Starting phenix.real_space_refine
on Tue Aug  4 20:21:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9z2p_73774/08_2026/9z2p_73774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9z2p_73774/08_2026/9z2p_73774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9z2p_73774/08_2026/9z2p_73774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9z2p_73774/08_2026/9z2p_73774.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9z2p_73774/08_2026/9z2p_73774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9z2p_73774/08_2026/9z2p_73774.map"
  }
  resolution = 2.91
  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=   0.007
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
     P      75      5.49       5
     S      31      5.16       5
     C    3794      2.51       5
     N    1116      2.21       5
     O    1396      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6412
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4812
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 592, 4790
          Classifications: {'peptide': 592}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 551}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 592, 4790
          Classifications: {'peptide': 592}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 551}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4885
    Chain: "B"
      Number of atoms: 1600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1600
          Classifications: {'RNA': 75}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 10, 'rna3p': 64}
  Time building chain proxies: 2.52, per 1000 atoms: 0.39
  Number of scatterers: 6412
  At special positions: 0
  Unit cell: (69.864, 98.4, 105.288, 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)
     S      31     16.00
     P      75     15.00
     O    1396      8.00
     N    1116      7.00
     C    3794      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: 0.48
  Conformation dependent library (CDL) restraints added in 575.2 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:  1134

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      42.9% alpha, 16.0% beta
      23 base pairs and 42 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 83 through 98
    Processing helix  chain 'A' and resid 121 through 124
      removed outlier: 3.648A  pdb=" N   GLU A 124 " --> pdb=" O   TYR A 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 121 through 124'
    Processing helix  chain 'A' and resid 132 through 139
    Processing helix  chain 'A' and resid 142 through 156
    Processing helix  chain 'A' and resid 162 through 165
    Processing helix  chain 'A' and resid 166 through 173
      removed outlier: 3.525A  pdb=" N   LEU A 170 " --> pdb=" O   MET A 166 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASN A 173 " --> pdb=" O   PRO A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 199
      removed outlier: 3.596A  pdb=" N   GLN A 193 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 242 through 246
      removed outlier: 4.002A  pdb=" N   ILE A 246 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 277
      removed outlier: 3.875A  pdb=" N   MET A 277 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 289 through 309
      removed outlier: 4.783A  pdb=" N   GLY A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   LEU A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 340
      removed outlier: 4.236A  pdb=" N   ALA A 330 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   VAL A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 385
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.552A  pdb=" N   PHE A 393 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.858A  pdb=" N   HIS A 405 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 408
      No H-bonds generated for 'chain 'A' and resid 406 through 408'
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 4.411A  pdb=" N   GLN A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 538
      removed outlier: 3.816A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 546
      No H-bonds generated for 'chain 'A' and resid 544 through 546'
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 607 through 612
    Processing helix  chain 'A' and resid 613 through 615
      No H-bonds generated for 'chain 'A' and resid 613 through 615'
    Processing helix  chain 'A' and resid 623 through 633
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 642 through 651
      removed outlier: 3.882A  pdb=" N   ASP A 651 " --> pdb=" O   SER A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 702
      removed outlier: 3.557A  pdb=" N   MET A 702 " --> pdb=" O   TYR A 698 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117
    Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107
    Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345
    Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345
      removed outlier: 4.337A  pdb=" N   GLY A 314 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TYR A 262 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   GLY A 313 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   ARG A 264 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ARG A 315 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LEU A 266 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL A 317 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LYS A 179 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   LEU A 266 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LEU A 181 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL A 211 " --> pdb=" O   MET A 237 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   VAL A 239 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ALA A 213 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   ILE A 236 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   THR A 583 " --> pdb=" O   ILE A 236 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   VAL A 238 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253
    Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367
    Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 522
      removed outlier: 6.911A  pdb=" N   LEU A 560 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 621
      removed outlier: 3.517A  pdb=" N   ILE A 675 " --> pdb=" O   TYR A 661 " (cutoff:3.500A)

