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG A 525 " --> pdb=" O   ARG A 521 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 545
      removed outlier: 3.743A  pdb=" N   ILE A 537 " --> pdb=" O   PRO A 533 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   MET A 545 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 568
    Processing helix  chain 'A' and resid 571 through 581
      removed outlier: 3.564A  pdb=" N  AHIS A 575 " --> pdb=" O   SER A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 591
      removed outlier: 4.021A  pdb=" N   THR A 588 " --> pdb=" O   LYS A 585 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 589 " --> pdb=" O   THR A 586 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 590 " --> pdb=" O   ARG A 587 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS A 591 " --> pdb=" O   THR A 588 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 585 through 591'
    Processing helix  chain 'A' and resid 592 through 603
      removed outlier: 3.562A  pdb=" N   ILE A 603 " --> pdb=" O   VAL A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
      removed outlier: 3.604A  pdb=" N   ILE A 608 " --> pdb=" O   PRO A 604 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A 610 " --> pdb=" O   THR A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 639
      removed outlier: 3.510A  pdb=" N   ILE A 636 " --> pdb=" O   VAL A 632 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   SER A 639 " --> pdb=" O   ARG A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 648
      removed outlier: 3.509A  pdb=" N   ILE A 644 " --> pdb=" O   ASP A 641 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ASP A 647 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL A 648 " --> pdb=" O   PHE A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 712
      removed outlier: 3.596A  pdb=" N   VAL A 676 " --> pdb=" O   TYR A 672 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET A 683 " --> pdb=" O   TYR A 679 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE A 686 " --> pdb=" O   VAL A 682 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 700 " --> pdb=" O   ARG A 696 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLU A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A 710 " --> pdb=" O   ARG A 706 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY A 712 " --> pdb=" O   ALA A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 733
      removed outlier: 3.931A  pdb=" N   THR A 733 " --> pdb=" O   THR A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 740
    Processing helix  chain 'A' and resid 750 through 761
      removed outlier: 4.096A  pdb=" N   GLN A 761 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 778
    Processing helix  chain 'A' and resid 778 through 783
      removed outlier: 3.767A  pdb=" N   ARG A 782 " --> pdb=" O   ILE A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 813
      removed outlier: 3.644A  pdb=" N   LEU A 800 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LYS A 811 " --> pdb=" O   SER A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 834
      removed outlier: 3.548A  pdb=" N   TYR A 826 " --> pdb=" O   LYS A 822 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 830 " --> pdb=" O   TYR A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 845
      removed outlier: 3.674A  pdb=" N   VAL A 841 " --> pdb=" O   CYS A 837 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS A 842 " --> pdb=" O   LYS A 838 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA A 843 " --> pdb=" O   ASP A 839 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR A 844 " --> pdb=" O   PHE A 840 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   CYS A 845 " --> pdb=" O   VAL A 841 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 837 through 845'
    Processing helix  chain 'A' and resid 846 through 849
    Processing helix  chain 'A' and resid 851 through 858
    Processing helix  chain 'A' and resid 860 through 864
    Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 197

    321 hydrogen bonds defined for protein.
