Starting phenix.real_space_refine
on Tue Apr 29 04:40:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n73_24218/04_2025/7n73_24218_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n73_24218/04_2025/7n73_24218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n73_24218/04_2025/7n73_24218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n73_24218/04_2025/7n73_24218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n73_24218/04_2025/7n73_24218_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n73_24218/04_2025/7n73_24218_trim.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.024
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       2      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    5088      2.51       5
     N    1322      2.21       5
     O    1398      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7866
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1036, 7759
          Classifications: {'peptide': 1036}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 329
          Unresolved non-hydrogen dihedrals: 227
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 177
    Chain: "A"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 107
          Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1, 'Y01': 2}
          Classifications: {'undetermined': 6, 'water': 3}
          Link IDs: {None: 8}
  Time building chain proxies: 5.42, per 1000 atoms: 0.69
  Number of scatterers: 7866
  At special positions: 0
  Unit cell: (92.312, 99.655, 125.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      49     16.00
     P       2     15.00
     Al      1     13.00
     Mg      2     11.99
     F       4      9.00
     O    1398      8.00
     N    1322      7.00
     C    5088      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.51
  Conformation dependent library (CDL) restraints added in 993.5 milliseconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 8 sheets defined
      51.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 57
    Processing helix  chain 'A' and resid 59 through 68
    Processing helix  chain 'A' and resid 68 through 77
      removed outlier: 3.988A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 188 through 196
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 3.778A  pdb=" N   ALA A 209 " --> pdb=" O   MET A 205 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE A 210 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 232
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 251 through 284
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    Processing helix  chain 'A' and resid 393 through 396
    Processing helix  chain 'A' and resid 397 through 408
    Processing helix  chain 'A' and resid 419 through 445
      removed outlier: 3.848A  pdb=" N   LEU A 430 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 463
      removed outlier: 3.722A  pdb=" N   ILE A 454 " --> pdb=" O   ASN A 450 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 487
    Processing helix  chain 'A' and resid 494 through 500
      removed outlier: 3.981A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY A 500 " --> pdb=" O   ILE A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 3.608A  pdb=" N   THR A 576 " --> pdb=" O   MET A 572 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A 577 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 659
    Processing helix  chain 'A' and resid 667 through 677
    Processing helix  chain 'A' and resid 695 through 700
    Processing helix  chain 'A' and resid 703 through 709
      removed outlier: 3.581A  pdb=" N   GLY A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 737
    Processing helix  chain 'A' and resid 748 through 759
    Processing helix  chain 'A' and resid 821 through 832
    Processing helix  chain 'A' and resid 835 through 842
      removed outlier: 3.665A  pdb=" N   GLN A 842 " --> pdb=" O   LYS A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 863
    Processing helix  chain 'A' and resid 874 through 876
      No H-bonds generated for 'chain 'A' and resid 874 through 876'
    Processing helix  chain 'A' and resid 877 through 884
    Processing helix  chain 'A' and resid 909 through 948
    Processing helix  chain 'A' and resid 954 through 964
      removed outlier: 3.761A  pdb=" N   LEU A 959 " --> pdb=" O   ASP A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 974
      removed outlier: 4.361A  pdb=" N   SER A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1020
      removed outlier: 3.647A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.875A  pdb=" N   LEU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1072
    Processing helix  chain 'A' and resid 1073 through 1093
    Processing helix  chain 'A' and resid 1109 through 1145
      removed outlier: 3.629A  pdb=" N   PHE A1127 " --> pdb=" O   PHE A1123 " (cutoff:3.500A)
      Proline residue:  A1138  - end of helix
    Processing helix  chain 'A' and resid 1152 through 1164
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90
    Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109
      removed outlier: 5.753A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE A 169 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A 178 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 292
    Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 315
      removed outlier: 4.522A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU A 387 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   ASP A 325 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350
      removed outlier: 6.852A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490
      removed outlier: 5.824A  pdb=" N   GLY A 887 " --> pdb=" O   PHE A 901 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   SER A 903 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER A 889 " --> pdb=" O   SER A 903 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   VAL A 505 " --> pdb=" O   VAL A 742 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL A 744 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   PHE A 507 " --> pdb=" O   VAL A 744 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ALA A 741 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   PHE A 846 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   MET A 743 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   THR A 844 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   LEU A 818 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   PHE A 846 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU A 820 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 525
      removed outlier: 3.532A  pdb=" N   GLY A 522 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   LEU A 713 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   SER A 687 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 631 " --> pdb=" O   PHE A 625 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   PHE A 625 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ALA A 637 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   VAL A 619 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   SER A 588 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 558

    443 hydrogen bonds defined for protein.
