Starting phenix.real_space_refine
on Wed Sep 17 07:56:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iw3_60944/09_2025/9iw3_60944_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iw3_60944/09_2025/9iw3_60944.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iw3_60944/09_2025/9iw3_60944.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iw3_60944/09_2025/9iw3_60944.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iw3_60944/09_2025/9iw3_60944_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iw3_60944/09_2025/9iw3_60944_neut.cif"
  }
  resolution = 3.58
  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=   0.015
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      51      5.49       5
     Mg      1      5.21       5
     S      22      5.16       5
     C    4226      2.51       5
     N    1211      2.21       5
     O    1368      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6879
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 515
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "B"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 305
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "D"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 224
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "A"
      Number of atoms: 5834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 712, 5834
          Classifications: {'peptide': 712}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 681}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.93, per 1000 atoms: 0.28
  Number of scatterers: 6879
  At special positions: 0
  Unit cell: (78.288, 96.928, 116.5, 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      22     16.00
     P      51     15.00
     Mg      1     11.99
     O    1368      8.00
     N    1211      7.00
     C    4226      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: 0.54
  Conformation dependent library (CDL) restraints added in 323.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1360

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      37.1% alpha, 20.2% beta
      11 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 25
    Processing helix  chain 'A' and resid 34 through 36
      No H-bonds generated for 'chain 'A' and resid 34 through 36'
    Processing helix  chain 'A' and resid 37 through 48
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.588A  pdb=" N   GLY A  92 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 107
      removed outlier: 3.545A  pdb=" N   LEU A 101 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 223 through 239
    Processing helix  chain 'A' and resid 266 through 272
      removed outlier: 3.582A  pdb=" N   LEU A 272 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 303 through 309
      removed outlier: 3.576A  pdb=" N   LYS A 307 " --> pdb=" O   GLN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 357
    Processing helix  chain 'A' and resid 378 through 381
    Processing helix  chain 'A' and resid 382 through 401
    Processing helix  chain 'A' and resid 406 through 415
    Processing helix  chain 'A' and resid 462 through 475
    Processing helix  chain 'A' and resid 480 through 486
      removed outlier: 3.872A  pdb=" N   TRP A 484 " --> pdb=" O   PHE A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 521
    Processing helix  chain 'A' and resid 528 through 540
    Processing helix  chain 'A' and resid 541 through 544
      removed outlier: 4.140A  pdb=" N   SER A 544 " --> pdb=" O   PRO A 541 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 541 through 544'
    Processing helix  chain 'A' and resid 548 through 562
      removed outlier: 3.564A  pdb=" N   GLY A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 580
    Processing helix  chain 'A' and resid 585 through 598
      removed outlier: 3.561A  pdb=" N   ASN A 598 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 680
      removed outlier: 4.303A  pdb=" N   ASP A 670 " --> pdb=" O   ALA A 666 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A 671 " --> pdb=" O   GLY A 667 " (cutoff:3.500A)
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 694 through 711
      removed outlier: 4.094A  pdb=" N   LYS A 698 " --> pdb=" O   PRO A 694 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN A 710 " --> pdb=" O   SER A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 715
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 5.210A  pdb=" N   LYS A  15 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55
      removed outlier: 3.537A  pdb=" N   PHE A  69 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127
      removed outlier: 4.063A  pdb=" N   LEU A 125 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN A 142 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127
      removed outlier: 4.063A  pdb=" N   LEU A 125 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TYR A 196 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 178
      removed outlier: 4.596A  pdb=" N   ILE A 175 " --> pdb=" O   CYS A 188 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 213
    Processing sheet with id=AA7, first strand: chain 'A' and resid 254 through 258
      removed outlier: 4.297A  pdb=" N   SER A 257 " --> pdb=" O   ILE A 622 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ILE A 622 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLU A 629 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   HIS A 633 " --> pdb=" O   GLU A 629 " (cutoff:3.500A)