    934 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      36 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      32 stacking parallelities
  Total time for adding SS restraints: 1.00

  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:
        1.22 -     1.34: 2063
        1.34 -     1.45: 1741
        1.45 -     1.57: 4018
        1.57 -     1.69: 133
        1.69 -     1.81: 34
  Bond restraints: 7989
  Sorted by residual:
  bond pdb=" O5'   G B   1 "
       pdb=" C5'   G B   1 "
    ideal  model  delta    sigma   weight residual
    1.420  1.449 -0.029 1.50e-02 4.44e+03 3.69e+00
  bond pdb=" O5'   C B  -1 "
       pdb=" C5'   C B  -1 "
    ideal  model  delta    sigma   weight residual
    1.424  1.451 -0.027 1.50e-02 4.44e+03 3.34e+00
  bond pdb=" P     C B  -1 "
       pdb=" OP1   C B  -1 "
    ideal  model  delta    sigma   weight residual
    1.485  1.516 -0.031 2.00e-02 2.50e+03 2.42e+00
  bond pdb=" P     C B  -1 "
       pdb=" OP2   C B  -1 "
    ideal  model  delta    sigma   weight residual
    1.485  1.514 -0.029 2.00e-02 2.50e+03 2.04e+00
  bond pdb=" C1'   G B   1 "
       pdb=" N9    G B   1 "
    ideal  model  delta    sigma   weight residual
    1.475  1.454  0.021 1.50e-02 4.44e+03 1.97e+00
  ... (remaining 7984 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 11038
        2.17 -     4.33: 62
        4.33 -     6.50: 11
        6.50 -     8.66: 0
        8.66 -    10.83: 1
  Bond angle restraints: 11112
  Sorted by residual:
  angle pdb=" C3'   C B  -1 "
        pdb=" O3'   C B  -1 "
        pdb=" P     G B   1 "
      ideal   model   delta    sigma   weight residual
     120.20  109.37   10.83 1.50e+00 4.44e-01 5.21e+01
  angle pdb=" N   ILE A 113 "
        pdb=" CA  ILE A 113 "
        pdb=" C   ILE A 113 "
      ideal   model   delta    sigma   weight residual
     113.53  109.63    3.90 9.80e-01 1.04e+00 1.58e+01
  angle pdb=" C3'   G B   1 "
        pdb=" O3'   G B   1 "
        pdb=" P     C B   2 "
      ideal   model   delta    sigma   weight residual
     120.20  115.51    4.69 1.50e+00 4.44e-01 9.77e+00
  angle pdb=" C   GLN A 172 "
        pdb=" N   THR A 173 "
        pdb=" CA  THR A 173 "
      ideal   model   delta    sigma   weight residual
     121.54  127.39   -5.85 1.91e+00 2.74e-01 9.40e+00
  angle pdb=" O3'   C B   2 "
        pdb=" C3'   C B   2 "
        pdb=" C2'   C B   2 "
      ideal   model   delta    sigma   weight residual
     113.70  117.91   -4.21 1.50e+00 4.44e-01 7.89e+00
  ... (remaining 11107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.29: 4318
       21.29 -    42.58: 403
       42.58 -    63.87: 104
       63.87 -    85.16: 43
       85.16 -   106.45: 4
  Dihedral angle restraints: 4872
    sinusoidal: 2621
      harmonic: 2251
  Sorted by residual:
  dihedral pdb=" CA  ARG A 185 "
           pdb=" C   ARG A 185 "
           pdb=" N   LYS A 186 "
           pdb=" CA  LYS A 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  LYS A 303 "
           pdb=" C   LYS A 303 "
           pdb=" N   SER A 304 "
           pdb=" CA  SER A 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.96   17.04     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" C4'   C B   2 "
           pdb=" C3'   C B   2 "
           pdb=" O3'   C B   2 "
           pdb=" P     C B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00  113.55  106.45     1      3.50e+01 8.16e-04 1.01e+01
  ... (remaining 4869 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1236
       0.078 -    0.156: 43
       0.156 -    0.234: 2
       0.234 -    0.312: 0
       0.312 -    0.390: 2
  Chirality restraints: 1283
  Sorted by residual:
  chirality pdb=" P     C B  -1 "
            pdb=" OP1   C B  -1 "
            pdb=" OP2   C B  -1 "
            pdb=" O5'   C B  -1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.80   -0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" P     G B   1 "
            pdb=" OP1   G B   1 "
            pdb=" OP2   G B   1 "
            pdb=" O5'   G B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.77   -0.36 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" C3'   G B   1 "
            pdb=" C4'   G B   1 "
            pdb=" O3'   G B   1 "
            pdb=" C2'   G B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.65    0.17 2.00e-01 2.50e+01 7.24e-01
  ... (remaining 1280 not shown)

  Planarity restraints: 1157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 480 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.70e+00
        pdb=" N   PRO A 481 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 481 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 481 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 510 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.54e+00
        pdb=" N   PRO A 511 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 511 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 511 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 648 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO A 649 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 649 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 649 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1154 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1978
