Starting phenix.real_space_refine
on Sat May  2 18:17:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nzt_49959/05_2026/9nzt_49959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nzt_49959/05_2026/9nzt_49959.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nzt_49959/05_2026/9nzt_49959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nzt_49959/05_2026/9nzt_49959.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nzt_49959/05_2026/9nzt_49959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nzt_49959/05_2026/9nzt_49959.map"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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
     Zn      1      6.06       5
     P     146      5.49       5
     S      33      5.16       5
     C    4448      2.51       5
     N    1437      2.21       5
     O    1862      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7927
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3386
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 11, 'TRANS': 411}
    Chain: "B"
      Number of atoms: 1430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1430
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 6, 'TRANS': 168}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 331
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "D"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 163
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "E"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 2616
          Classifications: {'RNA': 122}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 8, 'rna3p_pur': 58, 'rna3p_pyr': 44}
          Link IDs: {'rna2p': 20, 'rna3p': 101}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3013  SG  CYS A 377      17.508  84.302  72.414  1.00139.47           S
  ATOM   3036  SG  CYS A 380      14.551  86.975  71.158  1.00149.32           S
  ATOM   3157  SG  CYS A 396      18.270  87.848  71.320  1.00146.29           S
  ATOM   3179  SG  CYS A 399      16.413  87.527  74.240  1.00145.39           S

  Time building chain proxies: 1.91, per 1000 atoms: 0.24
  Number of scatterers: 7927
  At special positions: 0
  Unit cell: (84.6, 99.64, 121.26, 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)
     Zn      1     29.99
     S      33     16.00
     P     146     15.00
     O    1862      8.00
     N    1437      7.00
     C    4448      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: 0.74
  Conformation dependent library (CDL) restraints added in 149.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 399 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 396 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 380 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 377 "
      Number of angles added : 6


  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1120

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 7 sheets defined
      48.7% alpha, 8.4% beta
      42 base pairs and 80 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 62
      removed outlier: 3.730A  pdb=" N   ARG A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLU A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.734A  pdb=" N   GLU A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 3.752A  pdb=" N   HIS A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   GLY A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLN A  88 " --> pdb=" O   CYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 3.669A  pdb=" N   LYS A 107 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 117
    Processing helix  chain 'A' and resid 156 through 162
    Processing helix  chain 'A' and resid 178 through 188
    Processing helix  chain 'A' and resid 250 through 271
      removed outlier: 3.767A  pdb=" N   ALA A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 287 through 319
    Processing helix  chain 'A' and resid 347 through 361
      removed outlier: 3.574A  pdb=" N   GLU A 360 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   HIS A 361 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.585A  pdb=" N   ARG A 388 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 415
      removed outlier: 3.845A  pdb=" N   ILE A 415 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 427
      removed outlier: 3.907A  pdb=" N   ILE A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 54
    Processing helix  chain 'B' and resid 77 through 89
      removed outlier: 4.175A  pdb=" N   GLY B  87 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   GLN B  88 " --> pdb=" O   CYS B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 111
      removed outlier: 3.545A  pdb=" N   LYS B 107 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 117
    Processing helix  chain 'B' and resid 156 through 162
    Processing helix  chain 'B' and resid 178 through 188