    1275 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.36

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2157
        1.33 -     1.45: 1155
        1.45 -     1.57: 4636
        1.57 -     1.69: 11
        1.69 -     1.81: 77
  Bond restraints: 8036
  Sorted by residual:
  bond pdb=" F2  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.808 -0.123 2.00e-02 2.50e+03 3.80e+01
  bond pdb=" F3  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.792 -0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" F4  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.686  1.788 -0.102 2.00e-02 2.50e+03 2.62e+01
  bond pdb=" F1  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.684  1.779 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" CAV Y01 A1205 "
       pdb=" CBC Y01 A1205 "
    ideal  model  delta    sigma   weight residual
    1.523  1.605 -0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 8031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.01: 10983
       14.01 -    28.01: 6
       28.01 -    42.02: 0
       42.02 -    56.02: 0
       56.02 -    70.03: 2
  Bond angle restraints: 10991
  Sorted by residual:
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F2  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     108.68  178.71  -70.03 3.00e+00 1.11e-01 5.45e+02
  angle pdb=" F3  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.63  179.59  -69.96 3.00e+00 1.11e-01 5.44e+02
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     110.21   89.87   20.34 3.00e+00 1.11e-01 4.60e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.02   89.25   19.77 3.00e+00 1.11e-01 4.34e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F3  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.69   90.35   19.34 3.00e+00 1.11e-01 4.15e+01
  ... (remaining 10986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.30: 4679
       22.30 -    44.60: 223
       44.60 -    66.89: 20
       66.89 -    89.19: 4
       89.19 -   111.49: 2
  Dihedral angle restraints: 4928
    sinusoidal: 1934
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" C5' ADP A1201 "
           pdb=" O5' ADP A1201 "
           pdb=" PA  ADP A1201 "
           pdb=" O2A ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -171.49  111.49     1      2.00e+01 2.50e-03 3.28e+01
  dihedral pdb=" O2A ADP A1201 "
           pdb=" O3A ADP A1201 "
           pdb=" PA  ADP A1201 "
           pdb=" PB  ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   50.14 -110.14     1      2.00e+01 2.50e-03 3.23e+01
  dihedral pdb=" O1B ADP A1201 "
           pdb=" O3A ADP A1201 "
           pdb=" PB  ADP A1201 "
           pdb=" PA  ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -125.53   65.53     1      2.00e+01 2.50e-03 1.41e+01
  ... (remaining 4925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.231: 1328
       0.231 -    0.462: 6
       0.462 -    0.692: 0
       0.692 -    0.923: 0
       0.923 -    1.154: 1
  Chirality restraints: 1335
  Sorted by residual:
  chirality pdb=" CB  VAL A 617 "
            pdb=" CA  VAL A 617 "
            pdb=" CG1 VAL A 617 "
            pdb=" CG2 VAL A 617 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.48   -1.15 2.00e-01 2.50e+01 3.33e+01
  chirality pdb=" CBG Y01 A1205 "
            pdb=" CAQ Y01 A1205 "
            pdb=" CBD Y01 A1205 "
            pdb=" CBI Y01 A1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.73    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CBG Y01 A1206 "
            pdb=" CAQ Y01 A1206 "
            pdb=" CBD Y01 A1206 "
            pdb=" CBI Y01 A1206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.38 2.00e-01 2.50e+01 3.61e+00
  ... (remaining 1332 not shown)

  Planarity restraints: 1373
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 174 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" CD  GLN A 174 "    0.055 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 174 "   -0.021 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 174 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 451 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.17e+00
        pdb=" CD  GLU A 451 "   -0.052 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 451 "    0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 451 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 590 "   -0.018 2.00e-02 2.50e+03   1.68e-02 4.96e+00
        pdb=" CG  PHE A 590 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 590 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 590 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 590 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 590 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 590 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1370 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 48
