Starting phenix.real_space_refine
on Wed Aug  5 00:59:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m33_63597/08_2026/9m33_63597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m33_63597/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m33_63597/08_2026/9m33_63597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m33_63597/08_2026/9m33_63597.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m33_63597/08_2026/9m33_63597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m33_63597/08_2026/9m33_63597.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.57, per 1000 atoms: 0.33
  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: 0.67
  Conformation dependent library (CDL) restraints added in 416.4 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: 0.91
  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: 1.27

  Time building geometry restraints manager: 0.91 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=" C1'   G B   1 "
       pdb=" N9    G B   1 "
    ideal  model  delta    sigma   weight residual
    1.483  1.454  0.029 1.50e-02 4.44e+03 3.75e+00
  bond pdb=" O5'   C B  -1 "
       pdb=" C5'   C B  -1 "
    ideal  model  delta    sigma   weight residual
    1.424  1.451 -0.027 1.60e-02 3.91e+03 2.94e+00
  bond pdb=" P     C B  -1 "
       pdb=" O5'   C B  -1 "
    ideal  model  delta    sigma   weight residual
    1.593  1.610 -0.017 1.00e-02 1.00e+04 2.90e+00
  bond pdb=" P     G B   1 "
       pdb=" O5'   G B   1 "
    ideal  model  delta    sigma   weight residual
    1.593  1.610 -0.017 1.00e-02 1.00e+04 2.79e+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
  ... (remaining 7984 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 10876
        2.07 -     4.13: 221
        4.13 -     6.20: 14
        6.20 -     8.26: 0
        8.26 -    10.33: 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
     119.70  109.37   10.33 1.20e+00 6.94e-01 7.40e+01
  angle pdb=" O5'   A B  -2 "
        pdb=" C5'   A B  -2 "
        pdb=" C4'   A B  -2 "
      ideal   model   delta    sigma   weight residual
     109.40  112.79   -3.39 8.00e-01 1.56e+00 1.79e+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=" O5'   C B   3 "
        pdb=" C5'   C B   3 "
        pdb=" C4'   C B   3 "
      ideal   model   delta    sigma   weight residual
     109.40  112.53   -3.13 8.00e-01 1.56e+00 1.53e+01
  angle pdb=" C3'   C B   2 "
        pdb=" O3'   C B   2 "
        pdb=" P     C B   3 "
      ideal   model   delta    sigma   weight residual
     119.70  124.27   -4.57 1.20e+00 6.94e-01 1.45e+01
  ... (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: 1171
       0.078 -    0.156: 108
       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:             2.910
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.640
-------------------------------------------------------------------------------
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= 0.167
  Angle     :  0.565  10.326  11112  Z= 0.372
  Chirality :  0.047   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        0.00316 /  0.17 ( 7989)
  covalent geometry    : angle       0.56496 /  0.37 (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  : 0.251 
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: 0.1080
  time to fit residues: 14.5565
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  : 0.193 
-------------------------------------------------------------------------------
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 = 0.165738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118249 restraints weight = 20913.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 3.39
r_work: 0.3189 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    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 = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (19 function evaluations)
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7989  Z= 0.166
  Angle     :  0.594   9.322  11112  Z= 0.335
  Chirality :  0.039   0.200   1283
  Planarity :  0.005   0.049   1157
  Dihedral  : 18.025 106.752   1855
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.95 %
    Favored  : 93.47 %
  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:  0.27 (0.31), residues: 745
  helix:  0.92 (0.23), residues: 503
  sheet:  None (None), residues: 0
  loop : -1.35 (0.40), residues: 242

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   0.018   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        0.00323 /  0.17 ( 7989)
  covalent geometry    : angle       0.59379 /  0.33 (11112)
  hydrogen bonds       : bond        0.10399 /  6.67 (  341)
  hydrogen bonds       : angle       4.31793 /  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  : 0.249 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7461 (p0) cc_final: 0.7239 (p0)
REVERT: A  208 PHE cc_start: 0.8060 (t80) cc_final: 0.7733 (t80)
REVERT: A  829 ASN cc_start: 0.7768 (m110) cc_final: 0.7460 (m-40)
  outliers start: 3
  outliers final: 2
  residues processed: 106
  average time/residue: 0.1050
  time to fit residues: 14.6102
Evaluate side-chains
  98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0000
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 24 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5984