      removed outlier: 3.787A  pdb=" N   ASN B 184 " --> pdb=" O   ALA B 180 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 3.544A  pdb=" N   PHE A 205 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   CYS A 195 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL A 198 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A 131 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141
      removed outlier: 3.689A  pdb=" N   ILE A 148 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 226
      removed outlier: 6.065A  pdb=" N   LEU A 225 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237
      removed outlier: 3.736A  pdb=" N   LEU A 235 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 394
      removed outlier: 3.989A  pdb=" N   ALA A 403 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 15
      removed outlier: 3.709A  pdb=" N   PHE B 205 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 140
      removed outlier: 3.531A  pdb=" N   MET B 171 " --> pdb=" O   THR B 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 152 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   PHE B 169 " --> pdb=" O   THR B 152 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    666 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      108 hydrogen bonds
      208 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      80 stacking parallelities
  Total time for adding SS restraints: 1.48

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1643
        1.33 -     1.45: 2712
        1.45 -     1.58: 3703
        1.58 -     1.70: 288
        1.70 -     1.82: 50
  Bond restraints: 8396
  Sorted by residual:
  bond pdb=" CA  ASN B 128 "
       pdb=" CB  ASN B 128 "
    ideal  model  delta    sigma   weight residual
    1.530  1.565 -0.035 1.50e-02 4.44e+03 5.40e+00
  bond pdb=" C   PRO B 213 "
       pdb=" N   PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.341  1.378 -0.037 1.60e-02 3.91e+03 5.33e+00
  bond pdb=" C   ARG B 201 "
       pdb=" N   PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.24e+00
  bond pdb=" CG  LEU A 153 "
       pdb=" CD1 LEU A 153 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.65e+00
  bond pdb=" C   PRO A 213 "
       pdb=" N   PRO A 214 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 2.34e-02 1.83e+03 2.84e+00
  ... (remaining 8391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.54: 11828
        3.54 -     7.07: 166
        7.07 -    10.61: 21
       10.61 -    14.15: 3
       14.15 -    17.69: 1
  Bond angle restraints: 12019
  Sorted by residual:
  angle pdb=" C   ASN B 128 "
        pdb=" CA  ASN B 128 "
        pdb=" CB  ASN B 128 "
      ideal   model   delta    sigma   weight residual
     111.73  119.09   -7.36 1.42e+00 4.96e-01 2.68e+01
  angle pdb=" CA  LEU B 185 "
        pdb=" CB  LEU B 185 "
        pdb=" CG  LEU B 185 "
      ideal   model   delta    sigma   weight residual
     116.30  133.99  -17.69 3.50e+00 8.16e-02 2.55e+01
  angle pdb=" CA  ASN B 128 "
        pdb=" CB  ASN B 128 "
        pdb=" CG  ASN B 128 "
      ideal   model   delta    sigma   weight residual
     112.60  117.50   -4.90 1.00e+00 1.00e+00 2.41e+01
  angle pdb=" C   PHE B  23 "
        pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  130.85   -9.31 1.91e+00 2.74e-01 2.38e+01
  angle pdb=" C3'   A E  67 "
        pdb=" O3'   A E  67 "
        pdb=" P     C E  68 "
      ideal   model   delta    sigma   weight residual
     120.20  127.23   -7.03 1.50e+00 4.44e-01 2.20e+01
  ... (remaining 12014 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.50: 4483
       32.50 -    65.01: 583
       65.01 -    97.51: 58
       97.51 -   130.02: 3
      130.02 -   162.52: 5
  Dihedral angle restraints: 5132
    sinusoidal: 3391
      harmonic: 1741
  Sorted by residual:
  dihedral pdb=" O4'   C E  19 "
           pdb=" C1'   C E  19 "
           pdb=" N1    C E  19 "
           pdb=" C2    C E  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.12  155.88     1      1.50e+01 4.44e-03 8.16e+01
  dihedral pdb=" O4'   U E  86 "
           pdb=" C1'   U E  86 "
           pdb=" N1    U E  86 "
           pdb=" C2    U E  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   32.70 -160.70     1      1.70e+01 3.46e-03 6.46e+01
  dihedral pdb=" CA  PRO A 213 "
           pdb=" C   PRO A 213 "
           pdb=" N   PRO A 214 "
           pdb=" CA  PRO A 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.16   25.84     0      5.00e+00 4.00e-02 2.67e+01
  ... (remaining 5129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1086
       0.049 -    0.099: 251
       0.099 -    0.148: 54
       0.148 -    0.197: 14
       0.197 -    0.246: 5
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" C3'   A E  67 "
            pdb=" C4'   A E  67 "
            pdb=" O3'   A E  67 "
            pdb=" C2'   A E  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.50   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" P     C E  68 "