      removed outlier: 11.623A  pdb=" N   PHE A 634 " --> pdb=" O   PRO A 661 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   THR A 636 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLN A 497 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   LEU A 498 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   VAL A 490 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ILE A 500 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ASP A 488 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   PHE A 422 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL A 433 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 453 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A 435 " --> pdb=" O   LYS A 451 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314
      removed outlier: 6.241A  pdb=" N   SER A 276 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ILE A 324 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   ASN A 278 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   VAL A 326 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TYR A 280 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    660 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      27 hydrogen bonds
      54 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 0.73 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: 2046
        1.34 -     1.46: 1654
        1.46 -     1.58: 3289
        1.58 -     1.70: 98
        1.70 -     1.82: 39
  Bond restraints: 7126
  Sorted by residual:
  bond pdb=" C1'  DA D  12 "
       pdb=" N9   DA D  12 "
    ideal  model  delta    sigma   weight residual
    1.460  1.364  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" C1'  DA C  31 "
       pdb=" N9   DA C  31 "
    ideal  model  delta    sigma   weight residual
    1.460  1.368  0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" C1'  DG C  47 "
       pdb=" N9   DG C  47 "
    ideal  model  delta    sigma   weight residual
    1.460  1.372  0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" C1'  DA C  38 "
       pdb=" N9   DA C  38 "
    ideal  model  delta    sigma   weight residual
    1.460  1.377  0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" O3'  DA C  45 "
       pdb=" P    DC C  46 "
    ideal  model  delta    sigma   weight residual
    1.607  1.667 -0.060 1.50e-02 4.44e+03 1.58e+01
  ... (remaining 7121 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 9738
        3.47 -     6.95: 81
        6.95 -    10.42: 13
       10.42 -    13.89: 5
       13.89 -    17.36: 2
  Bond angle restraints: 9839
  Sorted by residual:
  angle pdb=" N   ASP A 548 "
        pdb=" CA  ASP A 548 "
        pdb=" C   ASP A 548 "
      ideal   model   delta    sigma   weight residual
     114.31   97.82   16.49 1.29e+00 6.01e-01 1.63e+02
  angle pdb=" O3'  DA D  10 "
        pdb=" C3'  DA D  10 "
        pdb=" C2'  DA D  10 "
      ideal   model   delta    sigma   weight residual
     111.50   98.99   12.51 1.50e+00 4.44e-01 6.95e+01
  angle pdb=" N   SER A 547 "
        pdb=" CA  SER A 547 "
        pdb=" C   SER A 547 "
      ideal   model   delta    sigma   weight residual
     110.80  128.16  -17.36 2.13e+00 2.20e-01 6.65e+01
  angle pdb=" C4'  DA B   3 "
        pdb=" C3'  DA B   3 "
        pdb=" O3'  DA B   3 "
      ideal   model   delta    sigma   weight residual
     110.00  122.06  -12.06 1.50e+00 4.44e-01 6.47e+01
  angle pdb=" N   ALA A  37 "
        pdb=" CA  ALA A  37 "
        pdb=" C   ALA A  37 "
      ideal   model   delta    sigma   weight residual
     111.75  122.04  -10.29 1.28e+00 6.10e-01 6.47e+01
  ... (remaining 9834 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.98: 3696
       29.98 -    59.96: 460
       59.96 -    89.93: 42
       89.93 -   119.91: 2
      119.91 -   149.89: 2
  Dihedral angle restraints: 4202
    sinusoidal: 2101
      harmonic: 2101
  Sorted by residual:
  dihedral pdb=" C   SER A  36 "
           pdb=" N   SER A  36 "
           pdb=" CA  SER A  36 "
           pdb=" CB  SER A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.52   15.92     0      2.50e+00 1.60e-01 4.05e+01
  dihedral pdb=" N   SER A  36 "
           pdb=" C   SER A  36 "
           pdb=" CA  SER A  36 "
           pdb=" CB  SER A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.13  -11.33     0      2.50e+00 1.60e-01 2.05e+01
  dihedral pdb=" C4'  DT C  34 "
           pdb=" C3'  DT C  34 "
           pdb=" O3'  DT C  34 "
           pdb=" P    DT C  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.11  149.89     1      3.50e+01 8.16e-04 1.46e+01
  ... (remaining 4199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 1047
       0.121 -    0.241: 27
       0.241 -    0.362: 2
       0.362 -    0.482: 2
       0.482 -    0.603: 2
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  SER A  36 "
            pdb=" N   SER A  36 "
            pdb=" C   SER A  36 "
            pdb=" CB  SER A  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 9.09e+00
  chirality pdb=" C3'  DA C  45 "
            pdb=" C4'  DA C  45 "
            pdb=" O3'  DA C  45 "
            pdb=" C2'  DA C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.14   -0.52 2.00e-01 2.50e+01 6.84e+00
  chirality pdb=" CA  SER A 547 "
            pdb=" N   SER A 547 "
            pdb=" C   SER A 547 "
            pdb=" CB  SER A 547 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.82e+00
  ... (remaining 1077 not shown)

  Planarity restraints: 1087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 250 "    0.015 2.00e-02 2.50e+03   3.13e-02 9.82e+00
        pdb=" C   HIS A 250 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   HIS A 250 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LYS A 251 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  39 "   -0.012 2.00e-02 2.50e+03   2.32e-02 5.39e+00
        pdb=" C   LYS A  39 "    0.040 2.00e-02 2.50e+03
        pdb=" O   LYS A  39 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A  40 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT D   7 "    0.031 2.00e-02 2.50e+03   1.46e-02 5.34e+00
        pdb=" N1   DT D   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DT D   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DT D   7 "   -0.016 2.00e-02 2.50e+03