    187 hydrogen bonds defined for protein.
    507 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      61 hydrogen bonds
      106 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      42 stacking parallelities
  Total time for adding SS restraints: 1.12

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1698
        1.34 -     1.45: 1492
        1.45 -     1.57: 3332
        1.57 -     1.69: 149
        1.69 -     1.81: 50
  Bond restraints: 6721
  Sorted by residual:
  bond pdb=" N   VAL A 114 "
       pdb=" CA  VAL A 114 "
    ideal  model  delta    sigma   weight residual
    1.468  1.459  0.010 1.05e-02 9.07e+03 8.23e-01
  bond pdb=" N   PRO A 544 "
       pdb=" CA  PRO A 544 "
    ideal  model  delta    sigma   weight residual
    1.469  1.480 -0.011 1.28e-02 6.10e+03 7.57e-01
  bond pdb=" N3    G B  10 "
       pdb=" C4    G B  10 "
    ideal  model  delta    sigma   weight residual
    1.350  1.344  0.006 7.00e-03 2.04e+04 7.07e-01
  bond pdb=" C2    U B  50 "
       pdb=" N3    U B  50 "
    ideal  model  delta    sigma   weight residual
    1.373  1.379 -0.006 7.00e-03 2.04e+04 6.37e-01
  bond pdb=" C6    G B  46 "
       pdb=" N1    G B  46 "
    ideal  model  delta    sigma   weight residual
    1.391  1.386  0.005 7.00e-03 2.04e+04 6.10e-01
  ... (remaining 6716 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 9095
        1.25 -     2.50: 248
        2.50 -     3.75: 119
        3.75 -     5.00: 4
        5.00 -     6.26: 2
  Bond angle restraints: 9468
  Sorted by residual:
  angle pdb=" O5'   G B  69 "
        pdb=" C5'   G B  69 "
        pdb=" C4'   G B  69 "
      ideal   model   delta    sigma   weight residual
     109.40  112.45   -3.05 8.00e-01 1.56e+00 1.45e+01
  angle pdb=" O5'   G B  19 "
        pdb=" C5'   G B  19 "
        pdb=" C4'   G B  19 "
      ideal   model   delta    sigma   weight residual
     109.40  112.41   -3.01 8.00e-01 1.56e+00 1.41e+01
  angle pdb=" O5'   G B  70 "
        pdb=" C5'   G B  70 "
        pdb=" C4'   G B  70 "
      ideal   model   delta    sigma   weight residual
     109.40  112.18   -2.78 8.00e-01 1.56e+00 1.20e+01
  angle pdb=" O5'   G B  30 "
        pdb=" C5'   G B  30 "
        pdb=" C4'   G B  30 "
      ideal   model   delta    sigma   weight residual
     109.40  112.11   -2.71 8.00e-01 1.56e+00 1.15e+01
  angle pdb=" O5'   G B  46 "
        pdb=" C5'   G B  46 "
        pdb=" C4'   G B  46 "
      ideal   model   delta    sigma   weight residual
     109.40  112.11   -2.71 8.00e-01 1.56e+00 1.15e+01
  ... (remaining 9463 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 4048
       35.61 -    71.21: 159
       71.21 -   106.82: 25
      106.82 -   142.42: 1
      142.42 -   178.03: 1
  Dihedral angle restraints: 4234
    sinusoidal: 2488
      harmonic: 1746
  Sorted by residual:
  dihedral pdb=" O4'   G B  45 "
           pdb=" C1'   G B  45 "
           pdb=" N9    G B  45 "
           pdb=" C4    G B  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.00  175.44   78.56     1      1.70e+01 3.46e-03 2.66e+01
  dihedral pdb=" C4'   A B  21 "
           pdb=" C3'   A B  21 "
           pdb=" O3'   A B  21 "
           pdb=" P     G B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.97  178.03     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" O4'   G B  15 "
           pdb=" C1'   G B  15 "
           pdb=" N9    G B  15 "
           pdb=" C4    G B  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -38.34  -51.66     1      2.00e+01 2.50e-03 9.11e+00
  ... (remaining 4231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 676
       0.028 -    0.057: 243
       0.057 -    0.085: 60
       0.085 -    0.113: 50
       0.113 -    0.142: 74
  Chirality restraints: 1103
  Sorted by residual:
  chirality pdb=" C2'   A B  14 "
            pdb=" C3'   A B  14 "
            pdb=" O2'   A B  14 "
            pdb=" C1'   A B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.76    0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" C2'   G B  70 "
            pdb=" C3'   G B  70 "
            pdb=" O2'   G B  70 "
            pdb=" C1'   G B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.76    0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" C2'   U B  20 "
            pdb=" C3'   U B  20 "
            pdb=" O2'   U B  20 "
            pdb=" C1'   U B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.76    0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1100 not shown)

