Starting phenix.real_space_refine
on Tue Feb  3 23:31:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m33_63597/02_2026/9m33_63597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m33_63597/02_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_63597/02_2026/9m33_63597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m33_63597/02_2026/9m33_63597.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m33_63597/02_2026/9m33_63597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m33_63597/02_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-2.0-5952/lib/python3.9/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: 2.27, per 1000 atoms: 0.30
  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: 0.57
  Conformation dependent library (CDL) restraints added in 327.0 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: 0.67
  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: 0.90

  Time building geometry restraints manager: 0.74 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:             2.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.040
  Process input model:                     8.260
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
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= 0.138
  Angle     :  0.478  10.826  11112  Z= 0.274
  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
  covalent geometry    : bond        0.00307 ( 7989)
  covalent geometry    : angle       0.47840 (11112)
  hydrogen bonds       : bond        0.29660 (  341)
  hydrogen bonds       : angle       6.55765 (  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  : 0.245 
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: 0.0786
  time to fit residues: 10.7309
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  : 0.188 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4026 r_free = 0.4026 target = 0.166347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.118571 restraints weight = 21011.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.49
r_work: 0.3205 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7989  Z= 0.152
  Angle     :  0.603   9.190  11112  Z= 0.317
  Chirality :  0.037   0.172   1283
  Planarity :  0.004   0.049   1157
  Dihedral  : 18.033 108.920   1855
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  5.81 %
    Favored  : 93.76 %
  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:  0.35 (0.31), residues: 745
  helix:  0.96 (0.24), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.29 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 543 
 TYR   0.024   0.002   TYR A 296 
 PHE   0.014   0.001   PHE A 433 
 TRP   0.011   0.002   TRP A 814 
 HIS   0.004   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7989)
  covalent geometry    : angle       0.60286 (11112)
  hydrogen bonds       : bond        0.08373 (  341)
  hydrogen bonds       : angle       4.02367 (  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
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7472 (p0) cc_final: 0.7242 (p0)
REVERT: A  208 PHE cc_start: 0.8068 (t80) cc_final: 0.7771 (t80)
REVERT: A  237 PHE cc_start: 0.8119 (m-80) cc_final: 0.7901 (m-80)
REVERT: A  570 GLU cc_start: 0.7254 (tm-30) cc_final: 0.7027 (tm-30)
REVERT: A  829 ASN cc_start: 0.7750 (m110) cc_final: 0.7417 (m-40)
  outliers start: 2
  outliers final: 2
  residues processed: 103
  average time/residue: 0.0906
  time to fit residues: 12.2241
Evaluate side-chains
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
A 219 GLN
** 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 = 0.3985 r_free = 0.3985 target = 0.163093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.116001 restraints weight = 21877.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 3.47
r_work: 0.3158 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7989  Z= 0.210
  Angle     :  0.608   7.654  11112  Z= 0.320
  Chirality :  0.040   0.177   1283
  Planarity :  0.004   0.048   1157
  Dihedral  : 18.218 107.898   1855
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  8.71 %
    Favored  : 90.57 %
  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:  0.20 (0.31), residues: 745
  helix:  0.86 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.38 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 202 
 TYR   0.029   0.002   TYR A 296 
 PHE   0.015   0.002   PHE A 420 
 TRP   0.010   0.002   TRP A 752 
 HIS   0.007   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 7989)
  covalent geometry    : angle       0.60839 (11112)
  hydrogen bonds       : bond        0.08755 (  341)
  hydrogen bonds       : angle       4.00107 (  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  : 0.270 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7620 (p0) cc_final: 0.7344 (p0)
REVERT: A  123 ASP cc_start: 0.7750 (t0) cc_final: 0.7526 (t0)
REVERT: A  208 PHE cc_start: 0.8178 (t80) cc_final: 0.7828 (t80)
REVERT: A  453 LEU cc_start: 0.7546 (mm) cc_final: 0.7215 (mp)
REVERT: A  570 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7100 (tm-30)
REVERT: A  829 ASN cc_start: 0.7754 (m110) cc_final: 0.7362 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 102
  average time/residue: 0.1052
  time to fit residues: 13.9668
Evaluate side-chains