            pdb=" OP1   C E  68 "
            pdb=" OP2   C E  68 "
            pdb=" O5'   C E  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.65   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" C3'   G E  28 "
            pdb=" C4'   G E  28 "
            pdb=" O3'   G E  28 "
            pdb=" C2'   G E  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.24   -0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1407 not shown)

  Planarity restraints: 992
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E 127 "    0.023 2.00e-02 2.50e+03   2.15e-02 1.39e+01
        pdb=" N9    G E 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8    G E 127 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G E 127 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    G E 127 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    G E 127 "   -0.018 2.00e-02 2.50e+03
        pdb=" O6    G E 127 "    0.028 2.00e-02 2.50e+03
        pdb=" N1    G E 127 "    0.014 2.00e-02 2.50e+03
        pdb=" C2    G E 127 "   -0.054 2.00e-02 2.50e+03
        pdb=" N2    G E 127 "    0.027 2.00e-02 2.50e+03
        pdb=" N3    G E 127 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    G E 127 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 213 "    0.049 5.00e-02 4.00e+02   7.54e-02 9.09e+00
        pdb=" N   PRO A 214 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 214 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 214 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 328 "   -0.014 2.00e-02 2.50e+03   2.85e-02 8.12e+00
        pdb=" CG  ASP A 328 "    0.049 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 328 "   -0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 328 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 989 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 2887
        2.92 -     3.41: 7409
        3.41 -     3.91: 14853
        3.91 -     4.40: 15906
        4.40 -     4.90: 23562
  Nonbonded interactions: 64617
  Sorted by model distance:
  nonbonded pdb=" N   ARG A 201 "
            pdb=" O   ARG A 201 "
     model   vdw
     2.420 2.496
  nonbonded pdb=" N1    A E  34 "
            pdb=" O6    G E  64 "
     model   vdw
     2.478 2.496
  nonbonded pdb=" N   ARG B 201 "
            pdb=" O   ARG B 201 "
     model   vdw
     2.489 2.496
  nonbonded pdb=" O4'   C E  70 "
            pdb=" C6    C E  70 "
     model   vdw
     2.506 2.672
  nonbonded pdb=" O5'   G E  61 "
            pdb=" O4'   G E  61 "
     model   vdw
     2.514 2.432
  ... (remaining 64612 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 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:             3.010
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.220
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
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   0.063   8400  Z= 0.226
  Angle     :  1.053  17.685  12025  Z= 0.534
  Chirality :  0.048   0.246   1410
  Planarity :  0.008   0.088    992
  Dihedral  : 23.983 162.521   4012
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 27.50 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.35), residues: 590
  helix:  1.26 (0.32), residues: 261
  sheet: -2.13 (0.48), residues: 111
  loop : -2.11 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG B  15 
 TYR   0.041   0.003   TYR A 125 
 PHE   0.039   0.002   PHE A 182 
 TRP   0.029   0.004   TRP A  31 
 HIS   0.021   0.002   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 8396)
  covalent geometry    : angle       1.03547 (12019)
  hydrogen bonds       : bond        0.15040 (  337)
  hydrogen bonds       : angle       5.39346 (  874)
  metal coordination   : bond        0.01882 (    4)
  metal coordination   : angle       8.73392 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 119
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  137 THR cc_start: 0.8311 (p) cc_final: 0.8097 (t)
  outliers start: 5
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1137
  time to fit residues: 17.8648
Evaluate side-chains
  90 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0870
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.4764

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS
B  25 ASN
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 HIS
B 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.086760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.066246 restraints weight = 28833.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 3.12
r_work: 0.3155 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8400  Z= 0.193
  Angle     :  0.710  13.067  12025  Z= 0.359
  Chirality :  0.037   0.193   1410
  Planarity :  0.005   0.052    992
  Dihedral  : 24.649 160.988   2812
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 27.12 %
    Favored  : 69.62 %
  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 are not related in a simple way.