        2.46 -     3.07: 5596
        3.07 -     3.68: 12005
        3.68 -     4.29: 17650
        4.29 -     4.90: 30591
  Nonbonded interactions: 65890
  Sorted by model distance:
  nonbonded pdb=" O   THR A 510 "
            pdb="MG    MG A1203 "
     model   vdw
     1.850 2.170
  nonbonded pdb=" NZ  LYS A1062 "
            pdb=" OD2 ASP A1134 "
     model   vdw
     2.043 3.120
  nonbonded pdb=" O   LEU A 672 "
            pdb=" OG1 THR A 676 "
     model   vdw
     2.062 3.040
  nonbonded pdb=" O   VAL A 462 "
            pdb=" O   HOH A1301 "
     model   vdw
     2.066 3.040
  nonbonded pdb=" OG1 THR A 745 "
            pdb=" F1  ALF A1202 "
     model   vdw
     2.070 2.990
  ... (remaining 65885 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.510
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:13.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
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      :  0.007   0.289   8037  Z= 0.436
  Angle     :  1.268  70.028  10991  Z= 0.490
  Chirality :  0.064   1.154   1335
  Planarity :  0.004   0.032   1373
  Dihedral  : 13.003 111.491   2994
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 1024
  helix:  1.63 (0.24), residues: 500
  sheet: -0.24 (0.42), residues: 158
  loop :  0.51 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 246 
 HIS   0.017   0.002   HIS A 385 
 PHE   0.038   0.001   PHE A 590 
 TYR   0.023   0.001   TYR A 443 
 ARG   0.008   0.001   ARG A1159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15235 (  443)
  hydrogen bonds       : angle       6.61867 ( 1275)
  covalent geometry    : bond        0.00604 ( 8036)
  covalent geometry    : angle       1.26794 (10991)
  Misc. bond           : bond        0.28880 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7833 (tttt) cc_final: 0.7505 (tttt)
REVERT: A  421 MET cc_start: 0.7532 (tpp) cc_final: 0.7115 (tmt)
REVERT: A 1151 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7917 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 1.2063
  time to fit residues: 76.4358
Evaluate side-chains
  38 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0970
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.3528 r_free = 0.3528 target = 0.090629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.068891 restraints weight = 16943.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.66
r_work: 0.2982 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8037  Z= 0.126
  Angle     :  0.866  33.050  10991  Z= 0.351
  Chirality :  0.042   0.142   1335
  Planarity :  0.005   0.037   1373
  Dihedral  :  7.788 122.441   1262
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  4.95 %
    Favored  : 94.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.27), residues: 1024
  helix:  1.94 (0.23), residues: 506
  sheet: -0.02 (0.42), residues: 157
  loop :  0.56 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 170 
 HIS   0.006   0.001   HIS A 554 
 PHE   0.013   0.001   PHE A 590 
 TYR   0.010   0.001   TYR A 931 
 ARG   0.008   0.000   ARG A1159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04198 (  443)
  hydrogen bonds       : angle       4.93269 ( 1275)
  covalent geometry    : bond        0.00287 ( 8036)
  covalent geometry    : angle       0.86584 (10991)
  Misc. bond           : bond        0.00075 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7412 (tttt) cc_final: 0.6829 (tttm)
REVERT: A  421 MET cc_start: 0.7629 (tpp) cc_final: 0.6933 (tmt)
  outliers start: 7
  outliers final: 3
  residues processed: 50
  average time/residue: 0.9379
  time to fit residues: 51.5393
Evaluate side-chains
  40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 CYS
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue 1001 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 94 optimal weight:    0.7980
   chunk 21 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0570
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
A 721 ASN
** A1122 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 = 0.3527 r_free = 0.3527 target = 0.090630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.068886 restraints weight = 17266.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.65
r_work: 0.2985 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8037  Z= 0.123
  Angle     :  0.836  31.356  10991  Z= 0.334
  Chirality :  0.041   0.142   1335
  Planarity :  0.004   0.039   1373
  Dihedral  :  7.397 119.111   1262
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  7.36 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.27), residues: 1024
  helix:  2.09 (0.23), residues: 507
  sheet:  0.04 (0.41), residues: 158