        pdb=" N3   DT D   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DT D   7 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT D   7 "    0.021 2.00e-02 2.50e+03
        pdb=" C5   DT D   7 "   -0.009 2.00e-02 2.50e+03
        pdb=" C7   DT D   7 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT D   7 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1084 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 75
        2.52 -     3.12: 5161
        3.12 -     3.71: 11526
        3.71 -     4.31: 15281
        4.31 -     4.90: 24429
  Nonbonded interactions: 56472
  Sorted by model distance:
  nonbonded pdb=" OP1  DA C  49 "
            pdb=" CB  ARG A 585 "
     model   vdw
     1.930 3.440
  nonbonded pdb=" OP2  DG B   2 "
            pdb=" N   THR A 352 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" O   LEU A 260 "
            pdb=" OH  TYR A 690 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" C7   DT B   1 "
            pdb=" CZ  TYR A 339 "
     model   vdw
     2.192 3.680
  nonbonded pdb=" OP1  DA B   3 "
            pdb="MG    MG B 101 "
     model   vdw
     2.217 2.170
  ... (remaining 56467 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.500
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.000
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
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      :  0.005   0.096   7126  Z= 0.268
  Angle     :  0.909  17.364   9839  Z= 0.548
  Chirality :  0.058   0.603   1080
  Planarity :  0.004   0.050   1087
  Dihedral  : 23.443 149.891   2842
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 22.54
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.76 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 24.38 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.29 %
  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 aren not related in a simple way.
  whole: -0.43 (0.31), residues: 710
  helix:  1.10 (0.35), residues: 225
  sheet: -0.09 (0.44), residues: 150
  loop : -1.35 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 502 
 TYR   0.010   0.001   TYR A 481 
 PHE   0.010   0.001   PHE A 673 
 TRP   0.005   0.001   TRP A 484 
 HIS   0.002   0.000   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 7126)
  covalent geometry    : angle       0.90935 ( 9839)
  hydrogen bonds       : bond        0.23860 (  253)
  hydrogen bonds       : angle       8.60734 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  709 ARG cc_start: 0.8343 (tpt170) cc_final: 0.8009 (ttm-80)
  outliers start: 15
  outliers final: 3
  residues processed: 59
  average time/residue: 0.1088
  time to fit residues: 8.3208
Evaluate side-chains
  41 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  429 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN
A 282 GLN
A 319 GLN
A 376 HIS
A 495 ASN
A 555 GLN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 711 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.076070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.060006 restraints weight = 22119.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.062008 restraints weight = 10780.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.063376 restraints weight = 6907.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.064263 restraints weight = 5176.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.064585 restraints weight = 4285.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7126  Z= 0.163
  Angle     :  0.639   7.149   9839  Z= 0.354
  Chirality :  0.042   0.182   1080
  Planarity :  0.005   0.053   1087
  Dihedral  : 24.693 166.193   1351
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.06 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.12 %
    Favored  : 74.22 %
  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 aren not related in a simple way.
  whole: -0.21 (0.31), residues: 710
  helix:  1.36 (0.34), residues: 231
  sheet: -0.23 (0.42), residues: 155
  loop : -1.19 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  57 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.017   0.001   PHE A 673 
 TRP   0.007   0.001   TRP A 484 
 HIS   0.002   0.000   HIS A 298 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7126)
  covalent geometry    : angle       0.63909 ( 9839)
  hydrogen bonds       : bond        0.04489 (  253)
  hydrogen bonds       : angle       5.06741 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  671 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8551 (tp30)
  outliers start: 17
  outliers final: 7
  residues processed: 63
  average time/residue: 0.0887
  time to fit residues: 7.5685
Evaluate side-chains
  46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  633 HIS
Chi-restraints excluded: chain A residue  671 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 HIS
A 325 GLN
** A 592 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 = 0.3260 r_free = 0.3260 target = 0.071949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.055984 restraints weight = 22440.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.057885 restraints weight = 11572.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.059024 restraints weight = 7643.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.059917 restraints weight = 5941.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.060353 restraints weight = 4989.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7126  Z= 0.256
  Angle     :  0.662   8.013   9839  Z= 0.358
  Chirality :  0.042   0.163   1080
  Planarity :  0.005   0.052   1087
  Dihedral  : 24.593 178.566   1349
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.20 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 22.81 %
    Favored  : 72.97 %
  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 aren not related in a simple way.
