Starting phenix.real_space_refine
on Tue Mar  3 12:25:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ckr_30391/03_2026/7ckr_30391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ckr_30391/03_2026/7ckr_30391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ckr_30391/03_2026/7ckr_30391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ckr_30391/03_2026/7ckr_30391.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ckr_30391/03_2026/7ckr_30391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ckr_30391/03_2026/7ckr_30391.map"
  }
  resolution = 3.0
  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=   0.004 sd=   0.070
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: 5
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     Cl      1      4.86       5
     C    2669      2.51       5
     N     687      2.21       5
     O     711      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4094
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2900
          Classifications: {'peptide': 382}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 364}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1166
          Classifications: {'peptide': 215}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 155}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 204}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 527
          Unresolved non-hydrogen angles: 675
          Unresolved non-hydrogen dihedrals: 438
          Unresolved non-hydrogen chiralities: 49
          Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 7, 'HIS:plan': 3, 'ARG:plan': 7, 'TRP:plan': 4, 'GLN:plan1': 6, 'TYR:plan': 3}
          Unresolved non-hydrogen planarities: 282
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'G5O': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.09, per 1000 atoms: 0.27
  Number of scatterers: 4094
  At special positions: 0
  Unit cell: (102.883, 58.1877, 112.159, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      26     16.00
     O     711      8.00
     N     687      7.00
     C    2669      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: 0.35
  Conformation dependent library (CDL) restraints added in 180.1 milliseconds
  

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1066

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 4 sheets defined
      65.7% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 41
      removed outlier: 3.942A  pdb=" N   VAL A  22 " --> pdb=" O   TRP A  18 " (cutoff:3.500A)
      Proline residue:  A  37  - end of helix
    Processing helix  chain 'A' and resid 43 through 52
      removed outlier: 3.663A  pdb=" N   ILE A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 72
      removed outlier: 3.983A  pdb=" N   TRP A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   SER A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   MET A  65 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 84 through 104
      removed outlier: 3.702A  pdb=" N   VAL A  88 " --> pdb=" O   GLY A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 139
      Proline residue:  A 130  - end of helix
      removed outlier: 3.634A  pdb=" N   THR A 133 " --> pdb=" O   ASN A 129 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 172
      removed outlier: 3.871A  pdb=" N   ALA A 146 " --> pdb=" O   ARG A 142 " (cutoff:3.500A)
      Proline residue:  A 155  - end of helix
      removed outlier: 3.802A  pdb=" N   LEU A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 174 through 184
    Processing helix  chain 'A' and resid 184 through 192
    Processing helix  chain 'A' and resid 254 through 259
    Processing helix  chain 'A' and resid 260 through 278
      removed outlier: 4.048A  pdb=" N   GLY A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   PHE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 291
      removed outlier: 5.024A  pdb=" N   SER A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   SER A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 321
      removed outlier: 3.576A  pdb=" N   ALA A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      Proline residue:  A 314  - end of helix
    Processing helix  chain 'A' and resid 325 through 327
      No H-bonds generated for 'chain 'A' and resid 325 through 327'
    Processing helix  chain 'A' and resid 328 through 347
      removed outlier: 3.945A  pdb=" N   HIS A 344 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 352 through 382
      removed outlier: 3.918A  pdb=" N   TYR A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   PHE A 375 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 416
      Proline residue:  A 401  - end of helix
      removed outlier: 4.226A  pdb=" N   LEU A 404 " --> pdb=" O   CYS A 400 " (cutoff:3.500A)
      Proline residue:  A 406  - end of helix
    Processing helix  chain 'A' and resid 419 through 449