  whole: -0.29 (0.36), residues: 590
  helix:  1.74 (0.33), residues: 263
  sheet: -1.75 (0.49), residues: 103
  loop : -1.79 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  15 
 TYR   0.019   0.002   TYR A 199 
 PHE   0.021   0.002   PHE B 158 
 TRP   0.014   0.002   TRP A  31 
 HIS   0.005   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8396)
  covalent geometry    : angle       0.69406 (12019)
  hydrogen bonds       : bond        0.05137 (  337)
  hydrogen bonds       : angle       4.18190 (  874)
  metal coordination   : bond        0.01181 (    4)
  metal coordination   : angle       6.63099 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8786 (ttt180)
REVERT: A  128 ASN cc_start: 0.8891 (t0) cc_final: 0.8686 (m-40)
REVERT: A  135 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9049 (ptpt)
REVERT: A  211 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7240 (tppt)
REVERT: B   15 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7951 (mtp85)
REVERT: B   51 TRP cc_start: 0.9038 (t60) cc_final: 0.8357 (t-100)
REVERT: B  114 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7944 (mm-30)
REVERT: B  196 GLN cc_start: 0.8105 (mp10) cc_final: 0.7752 (mp10)
REVERT: B  199 TYR cc_start: 0.7262 (m-10) cc_final: 0.7043 (m-80)
REVERT: B  207 PHE cc_start: 0.7232 (m-80) cc_final: 0.6618 (m-80)
  outliers start: 17
  outliers final: 4
  residues processed: 109
  average time/residue: 0.1161
  time to fit residues: 16.1597
Evaluate side-chains
  95 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue  124 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0470
   chunk 26 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.9680

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

Flipped N/Q/H residues before XYZ refinement:
** B 128 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 = 0.3798 r_free = 0.3798 target = 0.086416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.065309 restraints weight = 28852.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 3.19
r_work: 0.3145 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8400  Z= 0.150
  Angle     :  0.669  12.207  12025  Z= 0.336
  Chirality :  0.035   0.181   1410
  Planarity :  0.005   0.050    992
  Dihedral  : 24.613 164.957   2810
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 28.08 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.36), residues: 590
  helix:  1.85 (0.33), residues: 263
  sheet: -1.37 (0.46), residues: 108
  loop : -1.78 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 343 
 TYR   0.023   0.002   TYR A 199 
 PHE   0.012   0.001   PHE A 341 
 TRP   0.029   0.002   TRP A  31 
 HIS   0.006   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8396)
  covalent geometry    : angle       0.65407 (12019)
  hydrogen bonds       : bond        0.04734 (  337)
  hydrogen bonds       : angle       3.88126 (  874)
  metal coordination   : bond        0.01129 (    4)
  metal coordination   : angle       6.26889 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8749 (ttt180)
REVERT: A   31 TRP cc_start: 0.8577 (m-10) cc_final: 0.8136 (m-10)
REVERT: A  117 ARG cc_start: 0.8150 (tmm160) cc_final: 0.7930 (ttp80)
REVERT: A  128 ASN cc_start: 0.8626 (t0) cc_final: 0.8337 (m-40)
REVERT: A  135 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9036 (ptpt)
REVERT: A  211 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7223 (tppt)
REVERT: B   15 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8027 (mtp85)
REVERT: B   51 TRP cc_start: 0.9053 (t60) cc_final: 0.8369 (t-100)
REVERT: B   91 ASP cc_start: 0.9065 (m-30) cc_final: 0.8732 (t0)
REVERT: B  114 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8185 (mm-30)
REVERT: B  117 ARG cc_start: 0.7345 (tmm160) cc_final: 0.6998 (ttp80)
REVERT: B  199 TYR cc_start: 0.7334 (m-10) cc_final: 0.7008 (m-80)
REVERT: B  207 PHE cc_start: 0.7394 (m-80) cc_final: 0.6601 (m-80)
  outliers start: 19
  outliers final: 9
  residues processed: 101
  average time/residue: 0.1008
  time to fit residues: 13.2550
Evaluate side-chains
  93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  189 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 128 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 = 0.3830 r_free = 0.3830 target = 0.087336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.066830 restraints weight = 28918.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.07
r_work: 0.3177 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8400  Z= 0.130
  Angle     :  0.629  10.688  12025  Z= 0.315
  Chirality :  0.034   0.171   1410
  Planarity :  0.004   0.056    992
  Dihedral  : 24.480 169.734   2810
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 29.42 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.36), residues: 590
  helix:  2.02 (0.33), residues: 262
  sheet: -1.02 (0.48), residues: 103
  loop : -1.80 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 117 