  loop :  0.61 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.011   0.001   PHE A 590 
 TYR   0.009   0.001   TYR A 161 
 ARG   0.003   0.000   ARG A1159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  443)
  hydrogen bonds       : angle       4.65571 ( 1275)
  covalent geometry    : bond        0.00285 ( 8036)
  covalent geometry    : angle       0.83574 (10991)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7458 (tttt) cc_final: 0.6982 (tttt)
REVERT: A  421 MET cc_start: 0.7662 (tpp) cc_final: 0.6932 (tmt)
REVERT: A 1144 LEU cc_start: 0.8905 (tp) cc_final: 0.8490 (tt)
REVERT: A 1151 LYS cc_start: 0.8400 (ptpp) cc_final: 0.8109 (ptpp)
  outliers start: 13
  outliers final: 5
  residues processed: 52
  average time/residue: 1.0647
  time to fit residues: 59.8785
Evaluate side-chains
  46 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 721 ASN
** A1122 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 = 0.3517 r_free = 0.3517 target = 0.090109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.068377 restraints weight = 17114.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.63
r_work: 0.2973 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8037  Z= 0.140
  Angle     :  0.844  31.850  10991  Z= 0.335
  Chirality :  0.041   0.141   1335
  Planarity :  0.004   0.040   1373
  Dihedral  :  7.226 118.446   1262
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.29 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.27), residues: 1024
  helix:  2.17 (0.23), residues: 506
  sheet:  0.25 (0.42), residues: 148
  loop :  0.50 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.011   0.001   PHE A 590 
 TYR   0.010   0.001   TYR A 931 
 ARG   0.002   0.000   ARG A 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03703 (  443)
  hydrogen bonds       : angle       4.50174 ( 1275)
  covalent geometry    : bond        0.00335 ( 8036)
  covalent geometry    : angle       0.84377 (10991)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7339 (tttt) cc_final: 0.6976 (tttt)
REVERT: A  421 MET cc_start: 0.7694 (tpp) cc_final: 0.6960 (tmt)
REVERT: A  446 ARG cc_start: 0.8231 (tpm170) cc_final: 0.7859 (tpm170)
REVERT: A  719 MET cc_start: 0.9087 (mtm) cc_final: 0.8786 (mtm)
REVERT: A 1144 LEU cc_start: 0.8896 (tp) cc_final: 0.8485 (tt)
REVERT: A 1151 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8092 (ptpp)
  outliers start: 10
  outliers final: 6
  residues processed: 52
  average time/residue: 1.4538
  time to fit residues: 82.5740
Evaluate side-chains
  48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 1.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 58 optimal weight:    0.2980
   chunk 102 optimal weight:    0.5980
   chunk 93 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.3535 r_free = 0.3535 target = 0.091167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.069546 restraints weight = 16987.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.66
r_work: 0.2996 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8037  Z= 0.111
  Angle     :  0.820  31.445  10991  Z= 0.323
  Chirality :  0.040   0.139   1335
  Planarity :  0.004   0.039   1373
  Dihedral  :  7.059 117.315   1262
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 10.86 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.27), residues: 1024
  helix:  2.38 (0.23), residues: 500
  sheet:  0.23 (0.42), residues: 149
  loop :  0.46 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.010   0.001   PHE A 940 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  443)
  hydrogen bonds       : angle       4.31636 ( 1275)
  covalent geometry    : bond        0.00260 ( 8036)
  covalent geometry    : angle       0.81998 (10991)
  Misc. bond           : bond        0.00039 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7427 (tttt) cc_final: 0.6930 (tttm)
REVERT: A  421 MET cc_start: 0.7719 (tpp) cc_final: 0.6905 (tmt)
REVERT: A 1144 LEU cc_start: 0.8895 (tp) cc_final: 0.8479 (tt)
REVERT: A 1151 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8101 (ptpp)
  outliers start: 12
  outliers final: 8
  residues processed: 54
  average time/residue: 1.4171
  time to fit residues: 82.8883
Evaluate side-chains
  50 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 102 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0770
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.3537 r_free = 0.3537 target = 0.091465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.069740 restraints weight = 17115.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.68
r_work: 0.2994 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8037  Z= 0.113
  Angle     :  0.829  31.425  10991  Z= 0.326
  Chirality :  0.040   0.145   1335