  Planarity restraints: 934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 531 "    0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO A 532 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 532 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 532 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 167 "   -0.021 5.00e-02 4.00e+02   3.16e-02 1.59e+00
        pdb=" N   PRO A 168 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 168 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 168 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 540 "    0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 541 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 541 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 541 "    0.017 5.00e-02 4.00e+02
  ... (remaining 931 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1076
        2.77 -     3.30: 5727
        3.30 -     3.83: 11125
        3.83 -     4.37: 12943
        4.37 -     4.90: 20724
  Nonbonded interactions: 51595
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OD2 ASP A 274 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O2'   A B  21 "
            pdb=" OP1   G B  22 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   GLU A 525 "
            pdb=" NH1 ARG A 545 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OG1 THR A 368 "
            pdb=" OD1 ASP A 370 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   PRO A 270 "
            pdb=" NE2 GLN A 299 "
     model   vdw
     2.339 3.120
  ... (remaining 51590 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.44 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:             1.340
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.590
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6721  Z= 0.146
  Angle     :  0.552   6.256   9468  Z= 0.385
  Chirality :  0.049   0.142   1103
  Planarity :  0.004   0.037    934
  Dihedral  : 16.552 178.031   3100
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  2.42 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.48 (0.35), residues: 591
  helix:  1.98 (0.39), residues: 201
  sheet: -0.20 (0.54), residues: 93
  loop :  0.85 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 315 
 TYR   0.010   0.001   TYR A  51 
 PHE   0.010   0.001   PHE A  66 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.002   0.000   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 ( 6721)
  covalent geometry    : angle       0.55230 /  0.39 ( 9468)
  hydrogen bonds       : bond        0.14341 /  9.27 (  246)
  hydrogen bonds       : angle       5.90862 /  4.41 (  613)

*********************** 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
  62 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7739 (mmm-85)
REVERT: A  433 MET cc_start: 0.9266 (mmt) cc_final: 0.8908 (mmt)
REVERT: A  436 ASN cc_start: 0.8127 (t0) cc_final: 0.7530 (p0)
REVERT: A  651 ASP cc_start: 0.9096 (m-30) cc_final: 0.8826 (p0)
  outliers start: 3
  outliers final: 2
  residues processed: 62
  average time/residue: 0.7663
  time to fit residues: 49.1691
Evaluate side-chains
  35 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  693 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 569 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 = 0.3807 r_free = 0.3807 target = 0.121871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.065638 restraints weight = 20857.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 3.59
r_work: 0.2601 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2597 r_free = 0.2597    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6721  Z= 0.174
  Angle     :  0.520   8.243   9468  Z= 0.267
  Chirality :  0.039   0.167   1103
  Planarity :  0.005   0.053    934
  Dihedral  : 19.814 178.836   1853
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  7.99 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.44 (0.35), residues: 591
  helix:  1.98 (0.38), residues: 202
  sheet: -0.45 (0.52), residues: 91
  loop :  0.87 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 256 
 TYR   0.013   0.001   TYR A  52 
 PHE   0.014   0.002   PHE A 543 
 TRP   0.007   0.001   TRP A 680 
 HIS   0.002   0.001   HIS A 405 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.17 ( 6721)
  covalent geometry    : angle       0.51977 /  0.27 ( 9468)
  hydrogen bonds       : bond        0.04440 /  2.95 (  246)
  hydrogen bonds       : angle       4.66620 /  3.45 (  613)