 TYR   0.022   0.002   TYR A 199 
 PHE   0.023   0.001   PHE B 158 
 TRP   0.019   0.001   TRP A  31 
 HIS   0.003   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8396)
  covalent geometry    : angle       0.61753 (12019)
  hydrogen bonds       : bond        0.04434 (  337)
  hydrogen bonds       : angle       3.66110 (  874)
  metal coordination   : bond        0.00997 (    4)
  metal coordination   : angle       5.49449 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.8705 (m-10) cc_final: 0.8329 (m-10)
REVERT: A   53 CYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7458 (t)
REVERT: A  117 ARG cc_start: 0.8100 (tmm160) cc_final: 0.7896 (ttp80)
REVERT: A  128 ASN cc_start: 0.8620 (t0) cc_final: 0.8249 (m-40)
REVERT: A  135 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9103 (ptpt)
REVERT: A  211 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6942 (tppt)
REVERT: A  258 LYS cc_start: 0.9385 (pptt) cc_final: 0.9081 (ptmm)
REVERT: B   51 TRP cc_start: 0.9039 (t60) cc_final: 0.8357 (t-100)
REVERT: B   91 ASP cc_start: 0.9119 (m-30) cc_final: 0.8806 (t0)
REVERT: B  120 MET cc_start: 0.8852 (tmm) cc_final: 0.8585 (tmm)
REVERT: B  199 TYR cc_start: 0.7231 (m-10) cc_final: 0.6821 (m-80)
REVERT: B  207 PHE cc_start: 0.7524 (m-80) cc_final: 0.6979 (m-80)
  outliers start: 15
  outliers final: 6
  residues processed: 98
  average time/residue: 0.1059
  time to fit residues: 13.4942
Evaluate side-chains
  90 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  189 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0170
   chunk 22 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    2.1424

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
A  98 ASN
** A 217 HIS ** 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 = 0.3756 r_free = 0.3756 target = 0.083348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.062182 restraints weight = 28725.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 3.06
r_work: 0.3080 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8400  Z= 0.242
  Angle     :  0.704  13.041  12025  Z= 0.351
  Chirality :  0.037   0.182   1410
  Planarity :  0.005   0.050    992
  Dihedral  : 24.481 165.441   2810
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 28.65 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.36), residues: 590
  helix:  1.89 (0.33), residues: 261
  sheet: -0.86 (0.47), residues: 108
  loop : -1.69 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  15 
 TYR   0.034   0.002   TYR A 199 
 PHE   0.014   0.002   PHE B  49 
 TRP   0.013   0.001   TRP A  31 
 HIS   0.004   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 8396)
  covalent geometry    : angle       0.68834 (12019)
  hydrogen bonds       : bond        0.04992 (  337)
  hydrogen bonds       : angle       3.84413 (  874)
  metal coordination   : bond        0.01140 (    4)
  metal coordination   : angle       6.60268 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8933 (t0) cc_final: 0.8664 (m-40)
REVERT: A  135 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9139 (ptpt)
REVERT: A  199 TYR cc_start: 0.7329 (m-80) cc_final: 0.7067 (m-80)
REVERT: A  211 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7400 (tppt)
REVERT: A  371 ARG cc_start: 0.8981 (tpm170) cc_final: 0.8692 (tpm170)
REVERT: B   15 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8850 (mtp-110)
REVERT: B   16 TYR cc_start: 0.6534 (p90) cc_final: 0.6289 (p90)
REVERT: B   92 MET cc_start: 0.8588 (tmm) cc_final: 0.8330 (tmm)
REVERT: B  120 MET cc_start: 0.8745 (tmm) cc_final: 0.8456 (tmm)
REVERT: B  137 THR cc_start: 0.8427 (p) cc_final: 0.8114 (t)
REVERT: B  184 ASN cc_start: 0.9357 (m-40) cc_final: 0.9040 (p0)
REVERT: B  199 TYR cc_start: 0.7268 (m-10) cc_final: 0.6952 (m-80)
REVERT: B  207 PHE cc_start: 0.7974 (m-80) cc_final: 0.7101 (m-80)
  outliers start: 23
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0965
  time to fit residues: 12.0184
Evaluate side-chains
  93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   20 CYS
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  210 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 46 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 69 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0370
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
A 184 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.085744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.064599 restraints weight = 29163.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.08
r_work: 0.3138 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8400  Z= 0.130
  Angle     :  0.654  10.313  12025  Z= 0.325
  Chirality :  0.034   0.172   1410
  Planarity :  0.005   0.075    992
  Dihedral  : 24.407 171.602   2810
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 29.62 %
    Favored  : 67.12 %
  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 are not related in a simple way.