        2.80 -     3.32: 6819
        3.32 -     3.85: 12039
        3.85 -     4.37: 13871
        4.37 -     4.90: 23094
  Nonbonded interactions: 57801
  Sorted by model distance:
  nonbonded pdb=" O2'   A B  -3 "
            pdb=" OP1   A B  -2 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" NZ  LYS A 822 "
            pdb=" OE2 GLU A 825 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OG  SER A 512 "
            pdb=" N   ALA A 513 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OH  TYR A 692 "
            pdb=" OP2   A B  -3 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O2'   C B   2 "
            pdb=" OP1   C B   3 "
     model   vdw
     2.288 3.040
  ... (remaining 57796 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=0.01 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.840
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
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      :  0.003   0.031   7989  Z= 0.155
  Angle     :  0.478  10.826  11112  Z= 0.287
  Chirality :  0.038   0.390   1283
  Planarity :  0.004   0.048   1157
  Dihedral  : 18.091 106.450   3416
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.00 %
    Favored  : 99.85 %
  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: -0.52 (0.30), residues: 745
  helix:  0.23 (0.23), residues: 495
  sheet:  None (None), residues: 0
  loop : -1.38 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 587 
 TYR   0.024   0.001   TYR A 642 
 PHE   0.018   0.001   PHE A 840 
 TRP   0.005   0.001   TRP A 258 
 HIS   0.004   0.001   HIS A 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 ( 7989)
  covalent geometry    : angle       0.47844 /  0.29 (11112)
  hydrogen bonds       : bond        0.29660 / 19.75 (  341)
  hydrogen bonds       : angle       6.55765 /  4.51 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  208 PHE cc_start: 0.8240 (t80) cc_final: 0.7982 (t80)
REVERT: A  543 ARG cc_start: 0.8131 (tmm160) cc_final: 0.7846 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0953
  time to fit residues: 12.7186
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0570
   overall best weight:    0.3476

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.165707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.119057 restraints weight = 20933.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 3.27
r_work: 0.3202 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (15 function evaluations)
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7989  Z= 0.170
  Angle     :  0.578   8.910  11112  Z= 0.332
  Chirality :  0.038   0.150   1283
  Planarity :  0.005   0.049   1157
  Dihedral  : 18.067 108.870   1855
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.81 %
    Favored  : 93.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.31), residues: 745
  helix:  0.96 (0.24), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.35 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 750 
 TYR   0.018   0.002   TYR A 296 
 PHE   0.015   0.001   PHE A 701 
 TRP   0.011   0.002   TRP A 752 
 HIS   0.005   0.001   HIS A 802 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.17 ( 7989)
  covalent geometry    : angle       0.57845 /  0.33 (11112)
  hydrogen bonds       : bond        0.10214 /  6.56 (  341)
  hydrogen bonds       : angle       4.30288 /  3.09 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7461 (p0) cc_final: 0.7242 (p0)
REVERT: A  208 PHE cc_start: 0.8092 (t80) cc_final: 0.7764 (t80)
REVERT: A  829 ASN cc_start: 0.7788 (m110) cc_final: 0.7483 (m-40)
  outliers start: 3
  outliers final: 2
  residues processed: 106
  average time/residue: 0.0959
  time to fit residues: 13.3254
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  832 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 20 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 24 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
A 531 ASN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 806 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.164125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117781 restraints weight = 22006.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.25
r_work: 0.3176 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (10 function evaluations)
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7989  Z= 0.173
  Angle     :  0.535   8.557  11112  Z= 0.306
  Chirality :  0.038   0.171   1283
  Planarity :  0.004   0.050   1157
  Dihedral  : 18.166 108.067   1855
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.84 %
    Favored  : 91.44 %
  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:  0.31 (0.31), residues: 745
  helix:  0.95 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.34 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 610 
 TYR   0.024   0.002   TYR A 296 