  whole: -0.24 (0.32), residues: 710
  helix:  1.76 (0.35), residues: 225
  sheet: -0.49 (0.41), residues: 163
  loop : -1.38 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 184 
 TYR   0.018   0.001   TYR A 638 
 PHE   0.019   0.002   PHE A 673 
 TRP   0.009   0.001   TRP A 528 
 HIS   0.002   0.001   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 7126)
  covalent geometry    : angle       0.66183 ( 9839)
  hydrogen bonds       : bond        0.04647 (  253)
  hydrogen bonds       : angle       4.92053 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 38
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 LEU cc_start: 0.8778 (tp) cc_final: 0.8409 (tp)
REVERT: A  376 HIS cc_start: 0.8471 (m90) cc_final: 0.8099 (m-70)
REVERT: A  387 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8716 (tptm)
REVERT: A  584 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8811 (ttpt)
REVERT: A  679 MET cc_start: 0.8885 (mmm) cc_final: 0.8638 (mtt)
  outliers start: 27
  outliers final: 10
  residues processed: 59
  average time/residue: 0.0970
  time to fit residues: 7.7824
Evaluate side-chains
  45 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  598 ASN
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 GLN
** A 592 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 = 0.3263 r_free = 0.3263 target = 0.071980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.055940 restraints weight = 22521.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.057851 restraints weight = 11266.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.059143 restraints weight = 7354.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.059899 restraints weight = 5596.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.060420 restraints weight = 4744.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7126  Z= 0.191
  Angle     :  0.605   8.837   9839  Z= 0.328
  Chirality :  0.040   0.153   1080
  Planarity :  0.004   0.050   1087
  Dihedral  : 24.497 174.320   1349
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.49 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.91 %
    Favored  : 73.12 %
  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 aren not related in a simple way.
  whole: -0.15 (0.32), residues: 710
  helix:  1.87 (0.34), residues: 225
  sheet: -0.35 (0.42), residues: 163
  loop : -1.42 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 502 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.017   0.001   PHE A 673 
 TRP   0.007   0.001   TRP A  48 
 HIS   0.001   0.000   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 7126)
  covalent geometry    : angle       0.60482 ( 9839)
  hydrogen bonds       : bond        0.03690 (  253)
  hydrogen bonds       : angle       4.69864 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 38
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  584 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8853 (ttpt)
  outliers start: 19
  outliers final: 10
  residues processed: 52
  average time/residue: 0.0818
  time to fit residues: 5.7741
Evaluate side-chains
  42 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 710 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.069973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.053982 restraints weight = 22777.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.055787 restraints weight = 11897.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.057053 restraints weight = 7980.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.057797 restraints weight = 6132.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.058370 restraints weight = 5222.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   7126  Z= 0.287
  Angle     :  0.674   7.301   9839  Z= 0.362
  Chirality :  0.041   0.161   1080
  Planarity :  0.005   0.048   1087
  Dihedral  : 24.703 178.452   1349
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  7.32 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 25.00 %
    Favored  : 71.72 %
  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 aren not related in a simple way.
  whole: -0.24 (0.32), residues: 710
  helix:  1.76 (0.35), residues: 226
  sheet: -0.32 (0.43), residues: 157
  loop : -1.48 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 184 
 TYR   0.017   0.001   TYR A 638 
 PHE   0.018   0.002   PHE A 673 
 TRP   0.010   0.001   TRP A 528 
 HIS   0.002   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 ( 7126)
  covalent geometry    : angle       0.67374 ( 9839)
  hydrogen bonds       : bond        0.04183 (  253)
  hydrogen bonds       : angle       4.86755 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 38
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7360 (m-30)
REVERT: A  387 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8838 (tppt)
REVERT: A  413 LEU cc_start: 0.9231 (tp) cc_final: 0.9010 (tt)
REVERT: A  584 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8845 (ttpt)
REVERT: A  710 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8354 (pp30)
  outliers start: 21
  outliers final: 13
  residues processed: 55
  average time/residue: 0.0884
  time to fit residues: 6.7330
Evaluate side-chains
  51 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  633 HIS
Chi-restraints excluded: chain A residue  710 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 108 GLN
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 651 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.070923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.054897 restraints weight = 22863.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.056833 restraints weight = 11387.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.058118 restraints weight = 7365.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.058891 restraints weight = 5586.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.059525 restraints weight = 4733.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7126  Z= 0.193
  Angle     :  0.615   7.797   9839  Z= 0.332
  Chirality :  0.039   0.149   1080
  Planarity :  0.005   0.047   1087
  Dihedral  : 24.712 176.811   1349
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.20 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 25.62 %
    Favored  : 71.41 %
  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 aren not related in a simple way.