  whole:  0.11 (0.35), residues: 590
  helix:  1.88 (0.33), residues: 262
  sheet: -0.36 (0.48), residues: 106
  loop : -1.99 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 201 
 TYR   0.017   0.001   TYR A 199 
 PHE   0.012   0.001   PHE B 158 
 TRP   0.012   0.001   TRP A  31 
 HIS   0.002   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8396)
  covalent geometry    : angle       0.64393 (12019)
  hydrogen bonds       : bond        0.04575 (  337)
  hydrogen bonds       : angle       3.63938 (  874)
  metal coordination   : bond        0.00924 (    4)
  metal coordination   : angle       5.23825 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8672 (t0) cc_final: 0.8272 (m-40)
REVERT: A  135 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9095 (ptpt)
REVERT: A  211 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7283 (tppt)
REVERT: A  314 ASP cc_start: 0.8926 (m-30) cc_final: 0.8621 (m-30)
REVERT: A  371 ARG cc_start: 0.9014 (tpm170) cc_final: 0.8736 (tpm170)
REVERT: B   15 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8771 (mtp-110)
REVERT: B   51 TRP cc_start: 0.9111 (t60) cc_final: 0.8395 (t-100)
REVERT: B  120 MET cc_start: 0.8611 (tmm) cc_final: 0.8141 (tmm)
REVERT: B  134 ASP cc_start: 0.7911 (t0) cc_final: 0.7674 (t0)
REVERT: B  137 THR cc_start: 0.8399 (p) cc_final: 0.8134 (t)
REVERT: B  184 ASN cc_start: 0.9343 (m-40) cc_final: 0.9004 (p0)
REVERT: B  199 TYR cc_start: 0.7267 (m-10) cc_final: 0.6811 (m-80)
REVERT: B  207 PHE cc_start: 0.8005 (m-80) cc_final: 0.6928 (m-80)
  outliers start: 17
  outliers final: 9
  residues processed: 92
  average time/residue: 0.1035
  time to fit residues: 12.4980
Evaluate side-chains
  90 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  210 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 64 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 23 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 55 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.085917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.065092 restraints weight = 28458.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 3.05
r_work: 0.3142 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8400  Z= 0.136
  Angle     :  0.647   9.892  12025  Z= 0.322
  Chirality :  0.034   0.168   1410
  Planarity :  0.004   0.045    992
  Dihedral  : 24.341 172.361   2810
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 30.77 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.35), residues: 590
  helix:  2.02 (0.32), residues: 256
  sheet: -0.11 (0.49), residues: 106
  loop : -1.94 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 160 
 TYR   0.012   0.001   TYR A  16 
 PHE   0.013   0.001   PHE A 207 
 TRP   0.008   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8396)
  covalent geometry    : angle       0.63742 (12019)
  hydrogen bonds       : bond        0.04434 (  337)
  hydrogen bonds       : angle       3.59206 (  874)
  metal coordination   : bond        0.00900 (    4)
  metal coordination   : angle       5.04527 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8707 (t0) cc_final: 0.8260 (m-40)
REVERT: A  135 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9123 (ptpt)
REVERT: A  211 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7237 (tppt)
REVERT: A  314 ASP cc_start: 0.8939 (m-30) cc_final: 0.8601 (m-30)
REVERT: A  371 ARG cc_start: 0.9020 (tpm170) cc_final: 0.8734 (tpm170)
REVERT: B   51 TRP cc_start: 0.9069 (t60) cc_final: 0.8333 (t-100)
REVERT: B   92 MET cc_start: 0.8461 (tmm) cc_final: 0.8212 (tmm)
REVERT: B  119 SER cc_start: 0.6894 (m) cc_final: 0.6130 (t)
REVERT: B  120 MET cc_start: 0.8631 (tmm) cc_final: 0.8102 (tmm)
REVERT: B  184 ASN cc_start: 0.9363 (m-40) cc_final: 0.9046 (p0)
REVERT: B  199 TYR cc_start: 0.7198 (m-10) cc_final: 0.6703 (m-80)
REVERT: B  207 PHE cc_start: 0.8003 (m-80) cc_final: 0.6931 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1011
  time to fit residues: 12.0386
Evaluate side-chains