 PHE   0.012   0.001   PHE A 420 
 TRP   0.011   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 742 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.17 ( 7989)
  covalent geometry    : angle       0.53452 /  0.31 (11112)
  hydrogen bonds       : bond        0.09475 /  6.11 (  341)
  hydrogen bonds       : angle       4.06955 /  2.91 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7527 (p0) cc_final: 0.7279 (p0)
REVERT: A  208 PHE cc_start: 0.8075 (t80) cc_final: 0.7767 (t80)
REVERT: A  829 ASN cc_start: 0.7704 (m110) cc_final: 0.7318 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 101
  average time/residue: 0.0908
  time to fit residues: 12.2333
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Chi-restraints excluded: chain A residue  832 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   chunk 57 optimal weight:    0.5980
   chunk 29 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
A 531 ASN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.163166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115065 restraints weight = 25712.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.71
r_work: 0.3152 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (13 function evaluations)
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7989  Z= 0.178
  Angle     :  0.532   7.952  11112  Z= 0.304
  Chirality :  0.038   0.178   1283
  Planarity :  0.004   0.050   1157
  Dihedral  : 18.223 108.397   1855
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  9.29 %
    Favored  : 89.99 %
  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:  0.21 (0.31), residues: 745
  helix:  0.91 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.46 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 543 
 TYR   0.023   0.002   TYR A 296 
 PHE   0.013   0.002   PHE A 420 
 TRP   0.009   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 7989)
  covalent geometry    : angle       0.53166 /  0.30 (11112)
  hydrogen bonds       : bond        0.08749 /  5.63 (  341)
  hydrogen bonds       : angle       3.95934 /  2.84 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7589 (p0) cc_final: 0.7333 (p0)
REVERT: A  123 ASP cc_start: 0.7809 (t0) cc_final: 0.7574 (t0)
REVERT: A  208 PHE cc_start: 0.8158 (t80) cc_final: 0.7852 (t80)
REVERT: A  453 LEU cc_start: 0.7662 (mm) cc_final: 0.7303 (mp)
REVERT: A  829 ASN cc_start: 0.7732 (m110) cc_final: 0.7382 (m-40)
  outliers start: 4
  outliers final: 3
  residues processed: 100
  average time/residue: 0.0815
  time to fit residues: 11.0464
Evaluate side-chains
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 36 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 28 optimal weight:    6.9990
   chunk 11 optimal weight:    0.2980
   chunk 78 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
A 531 ASN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.164517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.118072 restraints weight = 20927.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.18
r_work: 0.3209 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7989  Z= 0.162
  Angle     :  0.509   7.073  11112  Z= 0.292
  Chirality :  0.038   0.178   1283
  Planarity :  0.004   0.051   1157
  Dihedral  : 18.277 108.602   1855
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  9.58 %
    Favored  : 89.70 %
  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:  0.25 (0.31), residues: 745
  helix:  0.94 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.45 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 294 
 TYR   0.021   0.002   TYR A 296 
 PHE   0.013   0.001   PHE A 553 
 TRP   0.010   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 ( 7989)
  covalent geometry    : angle       0.50944 /  0.29 (11112)
  hydrogen bonds       : bond        0.08331 /  5.34 (  341)
  hydrogen bonds       : angle       3.89895 /  2.79 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7591 (p0) cc_final: 0.7310 (p0)
REVERT: A  123 ASP cc_start: 0.7728 (t0) cc_final: 0.7468 (t0)
REVERT: A  208 PHE cc_start: 0.8033 (t80) cc_final: 0.7740 (t80)
REVERT: A  453 LEU cc_start: 0.7443 (mm) cc_final: 0.7101 (mp)
REVERT: A  829 ASN cc_start: 0.7662 (m110) cc_final: 0.7322 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 103
  average time/residue: 0.0940
  time to fit residues: 12.8676
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 67 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 HIS
A 219 GLN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.163821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118012 restraints weight = 22452.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 3.27
r_work: 0.3176 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7989  Z= 0.186
  Angle     :  0.532   7.173  11112  Z= 0.302
  Chirality :  0.039   0.179   1283
  Planarity :  0.004   0.049   1157
  Dihedral  : 18.308 109.105   1855
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 10.45 %
    Favored  : 88.82 %
  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:  0.18 (0.31), residues: 745