*********************** 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
  39 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7721 (mmm-85)
REVERT: A  433 MET cc_start: 0.9274 (mmt) cc_final: 0.8795 (mmt)
REVERT: A  436 ASN cc_start: 0.8153 (t0) cc_final: 0.7465 (p0)
REVERT: A  651 ASP cc_start: 0.9114 (m-30) cc_final: 0.8810 (p0)
  outliers start: 7
  outliers final: 2
  residues processed: 37
  average time/residue: 0.6207
  time to fit residues: 24.2445
Evaluate side-chains
  32 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  578 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 49 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 569 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 = 0.3816 r_free = 0.3816 target = 0.122402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.064726 restraints weight = 38524.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 4.54
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6721  Z= 0.115
  Angle     :  0.451   7.414   9468  Z= 0.231
  Chirality :  0.037   0.160   1103
  Planarity :  0.004   0.039    934
  Dihedral  : 19.774 177.612   1851
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.36 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.41 (0.35), residues: 591
  helix:  2.00 (0.38), residues: 202
  sheet: -0.52 (0.51), residues: 96
  loop :  0.88 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 256 
 TYR   0.008   0.001   TYR A  51 
 PHE   0.012   0.001   PHE A 422 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.002   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 6721)
  covalent geometry    : angle       0.45104 /  0.23 ( 9468)
  hydrogen bonds       : bond        0.03804 /  2.57 (  246)
  hydrogen bonds       : angle       4.37904 /  3.25 (  613)

*********************** 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
  36 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.7924 (mmt180) cc_final: 0.7513 (mmm-85)
REVERT: A  651 ASP cc_start: 0.9082 (m-30) cc_final: 0.8818 (p0)
  outliers start: 6
  outliers final: 1
  residues processed: 34
  average time/residue: 0.7065
  time to fit residues: 25.2720
Evaluate side-chains
  29 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 2 optimal weight:    0.0010
   chunk 52 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0870
   chunk 14 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.5166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 569 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.123017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.065591 restraints weight = 34057.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 4.38
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6721  Z= 0.093
  Angle     :  0.427   7.518   9468  Z= 0.219
  Chirality :  0.036   0.151   1103
  Planarity :  0.004   0.039    934
  Dihedral  : 19.754 176.628   1851
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.92 %
    Favored  : 89.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.47 (0.35), residues: 591
  helix:  2.02 (0.38), residues: 203
  sheet: -0.45 (0.52), residues: 96
  loop :  0.91 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 639 
 TYR   0.010   0.001   TYR A  52 
 PHE   0.010   0.001   PHE A  48 
 TRP   0.009   0.001   TRP A 435 
 HIS   0.001   0.000   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.09 ( 6721)
  covalent geometry    : angle       0.42652 /  0.22 ( 9468)
  hydrogen bonds       : bond        0.03466 /  2.36 (  246)
  hydrogen bonds       : angle       4.19490 /  3.11 (  613)