  89 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  210 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.084335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.063492 restraints weight = 28633.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 3.03
r_work: 0.3107 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8400  Z= 0.192
  Angle     :  0.687  11.069  12025  Z= 0.342
  Chirality :  0.036   0.173   1410
  Planarity :  0.005   0.052    992
  Dihedral  : 24.349 170.610   2810
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 29.42 %
    Favored  : 66.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.36), residues: 590
  helix:  2.02 (0.32), residues: 256
  sheet:  0.09 (0.50), residues: 106
  loop : -1.96 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 201 
 TYR   0.030   0.002   TYR A 199 
 PHE   0.012   0.002   PHE B 154 
 TRP   0.007   0.001   TRP B 204 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8396)
  covalent geometry    : angle       0.67555 (12019)
  hydrogen bonds       : bond        0.04641 (  337)
  hydrogen bonds       : angle       3.70056 (  874)
  metal coordination   : bond        0.00969 (    4)
  metal coordination   : angle       5.67497 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8726 (t0) cc_final: 0.8382 (t0)
REVERT: A  135 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9094 (ptpt)
REVERT: A  211 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7372 (tppt)
REVERT: A  371 ARG cc_start: 0.8990 (tpm170) cc_final: 0.8694 (tpm170)
REVERT: B   15 ARG cc_start: 0.9021 (mtm110) cc_final: 0.8755 (mtm110)
REVERT: B   92 MET cc_start: 0.8464 (tmm) cc_final: 0.8201 (tmm)
REVERT: B  120 MET cc_start: 0.8659 (tmm) cc_final: 0.8314 (tpt)
REVERT: B  136 ASN cc_start: 0.9305 (t0) cc_final: 0.9043 (t0)
REVERT: B  184 ASN cc_start: 0.9373 (m-40) cc_final: 0.9042 (p0)
REVERT: B  199 TYR cc_start: 0.7157 (m-10) cc_final: 0.6946 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0913
  time to fit residues: 11.3601
Evaluate side-chains
  90 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  169 PHE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  210 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   chunk 16 optimal weight:    0.0170
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 26 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.087016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.066308 restraints weight = 29299.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 3.15
r_work: 0.3190 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8400  Z= 0.122
  Angle     :  0.658   9.374  12025  Z= 0.324
  Chirality :  0.034   0.179   1410
  Planarity :  0.004   0.043    992
  Dihedral  : 24.309 176.272   2810
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 31.73 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.35), residues: 590
  helix:  2.02 (0.32), residues: 256
  sheet:  0.17 (0.51), residues: 106
  loop : -2.04 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.013   0.001   TYR A 199 
 PHE   0.011   0.001   PHE B 212 
 TRP   0.013   0.001   TRP B  51 
 HIS   0.003   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8396)
  covalent geometry    : angle       0.65033 (12019)
  hydrogen bonds       : bond        0.04417 (  337)
  hydrogen bonds       : angle       3.57215 (  874)
  metal coordination   : bond        0.00905 (    4)
  metal coordination   : angle       4.64779 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8739 (t0) cc_final: 0.8482 (t0)
REVERT: A  135 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9164 (ptmm)
REVERT: A  211 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6989 (tppt)
REVERT: A  258 LYS cc_start: 0.9381 (pptt) cc_final: 0.9046 (ptmm)
REVERT: A  269 LYS cc_start: 0.9008 (tppp) cc_final: 0.8305 (tttt)
REVERT: A  314 ASP cc_start: 0.8928 (m-30) cc_final: 0.8632 (m-30)
REVERT: A  371 ARG cc_start: 0.9017 (tpm170) cc_final: 0.8731 (tpm170)
REVERT: B   51 TRP cc_start: 0.9093 (t60) cc_final: 0.8323 (t-100)
REVERT: B   92 MET cc_start: 0.8331 (tmm) cc_final: 0.8090 (tmm)
REVERT: B  120 MET cc_start: 0.8533 (tmm) cc_final: 0.8029 (tmm)
REVERT: B  136 ASN cc_start: 0.9345 (t0) cc_final: 0.9045 (t0)