      removed outlier: 3.820A  pdb=" N   GLY A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 81
      No H-bonds generated for 'chain 'B' and resid 79 through 81'
    Processing helix  chain 'B' and resid 153 through 156
    Processing helix  chain 'B' and resid 208 through 237
      removed outlier: 4.080A  pdb=" N   PHE B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      Proline residue:  B 235  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 33
    Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63
      removed outlier: 4.067A  pdb=" N   GLY B  95 " --> pdb=" O   PHE B  89 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109
      removed outlier: 3.501A  pdb=" N   ARG B 166 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 117
      removed outlier: 6.449A  pdb=" N   GLU B 114 " --> pdb=" O   ARG B 201 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   ARG B 203 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ILE B 116 " --> pdb=" O   ARG B 203 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY B 192 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   TRP B 139 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    930 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 644
        1.31 -     1.43: 1150
        1.43 -     1.56: 2344
        1.56 -     1.69: 8
        1.69 -     1.81: 41
  Bond restraints: 4187
  Sorted by residual:
  bond pdb=" C12 G5O A 601 "
       pdb=" C13 G5O A 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.525 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" C10 G5O A 601 "
       pdb=" C11 G5O A 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.524 -0.136 2.00e-02 2.50e+03 4.62e+01
  bond pdb=" C14 G5O A 601 "
       pdb=" C15 G5O A 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.522 -0.135 2.00e-02 2.50e+03 4.59e+01
  bond pdb=" C17 G5O A 601 "
       pdb=" N18 G5O A 601 "
    ideal  model  delta    sigma   weight residual
    1.339  1.453 -0.114 2.00e-02 2.50e+03 3.22e+01
  bond pdb=" N   PRO B  91 "
       pdb=" CD  PRO B  91 "
    ideal  model  delta    sigma   weight residual
    1.474  1.538 -0.064 1.40e-02 5.10e+03 2.10e+01
  ... (remaining 4182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.64: 5599
        3.64 -     7.29: 112
        7.29 -    10.93: 5
       10.93 -    14.57: 3
       14.57 -    18.22: 1
  Bond angle restraints: 5720
  Sorted by residual:
  angle pdb=" CA  PRO B  91 "
        pdb=" N   PRO B  91 "
        pdb=" CD  PRO B  91 "
      ideal   model   delta    sigma   weight residual
     111.50   97.99   13.51 1.40e+00 5.10e-01 9.31e+01
  angle pdb=" CA  PRO B 132 "
        pdb=" N   PRO B 132 "
        pdb=" CD  PRO B 132 "
      ideal   model   delta    sigma   weight residual
     111.50   98.07   13.43 1.40e+00 5.10e-01 9.21e+01
  angle pdb=" CA  PRO B  93 "
        pdb=" N   PRO B  93 "
        pdb=" CD  PRO B  93 "
      ideal   model   delta    sigma   weight residual
     111.50   99.09   12.41 1.40e+00 5.10e-01 7.85e+01
  angle pdb=" O8  G5O A 601 "
        pdb=" S7  G5O A 601 "
        pdb=" O9  G5O A 601 "
      ideal   model   delta    sigma   weight residual
     119.81  101.59   18.22 3.00e+00 1.11e-01 3.69e+01
  angle pdb=" N   ILE B 142 "
        pdb=" CA  ILE B 142 "
        pdb=" C   ILE B 142 "
      ideal   model   delta    sigma   weight residual
     108.12  114.96   -6.84 1.34e+00 5.57e-01 2.61e+01
  ... (remaining 5715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 2056
       16.50 -    33.01: 200
       33.01 -    49.51: 82
       49.51 -    66.02: 27
       66.02 -    82.52: 4
  Dihedral angle restraints: 2369
    sinusoidal: 690
      harmonic: 1679
  Sorted by residual:
  dihedral pdb=" C   VAL B  50 "
           pdb=" N   VAL B  50 "
           pdb=" CA  VAL B  50 "
           pdb=" CB  VAL B  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.04   17.04     0      2.50e+00 1.60e-01 4.65e+01
  dihedral pdb=" N   VAL B  50 "
           pdb=" C   VAL B  50 "
           pdb=" CA  VAL B  50 "
           pdb=" CB  VAL B  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  139.11  -15.71     0      2.50e+00 1.60e-01 3.95e+01
  dihedral pdb=" CA  TYR A 293 "
           pdb=" C   TYR A 293 "
           pdb=" N   SER A 294 "
           pdb=" CA  SER A 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.26   29.74     0      5.00e+00 4.00e-02 3.54e+01
  ... (remaining 2366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 595
       0.112 -    0.224: 60
       0.224 -    0.336: 7
       0.336 -    0.448: 5
       0.448 -    0.560: 3
  Chirality restraints: 670
  Sorted by residual:
  chirality pdb=" CA  GLU B 172 "
            pdb=" N   GLU B 172 "
            pdb=" C   GLU B 172 "
            pdb=" CB  GLU B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.84e+00
  chirality pdb=" CA  VAL B  50 "