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.163882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.117531 restraints weight = 21995.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 3.25
r_work: 0.3167 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    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 = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (12 function evaluations)
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   7989  Z= 0.182
  Angle     :  0.552   8.670  11112  Z= 0.311
  Chirality :  0.039   0.226   1283
  Planarity :  0.005   0.049   1157
  Dihedral  : 18.109 106.834   1855
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  8.42 %
    Favored  : 90.86 %
  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:  0.27 (0.31), residues: 745
  helix:  0.92 (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   0.001   ARG A 610 
 TYR   0.025   0.002   TYR A 296 
 PHE   0.013   0.002   PHE A 553 
 TRP   0.010   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 742 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.18 ( 7989)
  covalent geometry    : angle       0.55235 /  0.31 (11112)
  hydrogen bonds       : bond        0.09662 /  6.25 (  341)
  hydrogen bonds       : angle       4.08718 /  2.92 (  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
  102 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7538 (p0) cc_final: 0.7286 (p0)
REVERT: A  208 PHE cc_start: 0.8073 (t80) cc_final: 0.7764 (t80)
REVERT: A  829 ASN cc_start: 0.7702 (m110) cc_final: 0.7323 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0894
  time to fit residues: 11.9804
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  : 0.284 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 57 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 42 optimal weight:    0.6980
   chunk 21 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 62 optimal weight:    0.1980
   chunk 32 optimal weight:    0.5980
   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 = 0.4002 r_free = 0.4002 target = 0.164325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117687 restraints weight = 25543.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.58
r_work: 0.3164 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    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 = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (11 function evaluations)
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7989  Z= 0.166
  Angle     :  0.536   8.205  11112  Z= 0.302
  Chirality :  0.038   0.226   1283
  Planarity :  0.004   0.050   1157
  Dihedral  : 18.158 108.264   1855
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  9.00 %
    Favored  : 90.28 %
  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:  0.93 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.43 (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 296 
 PHE   0.014   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        0.00365 /  0.17 ( 7989)
  covalent geometry    : angle       0.53607 /  0.30 (11112)
  hydrogen bonds       : bond        0.08779 /  5.64 (  341)
  hydrogen bonds       : angle       3.96163 /  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
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7577 (p0) cc_final: 0.7309 (p0)
REVERT: A  123 ASP cc_start: 0.7757 (t0) cc_final: 0.7517 (t0)
REVERT: A  208 PHE cc_start: 0.8077 (t80) cc_final: 0.7766 (t80)
REVERT: A  453 LEU cc_start: 0.7515 (mm) cc_final: 0.7161 (mp)
REVERT: A  829 ASN cc_start: 0.7688 (m110) cc_final: 0.7352 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 103
  average time/residue: 0.0912
  time to fit residues: 12.5125
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  : 0.153 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 HIS
A 219 GLN
A 531 ASN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.163854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.116517 restraints weight = 20579.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 3.30
r_work: 0.3189 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (16 function evaluations)
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7989  Z= 0.178
  Angle     :  0.537   7.042  11112  Z= 0.302
  Chirality :  0.039   0.234   1283
  Planarity :  0.004   0.050   1157
  Dihedral  : 18.169 109.054   1855
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 10.01 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.31), residues: 745
  helix:  0.88 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.47 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 561 
 TYR   0.023   0.002   TYR A 296 
 PHE   0.015   0.002   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        0.00407 /  0.18 ( 7989)
  covalent geometry    : angle       0.53689 /  0.30 (11112)
  hydrogen bonds       : bond        0.08612 /  5.52 (  341)
  hydrogen bonds       : angle       3.94393 /  2.82 (  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
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7598 (p0) cc_final: 0.7323 (p0)
REVERT: A  123 ASP cc_start: 0.7786 (t0) cc_final: 0.7548 (t0)
REVERT: A  208 PHE cc_start: 0.8151 (t80) cc_final: 0.7842 (t80)
REVERT: A  453 LEU cc_start: 0.7526 (mm) cc_final: 0.7183 (mp)
REVERT: A  829 ASN cc_start: 0.7713 (m110) cc_final: 0.7369 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 100
  average time/residue: 0.0929
  time to fit residues: 12.4984
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  : 0.168 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 52 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 78 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    0.4980
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 67 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.164553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118826 restraints weight = 22408.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.29
r_work: 0.3206 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    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 = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7989  Z= 0.160
  Angle     :  0.522   6.999  11112  Z= 0.294
  Chirality :  0.038   0.231   1283
  Planarity :  0.004   0.050   1157
  Dihedral  : 18.225 108.513   1855
  Min Nonbonded Distance : 2.171