  whole: -0.14 (0.32), residues: 710
  helix:  1.88 (0.35), residues: 226
  sheet: -0.25 (0.44), residues: 157
  loop : -1.47 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.014   0.001   TYR A 638 
 PHE   0.015   0.001   PHE A 673 
 TRP   0.007   0.001   TRP A 528 
 HIS   0.002   0.000   HIS A 711 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 7126)
  covalent geometry    : angle       0.61474 ( 9839)
  hydrogen bonds       : bond        0.03691 (  253)
  hydrogen bonds       : angle       4.65264 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 38
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8935 (tppp)
REVERT: A  413 LEU cc_start: 0.9268 (tp) cc_final: 0.9054 (tt)
REVERT: A  584 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8799 (ttpt)
REVERT: A  610 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8685 (mm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 53
  average time/residue: 0.0990
  time to fit residues: 7.1235
Evaluate side-chains
  51 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0050
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 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 = 0.3299 r_free = 0.3299 target = 0.073518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.057572 restraints weight = 22308.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.059534 restraints weight = 11041.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.060832 restraints weight = 7114.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.061629 restraints weight = 5373.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062134 restraints weight = 4529.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7126  Z= 0.134
  Angle     :  0.592   8.295   9839  Z= 0.315
  Chirality :  0.039   0.158   1080
  Planarity :  0.004   0.047   1087
  Dihedral  : 24.768 171.467   1349
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.06 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 26.56 %
    Favored  : 71.41 %
  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 aren not related in a simple way.
  whole:  0.03 (0.32), residues: 710
  helix:  2.07 (0.35), residues: 226
  sheet: -0.12 (0.43), residues: 162
  loop : -1.46 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 589 
 TYR   0.013   0.001   TYR A 638 
 PHE   0.011   0.001   PHE A 673 
 TRP   0.004   0.001   TRP A 528 
 HIS   0.001   0.000   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7126)
  covalent geometry    : angle       0.59155 ( 9839)
  hydrogen bonds       : bond        0.03381 (  253)
  hydrogen bonds       : angle       4.46127 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7127 (m-30)
REVERT: A  387 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8521 (tppt)
  outliers start: 13
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0827
  time to fit residues: 5.9673
Evaluate side-chains
  41 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 69 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 ASN
A 376 HIS
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 710 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.074037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.058058 restraints weight = 22540.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.060048 restraints weight = 11100.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.061336 restraints weight = 7119.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.062074 restraints weight = 5367.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.062740 restraints weight = 4547.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7126  Z= 0.135
  Angle     :  0.593   8.619   9839  Z= 0.311
  Chirality :  0.039   0.153   1080
  Planarity :  0.004   0.048   1087
  Dihedral  : 24.758 172.729   1349
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.34 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 26.72 %
    Favored  : 71.09 %
  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 aren not related in a simple way.
  whole:  0.15 (0.32), residues: 710
  helix:  2.18 (0.35), residues: 225
  sheet: -0.03 (0.43), residues: 162
  loop : -1.39 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.014   0.001   TYR A 638 
 PHE   0.013   0.001   PHE A 673 
 TRP   0.006   0.001   TRP A 528 
 HIS   0.001   0.000   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7126)
  covalent geometry    : angle       0.59268 ( 9839)
  hydrogen bonds       : bond        0.03419 (  253)
  hydrogen bonds       : angle       4.40294 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.8409 (mmt) cc_final: 0.8158 (mmt)
REVERT: A   64 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7122 (m-30)
REVERT: A  387 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8486 (tppt)
REVERT: A  584 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8637 (ttpt)
REVERT: A  611 LEU cc_start: 0.9217 (mm) cc_final: 0.8673 (tt)
REVERT: A  702 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8326 (mm-30)
  outliers start: 14
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0975
  time to fit residues: 6.6222
Evaluate side-chains
  44 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 711 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.073408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.057508 restraints weight = 22348.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.059486 restraints weight = 11093.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.060740 restraints weight = 7146.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.061583 restraints weight = 5440.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.062030 restraints weight = 4558.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7126  Z= 0.152
  Angle     :  0.605   9.233   9839  Z= 0.318
  Chirality :  0.039   0.161   1080
  Planarity :  0.004   0.051   1087
  Dihedral  : 24.720 173.830   1349
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.06 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 27.34 %
    Favored  : 70.94 %
  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 aren not related in a simple way.