            pdb=" N   VAL B  50 "
            pdb=" C   VAL B  50 "
            pdb=" CB  VAL B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.88    0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" CA  GLU B 155 "
            pdb=" N   GLU B 155 "
            pdb=" C   GLU B 155 "
            pdb=" CB  GLU B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.78e+00
  ... (remaining 667 not shown)

  Planarity restraints: 731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 131 "    0.117 5.00e-02 4.00e+02   1.63e-01 4.28e+01
        pdb=" N   PRO B 132 "   -0.281 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "    0.098 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "    0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  90 "   -0.081 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO B  91 "    0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO B  91 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO B  91 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  27 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.74e+00
        pdb=" C   PHE A  27 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PHE A  27 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ILE A  28 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 728 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 24
        2.50 -     3.10: 3316
        3.10 -     3.70: 6203
        3.70 -     4.30: 8787
        4.30 -     4.90: 14435
  Nonbonded interactions: 32765
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 173 "
            pdb=" OG  SER A 177 "
     model   vdw
     1.896 3.040
  nonbonded pdb=" O   PRO A 324 "
            pdb=" NH1 ARG A 328 "
     model   vdw
     1.989 3.120
  nonbonded pdb=" OE1 GLN A 330 "
            pdb=" OG1 THR A 377 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" O   LYS A  38 "
            pdb=" OG1 THR A  41 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OD1 ASP A 418 "
            pdb=" N   TYR A 419 "
     model   vdw
     2.157 3.120
  ... (remaining 32760 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:             1.320
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.930
  Find NCS groups from input model:        0.020
  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:7.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5791
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      :  0.009   0.138   4187  Z= 0.588
  Angle     :  1.223  18.216   5720  Z= 0.792
  Chirality :  0.085   0.560    670
  Planarity :  0.010   0.163    731
  Dihedral  : 17.221  82.520   1303
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.95 %
    Favored  : 91.88 %
  Rotamer:
    Outliers : 11.04 %
    Allowed  : 20.90 %
    Favored  : 68.06 %
  Cbeta Deviations :  1.69 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -2.89 (0.31), residues: 591
  helix: -1.92 (0.24), residues: 357
  sheet:  0.30 (0.53), residues: 94
  loop : -2.94 (0.43), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 386 
 TYR   0.011   0.001   TYR A 266 
 PHE   0.028   0.001   PHE A  27 
 TRP   0.009   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00918 ( 4187)
  covalent geometry    : angle       1.22296 ( 5720)
  hydrogen bonds       : bond        0.13969 (  318)
  hydrogen bonds       : angle       7.07699 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 71
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  128 LEU cc_start: 0.8649 (tp) cc_final: 0.8444 (tp)
REVERT: A  137 LYS cc_start: 0.8453 (tttt) cc_final: 0.8183 (ttmt)
REVERT: A  380 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5847 (m-30)
REVERT: B  204 SER cc_start: 0.5404 (OUTLIER) cc_final: 0.5163 (m)
  outliers start: 37
  outliers final: 14
  residues processed: 99
  average time/residue: 0.2949
  time to fit residues: 30.9179
Evaluate side-chains
  81 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  220 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    0.0050
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 127 ASN
A 270 ASN
A 330 GLN
B 115 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.231349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.201454 restraints weight = 5478.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4305 rms_B_bonded: 1.91
r_work: 0.4237 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.4153 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4187  Z= 0.168
  Angle     :  0.694   7.861   5720  Z= 0.366
  Chirality :  0.044   0.131    670
  Planarity :  0.007   0.065    731
  Dihedral  :  7.226  58.208    657
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 24.18 %
    Favored  : 70.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.59 (0.35), residues: 591
  helix: -0.02 (0.27), residues: 368
  sheet:  0.85 (0.53), residues: 101