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:  0.23 (0.31), residues: 745
  helix:  0.92 (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   0.020   0.002   TYR A 844 
 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        0.00355 /  0.16 ( 7989)
  covalent geometry    : angle       0.52154 /  0.29 (11112)
  hydrogen bonds       : bond        0.08154 /  5.21 (  341)
  hydrogen bonds       : angle       3.86534 /  2.77 (  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: 5
    poor density    : 99
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7610 (p0) cc_final: 0.7324 (p0)
REVERT: A  123 ASP cc_start: 0.7771 (t0) cc_final: 0.7523 (t0)
REVERT: A  208 PHE cc_start: 0.8083 (t80) cc_final: 0.7781 (t80)
REVERT: A  271 LYS cc_start: 0.7522 (ttpt) cc_final: 0.7231 (mtpp)
REVERT: A  453 LEU cc_start: 0.7448 (mm) cc_final: 0.7114 (mp)
REVERT: A  468 ASP cc_start: 0.7932 (t0) cc_final: 0.7582 (t0)
REVERT: A  829 ASN cc_start: 0.7666 (m110) cc_final: 0.7240 (m110)
  outliers start: 5
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1024
  time to fit residues: 13.8433
Evaluate side-chains
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   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:    0.0770
   overall best weight:    0.4436

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.165221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118819 restraints weight = 24926.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 3.46
r_work: 0.3195 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    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 (6 function evaluations)
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
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      :  0.003   0.050   7989  Z= 0.145
  Angle     :  0.505   6.827  11112  Z= 0.285
  Chirality :  0.037   0.229   1283
  Planarity :  0.004   0.051   1157
  Dihedral  : 18.276 108.103   1855
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.03 %
    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:  0.32 (0.31), residues: 745
  helix:  0.99 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.44 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 294 
 TYR   0.019   0.001   TYR A 296 
 PHE   0.013   0.001   PHE A 553 
 TRP   0.011   0.001   TRP A 752 
 HIS   0.005   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 7989)
  covalent geometry    : angle       0.50498 /  0.29 (11112)
  hydrogen bonds       : bond        0.07678 /  4.88 (  341)
  hydrogen bonds       : angle       3.78241 /  2.71 (  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
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7642 (p0) cc_final: 0.7354 (p0)
REVERT: A  123 ASP cc_start: 0.7741 (t0) cc_final: 0.7506 (t0)
REVERT: A  208 PHE cc_start: 0.8089 (t80) cc_final: 0.7792 (t80)
REVERT: A  271 LYS cc_start: 0.7490 (ttpt) cc_final: 0.7202 (mtpp)
REVERT: A  453 LEU cc_start: 0.7420 (mm) cc_final: 0.7066 (mp)
REVERT: A  468 ASP cc_start: 0.7952 (t0) cc_final: 0.7626 (t0)
REVERT: A  570 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6716 (tm-30)
REVERT: A  829 ASN cc_start: 0.7688 (m110) cc_final: 0.7280 (m110)
  outliers start: 6
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0882
  time to fit residues: 12.1445
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  831 LYS
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:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.7380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.163470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117717 restraints weight = 18359.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 3.09
r_work: 0.3210 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    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 = 0.3209 r_free = 0.3209    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 (4 function evaluations)
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7989  Z= 0.195
  Angle     :  0.543   6.839  11112  Z= 0.303
  Chirality :  0.039   0.241   1283
  Planarity :  0.004   0.050   1157
  Dihedral  : 18.374 107.529   1855
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 11.61 %
    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:  0.15 (0.31), residues: 745
  helix:  0.86 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.49 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 202 
 TYR   0.024   0.002   TYR A 844 
 PHE   0.015   0.002   PHE A 420 
 TRP   0.010   0.002   TRP A 752 
 HIS   0.007   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00455 /  0.20 ( 7989)
  covalent geometry    : angle       0.54255 /  0.30 (11112)
  hydrogen bonds       : bond        0.08210 /  5.23 (  341)
  hydrogen bonds       : angle       3.86101 /  2.76 (  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
  106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7601 (p0) cc_final: 0.7290 (p0)
REVERT: A  123 ASP cc_start: 0.7768 (t0) cc_final: 0.7518 (t0)
REVERT: A  208 PHE cc_start: 0.8114 (t80) cc_final: 0.7813 (t80)
REVERT: A  271 LYS cc_start: 0.7570 (ttpt) cc_final: 0.7276 (mtpp)
REVERT: A  453 LEU cc_start: 0.7451 (mm) cc_final: 0.7134 (mp)
REVERT: A  468 ASP cc_start: 0.7903 (t0) cc_final: 0.7555 (t0)
REVERT: A  514 ASP cc_start: 0.8073 (t0) cc_final: 0.7772 (t0)
REVERT: A  570 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6665 (tm-30)
REVERT: A  829 ASN cc_start: 0.7674 (m110) cc_final: 0.7245 (m110)
  outliers start: 4
  outliers final: 4
  residues processed: 104
  average time/residue: 0.0978
  time to fit residues: 13.5870
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  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
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:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 8 optimal weight:    0.3980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.163674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117359 restraints weight = 16262.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.61
r_work: 0.3242 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (11 function evaluations)
r_final: 0.3236
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7989  Z= 0.185
  Angle     :  0.533   7.228  11112  Z= 0.298
  Chirality :  0.039   0.240   1283
  Planarity :  0.004   0.051   1157
  Dihedral  : 18.466 107.880   1855
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  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:  0.12 (0.31), residues: 745
  helix:  0.86 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.55 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 610 
 TYR   0.022   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        0.00428 /  0.18 ( 7989)
  covalent geometry    : angle       0.53281 /  0.30 (11112)
  hydrogen bonds       : bond        0.08031 /  5.10 (  341)
  hydrogen bonds       : angle       3.85219 /  2.75 (  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
  101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7583 (p0) cc_final: 0.7269 (p0)
REVERT: A  123 ASP cc_start: 0.7724 (t0) cc_final: 0.7460 (t0)
REVERT: A  208 PHE cc_start: 0.8113 (t80) cc_final: 0.7786 (t80)
REVERT: A  271 LYS cc_start: 0.7604 (ttpt) cc_final: 0.7312 (mtpp)
REVERT: A  453 LEU cc_start: 0.7469 (mm) cc_final: 0.7150 (mp)
REVERT: A  468 ASP cc_start: 0.7891 (t0) cc_final: 0.7548 (t0)
REVERT: A  514 ASP cc_start: 0.8052 (t0) cc_final: 0.7561 (t0)
REVERT: A  570 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6583 (tm-30)
REVERT: A  829 ASN cc_start: 0.7659 (m110) cc_final: 0.7251 (m110)
  outliers start: 5
  outliers final: 5
  residues processed: 99
  average time/residue: 0.1037
  time to fit residues: 13.7402
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  : 0.249 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0000
   chunk 52 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0570
   chunk 45 optimal weight:    0.0570
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.3420