  helix:  0.88 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.48 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 610 
 TYR   0.023   0.002   TYR A 844 
 PHE   0.014   0.002   PHE A 420 
 TRP   0.010   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00427 /  0.19 ( 7989)
  covalent geometry    : angle       0.53164 /  0.30 (11112)
  hydrogen bonds       : bond        0.08378 /  5.36 (  341)
  hydrogen bonds       : angle       3.90786 /  2.80 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7625 (p0) cc_final: 0.7326 (p0)
REVERT: A  123 ASP cc_start: 0.7794 (t0) cc_final: 0.7541 (t0)
REVERT: A  208 PHE cc_start: 0.8108 (t80) cc_final: 0.7804 (t80)
REVERT: A  453 LEU cc_start: 0.7460 (mm) cc_final: 0.7138 (mp)
REVERT: A  514 ASP cc_start: 0.8073 (t0) cc_final: 0.7779 (t0)
REVERT: A  829 ASN cc_start: 0.7687 (m110) cc_final: 0.7338 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 102
  average time/residue: 0.0849
  time to fit residues: 11.8146
Evaluate side-chains
  101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 72 optimal weight:    0.4980
   chunk 7 optimal weight:    0.4980
   chunk 8 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
A 531 ASN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.164526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118337 restraints weight = 24880.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.40
r_work: 0.3133 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (12 function evaluations)
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7989  Z= 0.163
  Angle     :  0.519   7.507  11112  Z= 0.295
  Chirality :  0.038   0.177   1283
  Planarity :  0.004   0.051   1157
  Dihedral  : 18.306 109.706   1855
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.89 %
    Favored  : 88.24 %
  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:  0.24 (0.31), residues: 745
  helix:  0.94 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.48 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 294 
 TYR   0.019   0.002   TYR A 296 
 PHE   0.012   0.001   PHE A 420 
 TRP   0.011   0.002   TRP A 752 
 HIS   0.005   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.16 ( 7989)
  covalent geometry    : angle       0.51870 /  0.30 (11112)
  hydrogen bonds       : bond        0.07864 /  5.00 (  341)
  hydrogen bonds       : angle       3.82930 /  2.74 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7707 (p0) cc_final: 0.7359 (p0)
REVERT: A  123 ASP cc_start: 0.7754 (t0) cc_final: 0.7492 (t0)
REVERT: A  208 PHE cc_start: 0.7857 (t80) cc_final: 0.7543 (t80)
REVERT: A  271 LYS cc_start: 0.7481 (ttpt) cc_final: 0.7186 (mtpp)
REVERT: A  453 LEU cc_start: 0.7191 (mm) cc_final: 0.6862 (mp)
REVERT: A  514 ASP cc_start: 0.8045 (t0) cc_final: 0.7570 (t0)
REVERT: A  829 ASN cc_start: 0.7571 (m110) cc_final: 0.7158 (m110)
  outliers start: 5
  outliers final: 5
  residues processed: 101
  average time/residue: 0.1032
  time to fit residues: 13.8171
Evaluate side-chains
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 59 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 531 ASN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.163604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.118287 restraints weight = 18363.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 3.16
r_work: 0.3211 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7989  Z= 0.184
  Angle     :  0.533   7.044  11112  Z= 0.302
  Chirality :  0.038   0.175   1283
  Planarity :  0.004   0.053   1157
  Dihedral  : 18.364 108.310   1855
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.03 %
    Favored  : 88.10 %
  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:  0.16 (0.31), residues: 745
  helix:  0.87 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 610 
 TYR   0.023   0.002   TYR A 844 
 PHE   0.015   0.002   PHE A 420 
 TRP   0.010   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.18 ( 7989)
  covalent geometry    : angle       0.53313 /  0.30 (11112)
  hydrogen bonds       : bond        0.08062 /  5.13 (  341)
  hydrogen bonds       : angle       3.85182 /  2.75 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7606 (p0) cc_final: 0.7291 (p0)
REVERT: A  123 ASP cc_start: 0.7756 (t0) cc_final: 0.7536 (t0)
REVERT: A  208 PHE cc_start: 0.8125 (t80) cc_final: 0.7816 (t80)
REVERT: A  271 LYS cc_start: 0.7588 (ttpt) cc_final: 0.7294 (mtpp)
REVERT: A  453 LEU cc_start: 0.7458 (mm) cc_final: 0.7142 (mp)
REVERT: A  468 ASP cc_start: 0.7938 (t0) cc_final: 0.7589 (t0)
REVERT: A  514 ASP cc_start: 0.8081 (t0) cc_final: 0.7593 (t0)
REVERT: A  829 ASN cc_start: 0.7677 (m110) cc_final: 0.7275 (m110)
  outliers start: 5
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0828
  time to fit residues: 11.3822
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
A 531 ASN
A 694 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.162007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.114880 restraints weight = 16107.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.66