*********************** 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
  38 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7514 (tpp80)
REVERT: A  436 ASN cc_start: 0.8309 (t0) cc_final: 0.7551 (p0)
REVERT: A  651 ASP cc_start: 0.9029 (m-30) cc_final: 0.8793 (p0)
  outliers start: 6
  outliers final: 2
  residues processed: 35
  average time/residue: 0.6078
  time to fit residues: 22.4517
Evaluate side-chains
  32 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  211 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:   30.0000
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.5188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.120586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.063953 restraints weight = 26215.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 3.91
r_work: 0.2556 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6721  Z= 0.187
  Angle     :  0.496   7.013   9468  Z= 0.254
  Chirality :  0.038   0.152   1103
  Planarity :  0.004   0.041    934
  Dihedral  : 19.763 176.536   1851
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.29 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.36 (0.35), residues: 591
  helix:  1.96 (0.38), residues: 202
  sheet: -0.48 (0.52), residues: 96
  loop :  0.81 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 639 
 TYR   0.009   0.001   TYR A  51 
 PHE   0.012   0.002   PHE A  66 
 TRP   0.009   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 405 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00455 /  0.19 ( 6721)
  covalent geometry    : angle       0.49582 /  0.25 ( 9468)
  hydrogen bonds       : bond        0.04240 /  2.84 (  246)
  hydrogen bonds       : angle       4.34365 /  3.21 (  613)

*********************** 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
  34 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.8408 (mmt180) cc_final: 0.7907 (tpp80)
REVERT: A  651 ASP cc_start: 0.9095 (m-30) cc_final: 0.8765 (p0)
  outliers start: 5
  outliers final: 3
  residues processed: 32
  average time/residue: 0.6724
  time to fit residues: 22.5511
Evaluate side-chains
  32 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  578 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 42 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0000
   chunk 45 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0770
   overall best weight:    0.2942

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.122633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.065407 restraints weight = 29721.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 4.12
r_work: 0.2598 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6721  Z= 0.081
  Angle     :  0.433   7.624   9468  Z= 0.221
  Chirality :  0.036   0.140   1103
  Planarity :  0.004   0.039    934
  Dihedral  : 19.787 175.915   1851
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.85 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.47 (0.35), residues: 591
  helix:  2.04 (0.38), residues: 203
  sheet: -0.50 (0.52), residues: 96
  loop :  0.91 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 639 
 TYR   0.009   0.001   TYR A  52 
 PHE   0.012   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.002   0.000   HIS A 697 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00179 /  0.08 ( 6721)
  covalent geometry    : angle       0.43265 /  0.22 ( 9468)
  hydrogen bonds       : bond        0.03432 /  2.32 (  246)
  hydrogen bonds       : angle       4.15075 /  3.06 (  613)

*********************** 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
  34 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.8221 (mmt180) cc_final: 0.7734 (tpp80)
REVERT: A  651 ASP cc_start: 0.9094 (m-30) cc_final: 0.8775 (p0)
  outliers start: 3
  outliers final: 2
  residues processed: 34
  average time/residue: 0.6312
  time to fit residues: 22.6610
Evaluate side-chains
  33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  211 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0770
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:   20.0000
   chunk 7 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.5540

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.122903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.066194 restraints weight = 24981.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 3.93
r_work: 0.2606 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6721  Z= 0.095
  Angle     :  0.433   7.670   9468  Z= 0.222
  Chirality :  0.036   0.137   1103
  Planarity :  0.004   0.040    934
  Dihedral  : 19.753 175.852   1851
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.04 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.49 (0.35), residues: 591
  helix:  2.05 (0.38), residues: 203
  sheet: -0.50 (0.53), residues: 96
  loop :  0.94 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 639 
 TYR   0.009   0.001   TYR A  52 
 PHE   0.010   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.001   0.000   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.09 ( 6721)
  covalent geometry    : angle       0.43273 /  0.22 ( 9468)
  hydrogen bonds       : bond        0.03402 /  2.31 (  246)
  hydrogen bonds       : angle       4.08529 /  3.01 (  613)