  whole:  0.12 (0.32), residues: 710
  helix:  2.19 (0.35), residues: 225
  sheet: -0.06 (0.43), residues: 162
  loop : -1.42 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 333 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.012   0.001   PHE A 673 
 TRP   0.006   0.001   TRP A 528 
 HIS   0.006   0.001   HIS A 711 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7126)
  covalent geometry    : angle       0.60534 ( 9839)
  hydrogen bonds       : bond        0.03454 (  253)
  hydrogen bonds       : angle       4.38877 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.8475 (mmt) cc_final: 0.8216 (mmt)
REVERT: A   64 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7177 (m-30)
REVERT: A  369 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8936 (tppp)
REVERT: A  584 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8624 (ttpt)
REVERT: A  611 LEU cc_start: 0.9231 (mm) cc_final: 0.8661 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 44
  average time/residue: 0.0974
  time to fit residues: 5.7933
Evaluate side-chains
  44 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0020
   chunk 64 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 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 = 0.3321 r_free = 0.3321 target = 0.074620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.058664 restraints weight = 22320.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.060625 restraints weight = 11052.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.061952 restraints weight = 7165.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.062735 restraints weight = 5413.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.063340 restraints weight = 4572.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7126  Z= 0.131
  Angle     :  0.595   9.720   9839  Z= 0.311
  Chirality :  0.039   0.140   1080
  Planarity :  0.004   0.051   1087
  Dihedral  : 24.668 172.141   1349
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.20 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 27.97 %
    Favored  : 70.78 %
  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 aren not related in a simple way.
  whole:  0.17 (0.32), residues: 710
  helix:  2.21 (0.35), residues: 225
  sheet: -0.00 (0.43), residues: 162
  loop : -1.40 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 333 
 TYR   0.014   0.001   TYR A 638 
 PHE   0.013   0.001   PHE A 673 
 TRP   0.005   0.001   TRP A 528 
 HIS   0.001   0.000   HIS A 711 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7126)
  covalent geometry    : angle       0.59538 ( 9839)
  hydrogen bonds       : bond        0.03392 (  253)
  hydrogen bonds       : angle       4.31942 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7193 (m-30)
REVERT: A  584 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8606 (ttpt)
REVERT: A  611 LEU cc_start: 0.9205 (mm) cc_final: 0.8653 (tt)
REVERT: A  702 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8333 (mm-30)
  outliers start: 8
  outliers final: 5
  residues processed: 44
  average time/residue: 0.0975
  time to fit residues: 5.8566
Evaluate side-chains
  42 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0170
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.2980
   chunk 29 optimal weight:    0.0370
   chunk 31 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.2296

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
A 521 ASN
** A 592 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 = 0.3411 r_free = 0.3411 target = 0.079118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.063061 restraints weight = 22383.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.065218 restraints weight = 10766.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.066631 restraints weight = 6782.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.067556 restraints weight = 5051.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.067882 restraints weight = 4178.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7126  Z= 0.118
  Angle     :  0.589   9.946   9839  Z= 0.304
  Chirality :  0.039   0.134   1080
  Planarity :  0.004   0.052   1087
  Dihedral  : 24.436 168.236   1349
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.06 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 28.12 %
    Favored  : 70.62 %
  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 aren not related in a simple way.
  whole:  0.38 (0.32), residues: 710
  helix:  2.25 (0.34), residues: 226
  sheet:  0.32 (0.44), residues: 153
  loop : -1.25 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 333 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.015   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 711 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7126)
  covalent geometry    : angle       0.58854 ( 9839)
  hydrogen bonds       : bond        0.03246 (  253)
  hydrogen bonds       : angle       4.16840 (  714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1127.26 seconds
wall clock time: 20 minutes 14.53 seconds (1214.53 seconds total)