  loop : -2.31 (0.52), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 446 
 TYR   0.017   0.002   TYR B 229 
 PHE   0.028   0.002   PHE A  27 
 TRP   0.009   0.001   TRP A 174 
 HIS   0.007   0.002   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4187)
  covalent geometry    : angle       0.69410 ( 5720)
  hydrogen bonds       : bond        0.05368 (  318)
  hydrogen bonds       : angle       5.25249 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 LEU cc_start: 0.3886 (OUTLIER) cc_final: 0.3242 (pt)
REVERT: A  272 ILE cc_start: 0.8213 (mt) cc_final: 0.7929 (tt)
REVERT: B  204 SER cc_start: 0.5104 (p) cc_final: 0.4880 (t)
  outliers start: 19
  outliers final: 6
  residues processed: 95
  average time/residue: 0.2021
  time to fit residues: 20.7918
Evaluate side-chains
  87 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain B residue  220 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.226239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.197159 restraints weight = 5455.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.4255 rms_B_bonded: 1.91
r_work: 0.4181 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.4094 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4187  Z= 0.174
  Angle     :  0.687   7.579   5720  Z= 0.359
  Chirality :  0.046   0.170    670
  Planarity :  0.006   0.049    731
  Dihedral  :  6.478  54.395    641
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 26.57 %
    Favored  : 67.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.03 (0.35), residues: 591
  helix:  0.45 (0.28), residues: 366
  sheet:  1.06 (0.53), residues: 101
  loop : -2.16 (0.50), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 196 
 TYR   0.014   0.002   TYR A 266 
 PHE   0.024   0.002   PHE A  27 
 TRP   0.010   0.001   TRP A 174 
 HIS   0.004   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4187)
  covalent geometry    : angle       0.68720 ( 5720)
  hydrogen bonds       : bond        0.05609 (  318)
  hydrogen bonds       : angle       5.14987 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8206 (m-10) cc_final: 0.7849 (m-10)
REVERT: A  255 LEU cc_start: 0.4143 (OUTLIER) cc_final: 0.3494 (pt)
REVERT: A  272 ILE cc_start: 0.8327 (mt) cc_final: 0.8023 (tt)
REVERT: A  380 ASP cc_start: 0.6229 (m-30) cc_final: 0.5725 (m-30)
REVERT: B  204 SER cc_start: 0.5295 (p) cc_final: 0.5007 (t)
  outliers start: 21
  outliers final: 12
  residues processed: 103
  average time/residue: 0.2177
  time to fit residues: 24.0701
Evaluate side-chains
  93 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  220 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 39 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 127 ASN
** A 330 GLN ** 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 = 0.4530 r_free = 0.4530 target = 0.221456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.192233 restraints weight = 5392.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 1.91
r_work: 0.4122 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.4036 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4187  Z= 0.210
  Angle     :  0.733   8.942   5720  Z= 0.389
  Chirality :  0.048   0.176    670
  Planarity :  0.006   0.054    731
  Dihedral  :  6.643  50.348    641
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 29.25 %
    Favored  : 64.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.09 (0.35), residues: 591
  helix:  0.34 (0.28), residues: 363
  sheet:  0.99 (0.52), residues: 101
  loop : -1.86 (0.52), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 196 
 TYR   0.021   0.002   TYR A 423 
 PHE   0.024   0.002   PHE A  27 
 TRP   0.010   0.002   TRP A 174 
 HIS   0.004   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 4187)
  covalent geometry    : angle       0.73330 ( 5720)
  hydrogen bonds       : bond        0.06275 (  318)
  hydrogen bonds       : angle       5.34930 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8226 (m-10) cc_final: 0.7746 (m-80)
REVERT: A  255 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4099 (pt)
REVERT: A  272 ILE cc_start: 0.8388 (mt) cc_final: 0.8112 (mp)
REVERT: A  380 ASP cc_start: 0.6489 (m-30) cc_final: 0.6179 (m-30)
REVERT: A  416 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5065 (t80)
REVERT: B  204 SER cc_start: 0.5589 (p) cc_final: 0.5328 (m)
  outliers start: 20
  outliers final: 10
  residues processed: 114
  average time/residue: 0.2149
  time to fit residues: 26.3143
Evaluate side-chains
  102 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  399 CYS
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  416 TYR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  218 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
A 147 ASN
** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.220449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.190387 restraints weight = 5375.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.4190 rms_B_bonded: 1.97
r_work: 0.4103 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.4014 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4187  Z= 0.209
  Angle     :  0.742   9.302   5720  Z= 0.390
  Chirality :  0.048   0.191    670
  Planarity :  0.006   0.056    731
  Dihedral  :  6.128  46.778    637
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers : 10.15 %
    Allowed  : 28.06 %
    Favored  : 61.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.04 (0.35), residues: 591
  helix:  0.31 (0.28), residues: 365
  sheet:  0.96 (0.47), residues: 111
  loop : -1.82 (0.57), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 196 
 TYR   0.032   0.002   TYR A 266 
 PHE   0.026   0.002   PHE A  27 
 TRP   0.013   0.002   TRP A 174 
 HIS   0.004   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 4187)
  covalent geometry    : angle       0.74243 ( 5720)
  hydrogen bonds       : bond        0.06157 (  318)
  hydrogen bonds       : angle       5.34630 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 LEU cc_start: 0.4603 (OUTLIER) cc_final: 0.4192 (pt)
REVERT: A  272 ILE cc_start: 0.8458 (mt) cc_final: 0.8203 (mt)
REVERT: A  380 ASP cc_start: 0.6503 (m-30) cc_final: 0.6205 (m-30)
REVERT: A  415 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.5999 (mtp)
REVERT: A  416 TYR cc_start: 0.5899 (OUTLIER) cc_final: 0.4872 (t80)
REVERT: B  204 SER cc_start: 0.5719 (p) cc_final: 0.5458 (m)
  outliers start: 34
  outliers final: 16
  residues processed: 120
  average time/residue: 0.2028
  time to fit residues: 26.3577
Evaluate side-chains
  109 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   34 TYR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  399 CYS
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  416 TYR
Chi-restraints excluded: chain A residue  422 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 40 optimal weight:   40.0000
   chunk 57 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
** A 330 GLN ** 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 = 0.4539 r_free = 0.4539 target = 0.222074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.192320 restraints weight = 5430.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.4218 rms_B_bonded: 1.98
r_work: 0.4132 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.4041 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4187  Z= 0.190
  Angle     :  0.746   9.552   5720  Z= 0.389
  Chirality :  0.048   0.174    670
  Planarity :  0.006   0.055    731
  Dihedral  :  5.987  46.307    637
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  9.85 %
    Allowed  : 28.06 %
    Favored  : 62.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: 591
  helix:  0.43 (0.28), residues: 365
  sheet:  0.99 (0.48), residues: 111
  loop : -1.54 (0.59), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 386 
 TYR   0.016   0.002   TYR A 423 
 PHE   0.026   0.002   PHE A  27 
 TRP   0.009   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 4187)
  covalent geometry    : angle       0.74644 ( 5720)
  hydrogen bonds       : bond        0.05861 (  318)
  hydrogen bonds       : angle       5.26236 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8163 (m-10) cc_final: 0.7617 (m-80)
REVERT: A  255 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4193 (pt)
REVERT: A  272 ILE cc_start: 0.8452 (mt) cc_final: 0.8200 (mt)
REVERT: A  379 MET cc_start: 0.7876 (ttt) cc_final: 0.7675 (ttp)
REVERT: A  380 ASP cc_start: 0.6457 (m-30) cc_final: 0.6146 (m-30)
REVERT: A  400 CYS cc_start: 0.7369 (t) cc_final: 0.6768 (m)
REVERT: A  415 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5941 (mtp)
REVERT: A  416 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4678 (t80)
REVERT: A  435 ILE cc_start: 0.8524 (mp) cc_final: 0.8068 (mt)
REVERT: B  204 SER cc_start: 0.5789 (p) cc_final: 0.5436 (m)
  outliers start: 33
  outliers final: 16
  residues processed: 118
  average time/residue: 0.1927
  time to fit residues: 24.6045
Evaluate side-chains
  109 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  357 CYS
Chi-restraints excluded: chain A residue  399 CYS
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  416 TYR
Chi-restraints excluded: chain A residue  422 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 29 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 42 optimal weight:   30.0000
   chunk 58 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
A 129 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.224374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.194331 restraints weight = 5418.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.4241 rms_B_bonded: 2.00
r_work: 0.4159 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.4071 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4187  Z= 0.164