  102 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  825 GLU
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:    0.0970
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 29 optimal weight:    8.9990
   chunk 42 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4012 r_free = 0.4012 target = 0.165284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.119580 restraints weight = 25915.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.42
r_work: 0.3199 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    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 = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7989  Z= 0.153
  Angle     :  0.547   7.454  11112  Z= 0.291
  Chirality :  0.037   0.176   1283
  Planarity :  0.004   0.049   1157
  Dihedral  : 18.141 109.307   1855
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.00 %
    Favored  : 90.13 %
  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:  0.98 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.46 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 610 
 TYR   0.021   0.001   TYR A 296 
 PHE   0.012   0.001   PHE A 420 
 TRP   0.012   0.002   TRP A 752 
 HIS   0.005   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7989)
  covalent geometry    : angle       0.54686 (11112)
  hydrogen bonds       : bond        0.07479 (  341)
  hydrogen bonds       : angle       3.79556 (  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
  102 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7606 (p0) cc_final: 0.7315 (p0)
REVERT: A  123 ASP cc_start: 0.7732 (t0) cc_final: 0.7516 (t0)
REVERT: A  208 PHE cc_start: 0.8070 (t80) cc_final: 0.7759 (t80)
REVERT: A  453 LEU cc_start: 0.7392 (mm) cc_final: 0.7037 (mp)
REVERT: A  491 ASN cc_start: 0.7687 (t0) cc_final: 0.7378 (t0)
REVERT: A  829 ASN cc_start: 0.7731 (m110) cc_final: 0.7388 (m-40)
  outliers start: 5
  outliers final: 5
  residues processed: 100
  average time/residue: 0.0889
  time to fit residues: 11.7574
Evaluate side-chains
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  825 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 46 optimal weight:    0.2980
   chunk 25 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4003 r_free = 0.4003 target = 0.164510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117921 restraints weight = 20866.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.19
r_work: 0.3204 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    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 = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7989  Z= 0.170
  Angle     :  0.553   7.169  11112  Z= 0.294
  Chirality :  0.038   0.171   1283
  Planarity :  0.004   0.050   1157
  Dihedral  : 18.177 107.556   1855
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.43 %
    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:  0.28 (0.31), residues: 745
  helix:  0.96 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.46 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.022   0.002   TYR A 296 
 PHE   0.013   0.001   PHE A 420 
 TRP   0.012   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 7989)
  covalent geometry    : angle       0.55257 (11112)
  hydrogen bonds       : bond        0.07610 (  341)
  hydrogen bonds       : angle       3.79276 (  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
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7618 (p0) cc_final: 0.7327 (p0)
REVERT: A  123 ASP cc_start: 0.7750 (t0) cc_final: 0.7515 (t0)
REVERT: A  208 PHE cc_start: 0.8116 (t80) cc_final: 0.7801 (t80)
REVERT: A  271 LYS cc_start: 0.7570 (ttpt) cc_final: 0.7280 (mtpp)
REVERT: A  453 LEU cc_start: 0.7450 (mm) cc_final: 0.7127 (mp)
REVERT: A  829 ASN cc_start: 0.7743 (m110) cc_final: 0.7393 (m-40)
  outliers start: 5
  outliers final: 5
  residues processed: 102
  average time/residue: 0.0782
  time to fit residues: 10.7584
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  : 0.275 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  825 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 67 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3995 r_free = 0.3995 target = 0.163448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.115811 restraints weight = 22217.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.26
r_work: 0.3144 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7989  Z= 0.192
  Angle     :  0.560   6.966  11112  Z= 0.299
  Chirality :  0.038   0.169   1283
  Planarity :  0.004   0.049   1157
  Dihedral  : 18.228 107.641   1855
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.16 %
    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:  0.90 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.51 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.024   0.002   TYR A 844 
 PHE   0.014   0.002   PHE A 420 
 TRP   0.011   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7989)
  covalent geometry    : angle       0.56029 (11112)
  hydrogen bonds       : bond        0.07859 (  341)
  hydrogen bonds       : angle       3.85388 (  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
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7665 (p0) cc_final: 0.7326 (p0)