r_work: 0.3140 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   7989  Z= 0.235
  Angle     :  0.577   7.519  11112  Z= 0.324
  Chirality :  0.041   0.175   1283
  Planarity :  0.005   0.049   1157
  Dihedral  : 18.487 108.525   1855
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.76 %
    Favored  : 87.37 %
  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: -0.05 (0.31), residues: 745
  helix:  0.71 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.57 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 202 
 TYR   0.029   0.002   TYR A 844 
 PHE   0.017   0.002   PHE A 420 
 TRP   0.009   0.002   TRP A 752 
 HIS   0.008   0.002   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00559 /  0.24 ( 7989)
  covalent geometry    : angle       0.57712 /  0.32 (11112)
  hydrogen bonds       : bond        0.08680 /  5.53 (  341)
  hydrogen bonds       : angle       3.97321 /  2.84 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7636 (p0) cc_final: 0.7405 (p0)
REVERT: A  123 ASP cc_start: 0.7764 (t0) cc_final: 0.7502 (t0)
REVERT: A  208 PHE cc_start: 0.8049 (t80) cc_final: 0.7716 (t80)
REVERT: A  453 LEU cc_start: 0.7380 (mm) cc_final: 0.7098 (mp)
REVERT: A  514 ASP cc_start: 0.8070 (t0) cc_final: 0.7589 (t0)
REVERT: A  829 ASN cc_start: 0.7682 (m110) cc_final: 0.7271 (m-40)
REVERT: A  841 VAL cc_start: 0.8387 (m) cc_final: 0.8141 (t)
  outliers start: 5
  outliers final: 5
  residues processed: 104
  average time/residue: 0.1006
  time to fit residues: 13.7104
Evaluate side-chains
  106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0070
   chunk 52 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0870
   chunk 45 optimal weight:    0.1980
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.2776

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
A 531 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.166107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118922 restraints weight = 25651.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.67
r_work: 0.3174 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (15 function evaluations)
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7989  Z= 0.130
  Angle     :  0.501   8.642  11112  Z= 0.285
  Chirality :  0.036   0.172   1283
  Planarity :  0.004   0.054   1157
  Dihedral  : 18.476 108.618   1855
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 12.63 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.28 (0.31), residues: 745
  helix:  1.00 (0.24), residues: 503
  sheet:  None (None), residues: 0
  loop : -1.53 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 610 
 TYR   0.016   0.001   TYR A 296 
 PHE   0.012   0.001   PHE A 433 
 TRP   0.013   0.001   TRP A 752 
 HIS   0.003   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.13 ( 7989)
  covalent geometry    : angle       0.50122 /  0.29 (11112)
  hydrogen bonds       : bond        0.06962 /  4.37 (  341)
  hydrogen bonds       : angle       3.71406 /  2.66 (  970)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7686 (p0) cc_final: 0.7370 (p0)
REVERT: A  186 LYS cc_start: 0.8305 (ptmt) cc_final: 0.7912 (ptmt)
REVERT: A  208 PHE cc_start: 0.8061 (t80) cc_final: 0.7719 (t80)
REVERT: A  271 LYS cc_start: 0.7511 (ttpt) cc_final: 0.7219 (mtpp)
REVERT: A  514 ASP cc_start: 0.8094 (t0) cc_final: 0.7567 (t0)
REVERT: A  829 ASN cc_start: 0.7768 (m110) cc_final: 0.7362 (m110)
  outliers start: 3
  outliers final: 3
  residues processed: 96
  average time/residue: 0.0851
  time to fit residues: 11.2410
Evaluate side-chains
  98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  764 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 72 optimal weight:    0.1980
   chunk 77 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 54 optimal weight:    0.5980
   chunk 20 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 219 GLN
A 531 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.165105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.118963 restraints weight = 23531.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.31
r_work: 0.3195 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7989  Z= 0.148
  Angle     :  0.502   6.941  11112  Z= 0.285
  Chirality :  0.037   0.167   1283
  Planarity :  0.004   0.053   1157
  Dihedral  : 18.352 107.516   1855
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 12.19 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.30 (0.31), residues: 745
  helix:  1.00 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 610 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.013   0.001   PHE A 420 
 TRP   0.012   0.001   TRP A 752 
 HIS   0.005   0.001   HIS A 802 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 7989)
  covalent geometry    : angle       0.50197 /  0.28 (11112)
  hydrogen bonds       : bond        0.07128 /  4.49 (  341)
  hydrogen bonds       : angle       3.69275 /  2.65 (  970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2003.29 seconds
wall clock time: 34 minutes 57.67 seconds (2097.67 seconds total)