  Planarity :  0.004   0.039   1373
  Dihedral  :  6.965 115.567   1262
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.98 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.27), residues: 1024
  helix:  2.46 (0.23), residues: 500
  sheet:  0.32 (0.43), residues: 144
  loop :  0.51 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03380 (  443)
  hydrogen bonds       : angle       4.26937 ( 1275)
  covalent geometry    : bond        0.00263 ( 8036)
  covalent geometry    : angle       0.82937 (10991)
  Misc. bond           : bond        0.00045 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: A  415 LYS cc_start: 0.7360 (tttt) cc_final: 0.6807 (tttt)
REVERT: A  421 MET cc_start: 0.7718 (tpp) cc_final: 0.6883 (tmt)
REVERT: A 1144 LEU cc_start: 0.8897 (tp) cc_final: 0.8477 (tt)
REVERT: A 1151 LYS cc_start: 0.8388 (ptpp) cc_final: 0.8109 (ptpp)
  outliers start: 14
  outliers final: 7
  residues processed: 52
  average time/residue: 1.1223
  time to fit residues: 63.3080
Evaluate side-chains
  49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 92 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.3532 r_free = 0.3532 target = 0.091133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.069438 restraints weight = 17120.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.67
r_work: 0.2990 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8037  Z= 0.121
  Angle     :  0.828  31.492  10991  Z= 0.327
  Chirality :  0.040   0.139   1335
  Planarity :  0.004   0.039   1373
  Dihedral  :  6.898 113.388   1262
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.46 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.27), residues: 1024
  helix:  2.43 (0.23), residues: 506
  sheet:  0.35 (0.43), residues: 144
  loop :  0.54 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.006   0.001   HIS A 554 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.011   0.001   TYR A 161 
 ARG   0.002   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03382 (  443)
  hydrogen bonds       : angle       4.24731 ( 1275)
  covalent geometry    : bond        0.00284 ( 8036)
  covalent geometry    : angle       0.82787 (10991)
  Misc. bond           : bond        0.00053 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8207 (pp)
REVERT: A   90 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8469 (mp)
REVERT: A  227 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7982 (mp)
REVERT: A  415 LYS cc_start: 0.7332 (tttt) cc_final: 0.6993 (tttt)
REVERT: A  421 MET cc_start: 0.7733 (tpp) cc_final: 0.6895 (tmt)
REVERT: A 1144 LEU cc_start: 0.8837 (tp) cc_final: 0.8408 (tt)
REVERT: A 1151 LYS cc_start: 0.8390 (ptpp) cc_final: 0.8033 (ptpp)
  outliers start: 13
  outliers final: 8
  residues processed: 51
  average time/residue: 1.0142
  time to fit residues: 56.2910
Evaluate side-chains
  52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0170
   chunk 66 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 73 optimal weight:    0.0970
   chunk 88 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0570
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
** A1122 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 = 0.3551 r_free = 0.3551 target = 0.092154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.070539 restraints weight = 17109.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.67
r_work: 0.3018 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8037  Z= 0.097
  Angle     :  0.818  30.747  10991  Z= 0.320
  Chirality :  0.040   0.137   1335
  Planarity :  0.004   0.038   1373
  Dihedral  :  6.704 108.094   1262
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.34 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.27), residues: 1024
  helix:  2.55 (0.23), residues: 506
  sheet:  0.37 (0.43), residues: 144
  loop :  0.54 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.009   0.001   PHE A 940 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 558 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03161 (  443)
  hydrogen bonds       : angle       4.12234 ( 1275)
  covalent geometry    : bond        0.00222 ( 8036)
  covalent geometry    : angle       0.81815 (10991)
  Misc. bond           : bond        0.00033 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8284 (pp)
REVERT: A  227 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7984 (mp)
REVERT: A  415 LYS cc_start: 0.7315 (tttt) cc_final: 0.6795 (tttm)
REVERT: A  421 MET cc_start: 0.7870 (tpp) cc_final: 0.7010 (tmt)
REVERT: A  446 ARG cc_start: 0.8232 (tpm170) cc_final: 0.7944 (tpm170)
REVERT: A 1144 LEU cc_start: 0.8808 (tp) cc_final: 0.8373 (tt)
REVERT: A 1151 LYS cc_start: 0.8427 (ptpp) cc_final: 0.8055 (ptpp)
  outliers start: 14
  outliers final: 7