  Angle     :  0.725   9.736   5720  Z= 0.373
  Chirality :  0.047   0.192    670
  Planarity :  0.006   0.056    731
  Dihedral  :  5.487  47.268    635
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  7.76 %
    Allowed  : 30.45 %
    Favored  : 61.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.41 (0.36), residues: 591
  helix:  0.60 (0.29), residues: 362
  sheet:  1.23 (0.49), residues: 109
  loop : -1.41 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 411 
 TYR   0.012   0.001   TYR A 423 
 PHE   0.025   0.002   PHE A 332 
 TRP   0.010   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4187)
  covalent geometry    : angle       0.72544 ( 5720)
  hydrogen bonds       : bond        0.05364 (  318)
  hydrogen bonds       : angle       5.09424 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8100 (m-10) cc_final: 0.7563 (m-80)
REVERT: A  129 ASN cc_start: 0.8262 (t0) cc_final: 0.8060 (t0)
REVERT: A  255 LEU cc_start: 0.4435 (OUTLIER) cc_final: 0.4033 (pt)
REVERT: A  270 ASN cc_start: 0.8179 (m-40) cc_final: 0.7959 (m-40)
REVERT: A  272 ILE cc_start: 0.8427 (mt) cc_final: 0.8200 (mt)
REVERT: A  379 MET cc_start: 0.7739 (ttt) cc_final: 0.7535 (ttp)
REVERT: A  380 ASP cc_start: 0.6452 (m-30) cc_final: 0.6242 (m-30)
REVERT: A  400 CYS cc_start: 0.7289 (t) cc_final: 0.6794 (m)
REVERT: A  435 ILE cc_start: 0.8506 (mp) cc_final: 0.8067 (mt)
REVERT: B  204 SER cc_start: 0.5759 (p) cc_final: 0.5334 (m)
  outliers start: 26
  outliers final: 13
  residues processed: 112
  average time/residue: 0.2159
  time to fit residues: 26.0421
Evaluate side-chains
  107 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  357 CYS
Chi-restraints excluded: chain A residue  399 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 54 optimal weight:   30.0000
   chunk 5 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 43 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
A 321 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.226206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.196640 restraints weight = 5308.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.4257 rms_B_bonded: 1.97
r_work: 0.4176 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.4086 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.5091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4187  Z= 0.154
  Angle     :  0.713   9.541   5720  Z= 0.369
  Chirality :  0.047   0.183    670
  Planarity :  0.006   0.057    731
  Dihedral  :  5.347  48.311    635
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 33.43 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.58 (0.36), residues: 591
  helix:  0.71 (0.29), residues: 363
  sheet:  1.36 (0.50), residues: 109
  loop : -1.35 (0.59), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 196 
 TYR   0.010   0.001   TYR A 423 
 PHE   0.030   0.002   PHE A 332 
 TRP   0.012   0.001   TRP A 174 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4187)
  covalent geometry    : angle       0.71338 ( 5720)
  hydrogen bonds       : bond        0.05134 (  318)
  hydrogen bonds       : angle       4.95540 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8089 (m-10) cc_final: 0.7538 (m-80)
REVERT: A  255 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.3873 (pt)
REVERT: A  271 VAL cc_start: 0.8116 (t) cc_final: 0.7864 (m)
REVERT: A  272 ILE cc_start: 0.8384 (mt) cc_final: 0.8139 (tt)
REVERT: A  289 LYS cc_start: 0.8442 (mptt) cc_final: 0.8203 (mmmt)
REVERT: A  400 CYS cc_start: 0.7320 (t) cc_final: 0.6876 (m)
REVERT: A  435 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8088 (mt)
REVERT: B  204 SER cc_start: 0.5769 (p) cc_final: 0.5289 (m)
  outliers start: 22
  outliers final: 12
  residues processed: 108
  average time/residue: 0.2349
  time to fit residues: 27.1101
Evaluate side-chains
  104 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  357 CYS
Chi-restraints excluded: chain A residue  399 CYS
Chi-restraints excluded: chain A residue  435 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 13 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 127 ASN
** A 330 GLN ** 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 = 0.4565 r_free = 0.4565 target = 0.225619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.197193 restraints weight = 5451.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.4251 rms_B_bonded: 1.95
r_work: 0.4174 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.4085 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4187  Z= 0.161
  Angle     :  0.730   9.743   5720  Z= 0.377
  Chirality :  0.047   0.215    670
  Planarity :  0.006   0.054    731
  Dihedral  :  5.351  48.446    635
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 34.93 %
    Favored  : 59.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.66 (0.36), residues: 591
  helix:  0.72 (0.28), residues: 364