REVERT: A  123 ASP cc_start: 0.7758 (t0) cc_final: 0.7519 (t0)
REVERT: A  208 PHE cc_start: 0.8094 (t80) cc_final: 0.7774 (t80)
REVERT: A  271 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7308 (mtpp)
REVERT: A  453 LEU cc_start: 0.7426 (mm) cc_final: 0.7098 (mp)
REVERT: A  468 ASP cc_start: 0.7895 (t0) cc_final: 0.7569 (t0)
REVERT: A  514 ASP cc_start: 0.8108 (t0) cc_final: 0.7574 (t0)
REVERT: A  543 ARG cc_start: 0.8305 (tmm160) cc_final: 0.8066 (ttt-90)
REVERT: A  829 ASN cc_start: 0.7747 (m110) cc_final: 0.7381 (m-40)
  outliers start: 6
  outliers final: 6
  residues processed: 101
  average time/residue: 0.0996
  time to fit residues: 13.2530
Evaluate side-chains
  101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  544 THR
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Chi-restraints excluded: chain A residue  825 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 26 optimal weight:    8.9990
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3999 r_free = 0.3999 target = 0.163774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.116995 restraints weight = 24705.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 3.51
r_work: 0.3147 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
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:        3 |
|-----------------------------------------------------------------------------|
|-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 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7989  Z= 0.184
  Angle     :  0.554   6.758  11112  Z= 0.296
  Chirality :  0.038   0.168   1283
  Planarity :  0.004   0.051   1157
  Dihedral  : 18.248 107.544   1855
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.45 %
    Favored  : 88.53 %
  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:  0.89 (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 493 
 TYR   0.022   0.002   TYR A 844 
 PHE   0.015   0.002   PHE A 560 
 TRP   0.011   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7989)
  covalent geometry    : angle       0.55367 (11112)
  hydrogen bonds       : bond        0.07717 (  341)
  hydrogen bonds       : angle       3.83706 (  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
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7688 (p0) cc_final: 0.7346 (p0)
REVERT: A  123 ASP cc_start: 0.7801 (t0) cc_final: 0.7574 (t0)
REVERT: A  208 PHE cc_start: 0.8143 (t80) cc_final: 0.7814 (t80)
REVERT: A  271 LYS cc_start: 0.7623 (ttpt) cc_final: 0.7332 (mtpp)
REVERT: A  453 LEU cc_start: 0.7472 (mm) cc_final: 0.7135 (mp)
REVERT: A  514 ASP cc_start: 0.8127 (t0) cc_final: 0.7591 (t0)
REVERT: A  829 ASN cc_start: 0.7797 (m110) cc_final: 0.7376 (m110)
  outliers start: 6
  outliers final: 6
  residues processed: 97
  average time/residue: 0.0693
  time to fit residues: 9.2277
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  718 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  764 ASP
Chi-restraints excluded: chain A residue  825 GLU
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:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3996 r_free = 0.3996 target = 0.163587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117298 restraints weight = 18261.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 3.06
r_work: 0.3197 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
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 = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7989  Z= 0.188
  Angle     :  0.557   6.979  11112  Z= 0.298
  Chirality :  0.038   0.168   1283
  Planarity :  0.004   0.051   1157
  Dihedral  : 18.269 107.531   1855
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.18 %
    Favored  : 87.95 %
  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:  0.88 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.52 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 610 
 TYR   0.022   0.002   TYR A 844 
 PHE   0.013   0.002   PHE A 560 
 TRP   0.011   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 7989)
  covalent geometry    : angle       0.55709 (11112)
  hydrogen bonds       : bond        0.07728 (  341)
  hydrogen bonds       : angle       3.83512 (  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
  98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7602 (p0) cc_final: 0.7272 (p0)
REVERT: A  208 PHE cc_start: 0.8173 (t80) cc_final: 0.7850 (t80)
REVERT: A  271 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7343 (mtpp)
REVERT: A  453 LEU cc_start: 0.7506 (mm) cc_final: 0.7179 (mp)
REVERT: A  514 ASP cc_start: 0.8112 (t0) cc_final: 0.7570 (t0)
REVERT: A  543 ARG cc_start: 0.8363 (tmm160) cc_final: 0.8108 (ttt-90)
REVERT: A  829 ASN cc_start: 0.7772 (m110) cc_final: 0.7333 (m110)
REVERT: A  841 VAL cc_start: 0.8463 (m) cc_final: 0.8196 (t)
  outliers start: 5
  outliers final: 5
  residues processed: 95
  average time/residue: 0.0893
  time to fit residues: 11.5448
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  825 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0870
   chunk 69 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4011 r_free = 0.4011 target = 0.164766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117659 restraints weight = 16151.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.68