REVERT: B  184 ASN cc_start: 0.9346 (m-40) cc_final: 0.9062 (p0)
REVERT: B  199 TYR cc_start: 0.7122 (m-10) cc_final: 0.6753 (m-80)
REVERT: B  207 PHE cc_start: 0.8161 (m-80) cc_final: 0.7190 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1067
  time to fit residues: 12.7120
Evaluate side-chains
  86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  189 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
B  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.086257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.065624 restraints weight = 29433.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 3.06
r_work: 0.3180 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8400  Z= 0.144
  Angle     :  0.669  11.095  12025  Z= 0.330
  Chirality :  0.034   0.168   1410
  Planarity :  0.005   0.076    992
  Dihedral  : 24.265 174.209   2810
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 31.54 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.35), residues: 590
  helix:  2.15 (0.32), residues: 256
  sheet:  0.17 (0.51), residues: 106
  loop : -2.06 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 201 
 TYR   0.016   0.001   TYR A 199 
 PHE   0.012   0.001   PHE B 158 
 TRP   0.010   0.001   TRP B  51 
 HIS   0.002   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8396)
  covalent geometry    : angle       0.65930 (12019)
  hydrogen bonds       : bond        0.04440 (  337)
  hydrogen bonds       : angle       3.52796 (  874)
  metal coordination   : bond        0.00901 (    4)
  metal coordination   : angle       5.05365 (    6)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8613 (t0) cc_final: 0.8174 (m-40)
REVERT: A  135 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9181 (ptmm)
REVERT: A  211 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7269 (tppt)
REVERT: A  269 LYS cc_start: 0.9078 (tppp) cc_final: 0.8377 (tttt)
REVERT: A  314 ASP cc_start: 0.8896 (m-30) cc_final: 0.8600 (m-30)
REVERT: A  349 ASP cc_start: 0.8742 (t0) cc_final: 0.8245 (t0)
REVERT: A  371 ARG cc_start: 0.8980 (tpm170) cc_final: 0.8702 (tpm170)
REVERT: B   15 ARG cc_start: 0.9028 (mtm110) cc_final: 0.8384 (mtp85)
REVERT: B   51 TRP cc_start: 0.9081 (t60) cc_final: 0.8291 (t-100)
REVERT: B   92 MET cc_start: 0.8320 (tmm) cc_final: 0.8110 (tmm)
REVERT: B  136 ASN cc_start: 0.9319 (t0) cc_final: 0.9068 (t0)
REVERT: B  184 ASN cc_start: 0.9331 (m-40) cc_final: 0.9044 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0989
  time to fit residues: 11.2916
Evaluate side-chains
  86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  189 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 16 optimal weight:    0.2980
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 HIS ** 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 = 0.3718 r_free = 0.3718 target = 0.081159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.059995 restraints weight = 28672.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.98
r_work: 0.3040 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.4083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   8400  Z= 0.288
  Angle     :  0.771  13.951  12025  Z= 0.385
  Chirality :  0.040   0.193   1410
  Planarity :  0.006   0.078    992
  Dihedral  : 24.479 166.534   2810
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 31.35 %
    Favored  : 65.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.35), residues: 590
  helix:  1.86 (0.32), residues: 256
  sheet:  0.09 (0.55), residues: 93
  loop : -1.91 (0.38), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  15 
 TYR   0.018   0.002   TYR A  16 
 PHE   0.016   0.002   PHE A 212 
 TRP   0.020   0.002   TRP B 204 
 HIS   0.005   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 ( 8396)
  covalent geometry    : angle       0.75427 (12019)
  hydrogen bonds       : bond        0.05449 (  337)
  hydrogen bonds       : angle       3.87027 (  874)
  metal coordination   : bond        0.01411 (    4)
  metal coordination   : angle       7.26695 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1978.84 seconds
wall clock time: 34 minutes 34.42 seconds (2074.42 seconds total)