  sheet:  1.49 (0.50), residues: 109
  loop : -1.26 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 196 
 TYR   0.012   0.002   TYR A 423 
 PHE   0.031   0.002   PHE A 332 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4187)
  covalent geometry    : angle       0.73029 ( 5720)
  hydrogen bonds       : bond        0.05291 (  318)
  hydrogen bonds       : angle       4.95431 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8050 (m-10) cc_final: 0.7568 (m-80)
REVERT: A  255 LEU cc_start: 0.4432 (OUTLIER) cc_final: 0.4018 (pt)
REVERT: A  271 VAL cc_start: 0.8122 (t) cc_final: 0.7891 (m)
REVERT: A  272 ILE cc_start: 0.8452 (mt) cc_final: 0.8188 (tt)
REVERT: A  289 LYS cc_start: 0.8416 (mptt) cc_final: 0.8192 (mmmt)
REVERT: A  400 CYS cc_start: 0.7309 (t) cc_final: 0.6883 (m)
REVERT: A  435 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8120 (mt)
REVERT: B  204 SER cc_start: 0.5758 (p) cc_final: 0.5555 (t)
  outliers start: 18
  outliers final: 9
  residues processed: 105
  average time/residue: 0.2143
  time to fit residues: 24.1874
Evaluate side-chains
  102 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  357 CYS
Chi-restraints excluded: chain A residue  399 CYS
Chi-restraints excluded: chain A residue  435 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:   20.0000
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 41 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** 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 = 0.4577 r_free = 0.4577 target = 0.226911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.197491 restraints weight = 5298.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.4259 rms_B_bonded: 1.99
r_work: 0.4178 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.4088 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.5309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4187  Z= 0.157
  Angle     :  0.730   9.730   5720  Z= 0.377
  Chirality :  0.048   0.203    670
  Planarity :  0.006   0.054    731
  Dihedral  :  5.294  48.707    635
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 37.01 %
    Favored  : 59.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.73 (0.36), residues: 591
  helix:  0.73 (0.28), residues: 364
  sheet:  1.61 (0.51), residues: 109
  loop : -1.17 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 328 
 TYR   0.010   0.002   TYR A 266 
 PHE   0.036   0.002   PHE A 332 
 TRP   0.007   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4187)
  covalent geometry    : angle       0.73038 ( 5720)
  hydrogen bonds       : bond        0.05198 (  318)
  hydrogen bonds       : angle       4.91303 (  930)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8030 (m-10) cc_final: 0.7513 (m-80)
REVERT: A  255 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.3913 (pt)
REVERT: A  271 VAL cc_start: 0.8095 (t) cc_final: 0.7890 (m)
REVERT: A  272 ILE cc_start: 0.8474 (mt) cc_final: 0.8205 (tt)
REVERT: A  400 CYS cc_start: 0.7298 (t) cc_final: 0.6909 (m)
REVERT: A  435 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8113 (mt)
REVERT: B  204 SER cc_start: 0.5721 (p) cc_final: 0.5500 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2324
  time to fit residues: 24.8516
Evaluate side-chains
  97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  357 CYS
Chi-restraints excluded: chain A residue  399 CYS
Chi-restraints excluded: chain A residue  435 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 54 optimal weight:   40.0000
   chunk 55 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:   50.0000
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.223455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.193704 restraints weight = 5385.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 2.02
r_work: 0.4132 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.4043 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.5447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4187  Z= 0.183
  Angle     :  0.768   9.744   5720  Z= 0.400
  Chirality :  0.049   0.200    670
  Planarity :  0.006   0.052    731
  Dihedral  :  5.485  48.448    635
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 36.42 %
    Favored  : 58.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.59 (0.36), residues: 591
  helix:  0.63 (0.28), residues: 364
  sheet:  1.56 (0.51), residues: 109
  loop : -1.27 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 328 
 TYR   0.015   0.002   TYR A 423 
 PHE   0.036   0.002   PHE A 332 
 TRP   0.010   0.002   TRP A 174 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 4187)
  covalent geometry    : angle       0.76808 ( 5720)
  hydrogen bonds       : bond        0.05673 (  318)
  hydrogen bonds       : angle       5.06628 (  930)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1586.62 seconds
wall clock time: 27 minutes 40.79 seconds (1660.79 seconds total)