r_work: 0.3240 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7989  Z= 0.160
  Angle     :  0.534   6.755  11112  Z= 0.287
  Chirality :  0.037   0.165   1283
  Planarity :  0.004   0.052   1157
  Dihedral  : 18.278 107.062   1855
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.32 %
    Favored  : 87.66 %
  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:  0.98 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 543 
 TYR   0.018   0.001   TYR A 844 
 PHE   0.012   0.001   PHE A 420 
 TRP   0.012   0.001   TRP A 752 
 HIS   0.005   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7989)
  covalent geometry    : angle       0.53411 (11112)
  hydrogen bonds       : bond        0.07184 (  341)
  hydrogen bonds       : angle       3.73878 (  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
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7580 (p0) cc_final: 0.7274 (p0)
REVERT: A  208 PHE cc_start: 0.8112 (t80) cc_final: 0.7791 (t80)
REVERT: A  271 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7305 (mtpp)
REVERT: A  453 LEU cc_start: 0.7433 (mm) cc_final: 0.7085 (mp)
REVERT: A  468 ASP cc_start: 0.7884 (t0) cc_final: 0.7541 (t0)
REVERT: A  514 ASP cc_start: 0.8040 (t0) cc_final: 0.7488 (t0)
REVERT: A  543 ARG cc_start: 0.8358 (tmm160) cc_final: 0.8083 (ttt-90)
REVERT: A  829 ASN cc_start: 0.7736 (m110) cc_final: 0.7333 (m-40)
  outliers start: 6
  outliers final: 5
  residues processed: 96
  average time/residue: 0.0856
  time to fit residues: 10.9174
Evaluate side-chains
  96 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  825 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0060
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0670
   chunk 40 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 72 optimal weight:    0.4980
   chunk 45 optimal weight:    0.4980
   chunk 56 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.2734

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4052 r_free = 0.4052 target = 0.168317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.121388 restraints weight = 25616.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 3.70
r_work: 0.3224 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7989  Z= 0.119
  Angle     :  0.496   7.226  11112  Z= 0.268
  Chirality :  0.035   0.155   1283
  Planarity :  0.004   0.055   1157
  Dihedral  : 18.203 104.941   1855
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.32 %
    Favored  : 87.81 %
  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:  0.51 (0.31), residues: 745
  helix:  1.23 (0.24), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.55 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 610 
 TYR   0.013   0.001   TYR A 296 
 PHE   0.011   0.001   PHE A 420 
 TRP   0.013   0.001   TRP A 752 
 HIS   0.005   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7989)
  covalent geometry    : angle       0.49617 (11112)
  hydrogen bonds       : bond        0.05962 (  341)
  hydrogen bonds       : angle       3.54505 (  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
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7634 (p0) cc_final: 0.7351 (p0)
REVERT: A  208 PHE cc_start: 0.8036 (t80) cc_final: 0.7760 (t80)
REVERT: A  271 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7132 (mtpp)
REVERT: A  468 ASP cc_start: 0.7906 (t0) cc_final: 0.7528 (t0)
REVERT: A  498 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7884 (mt-10)
REVERT: A  514 ASP cc_start: 0.8069 (t0) cc_final: 0.7530 (t0)
REVERT: A  543 ARG cc_start: 0.8387 (tmm160) cc_final: 0.8148 (ttt-90)
REVERT: A  829 ASN cc_start: 0.7750 (m110) cc_final: 0.7413 (m-40)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 0.0890
  time to fit residues: 11.8127
Evaluate side-chains
  98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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  764 ASP
Chi-restraints excluded: chain A residue  825 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0980
   chunk 77 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4012 r_free = 0.4012 target = 0.164789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.118064 restraints weight = 23496.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.45
r_work: 0.3182 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7989  Z= 0.171
  Angle     :  0.538   6.668  11112  Z= 0.288
  Chirality :  0.037   0.148   1283
  Planarity :  0.004   0.053   1157
  Dihedral  : 18.263 104.577   1855
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.76 %
    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:  0.39 (0.31), residues: 745
  helix:  1.09 (0.24), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.54 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 610 
 TYR   0.020   0.002   TYR A 844 
 PHE   0.014   0.001   PHE A 553 
 TRP   0.013   0.002   TRP A 752 
 HIS   0.005   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7989)
  covalent geometry    : angle       0.53788 (11112)
  hydrogen bonds       : bond        0.07232 (  341)
  hydrogen bonds       : angle       3.69210 (  970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1800.03 seconds
wall clock time: 31 minutes 27.05 seconds (1887.05 seconds total)