  residues processed: 56
  average time/residue: 1.0404
  time to fit residues: 63.4776
Evaluate side-chains
  53 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0670
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.3547 r_free = 0.3547 target = 0.091936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.070270 restraints weight = 17427.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.70
r_work: 0.3008 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8037  Z= 0.107
  Angle     :  0.828  30.838  10991  Z= 0.326
  Chirality :  0.040   0.136   1335
  Planarity :  0.004   0.039   1373
  Dihedral  :  6.577 102.478   1262
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.82 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.27), residues: 1024
  helix:  2.58 (0.23), residues: 506
  sheet:  0.41 (0.43), residues: 144
  loop :  0.56 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  443)
  hydrogen bonds       : angle       4.12749 ( 1275)
  covalent geometry    : bond        0.00250 ( 8036)
  covalent geometry    : angle       0.82803 (10991)
  Misc. bond           : bond        0.00035 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8360 (pp)
REVERT: A  227 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7936 (mp)
REVERT: A  415 LYS cc_start: 0.7298 (tttt) cc_final: 0.6771 (tttm)
REVERT: A  421 MET cc_start: 0.7871 (tpp) cc_final: 0.7002 (tmt)
REVERT: A  446 ARG cc_start: 0.8257 (tpm170) cc_final: 0.7957 (tpm170)
REVERT: A 1134 ASP cc_start: 0.8421 (m-30) cc_final: 0.8175 (m-30)
REVERT: A 1144 LEU cc_start: 0.8800 (tp) cc_final: 0.8359 (tt)
REVERT: A 1151 LYS cc_start: 0.8387 (ptpp) cc_final: 0.8019 (ptpp)
  outliers start: 12
  outliers final: 9
  residues processed: 54
  average time/residue: 1.0427
  time to fit residues: 61.2162
Evaluate side-chains
  56 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0870
   chunk 80 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.3549 r_free = 0.3549 target = 0.092025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.070435 restraints weight = 17275.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.68
r_work: 0.3017 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8037  Z= 0.104
  Angle     :  0.825  30.293  10991  Z= 0.324
  Chirality :  0.040   0.136   1335
  Planarity :  0.004   0.040   1373
  Dihedral  :  6.372  97.075   1262
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.06 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.27), residues: 1024
  helix:  2.58 (0.23), residues: 508
  sheet:  0.40 (0.42), residues: 144
  loop :  0.55 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 (  443)
  hydrogen bonds       : angle       4.09604 ( 1275)
  covalent geometry    : bond        0.00243 ( 8036)
  covalent geometry    : angle       0.82464 (10991)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8383 (pp)
REVERT: A  227 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7904 (mp)
REVERT: A  415 LYS cc_start: 0.7132 (tttt) cc_final: 0.6725 (tttt)
REVERT: A  421 MET cc_start: 0.7830 (tpp) cc_final: 0.6988 (tmt)
REVERT: A 1134 ASP cc_start: 0.8429 (m-30) cc_final: 0.8179 (m-30)
REVERT: A 1144 LEU cc_start: 0.8758 (tp) cc_final: 0.8325 (tt)
REVERT: A 1151 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8050 (ptpp)
  outliers start: 12
  outliers final: 6
  residues processed: 54
  average time/residue: 1.0211
  time to fit residues: 59.9034
Evaluate side-chains
  52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue 1000 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0770
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.3539 r_free = 0.3539 target = 0.091482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.069843 restraints weight = 17265.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.68
r_work: 0.3003 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8037  Z= 0.120
  Angle     :  0.834  30.374  10991  Z= 0.329
  Chirality :  0.040   0.137   1335
  Planarity :  0.004   0.039   1373
  Dihedral  :  6.299  96.075   1262
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.30 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.27), residues: 1024
  helix:  2.51 (0.23), residues: 512
  sheet:  0.45 (0.42), residues: 143
  loop :  0.62 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.015   0.001   TYR A 935 
 ARG   0.001   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  443)
  hydrogen bonds       : angle       4.12825 ( 1275)
  covalent geometry    : bond        0.00284 ( 8036)
  covalent geometry    : angle       0.83419 (10991)
  Misc. bond           : bond        0.00011 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4637.84 seconds
wall clock time: 81 minutes 38.54 seconds (4898.54 seconds total)