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.166301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.119082 restraints weight = 25598.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.66
r_work: 0.3161 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    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 = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7989  Z= 0.128
  Angle     :  0.492   8.581  11112  Z= 0.275
  Chirality :  0.036   0.230   1283
  Planarity :  0.004   0.054   1157
  Dihedral  : 18.445 108.169   1855
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 11.61 %
    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:  0.37 (0.31), residues: 745
  helix:  1.05 (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 561 
 TYR   0.016   0.001   TYR A 296 
 PHE   0.011   0.001   PHE A 553 
 TRP   0.013   0.001   TRP A 752 
 HIS   0.004   0.001   HIS A 702 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 ( 7989)
  covalent geometry    : angle       0.49238 /  0.28 (11112)
  hydrogen bonds       : bond        0.06934 /  4.36 (  341)
  hydrogen bonds       : angle       3.68261 /  2.64 (  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: 4
    poor density    : 96
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.7703 (p0) cc_final: 0.7403 (p0)
REVERT: A  186 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7918 (ptmt)
REVERT: A  208 PHE cc_start: 0.8021 (t80) cc_final: 0.7710 (t80)
REVERT: A  237 PHE cc_start: 0.8084 (m-10) cc_final: 0.7849 (m-80)
REVERT: A  271 LYS cc_start: 0.7463 (ttpt) cc_final: 0.7180 (mtpp)
REVERT: A  453 LEU cc_start: 0.7334 (mm) cc_final: 0.6946 (mp)
REVERT: A  468 ASP cc_start: 0.7896 (t0) cc_final: 0.7547 (t0)
REVERT: A  514 ASP cc_start: 0.8101 (t0) cc_final: 0.7594 (t0)
REVERT: A  570 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6656 (tm-30)
REVERT: A  829 ASN cc_start: 0.7711 (m110) cc_final: 0.7296 (m110)
  outliers start: 4
  outliers final: 4
  residues processed: 98
  average time/residue: 0.0933
  time to fit residues: 12.4732
Evaluate side-chains
  97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  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  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:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 72 optimal weight:    0.1980
   chunk 77 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 54 optimal weight:    0.4980
   chunk 20 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.164557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.117136 restraints weight = 23457.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.41
r_work: 0.3132 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
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:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| 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:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2315

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= 0.168
  Angle     :  0.525  11.194  11112  Z= 0.290
  Chirality :  0.038   0.240   1283
  Planarity :  0.004   0.052   1157
  Dihedral  : 18.316 107.293   1855
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 11.90 %
    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:  0.29 (0.31), residues: 745
  helix:  0.98 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.48 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 543 
 TYR   0.021   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/Z
  covalent geometry    : bond        0.00384 /  0.17 ( 7989)
  covalent geometry    : angle       0.52515 /  0.29 (11112)
  hydrogen bonds       : bond        0.07475 /  4.72 (  341)
  hydrogen bonds       : angle       3.73923 /  2.67 (  970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2146.46 seconds
wall clock time: 37 minutes 28.17 seconds (2248.17 seconds total)