*********************** 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
  35 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7678 (tpp80)
REVERT: A  277 MET cc_start: 0.9144 (mtp) cc_final: 0.8904 (ttt)
REVERT: A  651 ASP cc_start: 0.9093 (m-30) cc_final: 0.8763 (p0)
  outliers start: 3
  outliers final: 2
  residues processed: 35
  average time/residue: 0.6204
  time to fit residues: 22.7875
Evaluate side-chains
  33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  211 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0970
   chunk 53 optimal weight:    0.0770
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 64 optimal weight:   20.0000
   chunk 62 optimal weight:   30.0000
   overall best weight:    0.5536

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.122931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.066878 restraints weight = 23655.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 3.77
r_work: 0.2629 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2620 r_free = 0.2620    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2620 r_free = 0.2620    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6721  Z= 0.093
  Angle     :  0.439   8.526   9468  Z= 0.224
  Chirality :  0.036   0.135   1103
  Planarity :  0.004   0.039    934
  Dihedral  : 19.749 175.713   1851
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.41 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.52 (0.36), residues: 591
  helix:  2.06 (0.38), residues: 203
  sheet: -0.48 (0.53), residues: 96
  loop :  0.97 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 639 
 TYR   0.009   0.001   TYR A  52 
 PHE   0.010   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.002   0.000   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00216 /  0.09 ( 6721)
  covalent geometry    : angle       0.43898 /  0.22 ( 9468)
  hydrogen bonds       : bond        0.03340 /  2.26 (  246)
  hydrogen bonds       : angle       4.03725 /  2.98 (  613)

*********************** 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
  35 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.8196 (mmt180) cc_final: 0.7713 (tpp80)
REVERT: A  578 MET cc_start: 0.9028 (ttm) cc_final: 0.8597 (ptm)
REVERT: A  651 ASP cc_start: 0.9084 (m-30) cc_final: 0.8754 (p0)
  outliers start: 4
  outliers final: 2
  residues processed: 34
  average time/residue: 0.6255
  time to fit residues: 22.4072
Evaluate side-chains
  34 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  211 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0570
   chunk 65 optimal weight:    9.9990
   chunk 60 optimal weight:   40.0000
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.5898

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.122732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.065678 restraints weight = 37396.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 4.49
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2810
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6721  Z= 0.097
  Angle     :  0.431   7.610   9468  Z= 0.221
  Chirality :  0.036   0.132   1103
  Planarity :  0.004   0.040    934
  Dihedral  : 19.736 175.592   1851
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 10.41 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.59 (0.36), residues: 591
  helix:  2.07 (0.38), residues: 203
  sheet: -0.54 (0.51), residues: 104
  loop :  1.14 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 639 
 TYR   0.012   0.001   TYR A  52 
 PHE   0.009   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.001   0.000   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.10 ( 6721)
  covalent geometry    : angle       0.43148 /  0.22 ( 9468)
  hydrogen bonds       : bond        0.03330 /  2.25 (  246)
  hydrogen bonds       : angle       3.98253 /  2.94 (  613)

*********************** 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
  33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7515 (tpp80)
REVERT: A  402 GLN cc_start: 0.8693 (tt0) cc_final: 0.8490 (tm-30)
REVERT: A  639 ARG cc_start: 0.8861 (ptt90) cc_final: 0.8620 (pmt-80)
REVERT: A  651 ASP cc_start: 0.9039 (m-30) cc_final: 0.8775 (p0)
  outliers start: 2
  outliers final: 2
  residues processed: 33
  average time/residue: 0.7226
  time to fit residues: 24.9545
Evaluate side-chains
  33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  211 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0040
   chunk 32 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.7194

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.122602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.065787 restraints weight = 27308.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 4.04
r_work: 0.2597 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6721  Z= 0.107
  Angle     :  0.437   7.119   9468  Z= 0.223
  Chirality :  0.036   0.132   1103
  Planarity :  0.004   0.040    934
  Dihedral  : 19.733 175.568   1851
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 10.59 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.58 (0.36), residues: 591
  helix:  2.08 (0.38), residues: 203
  sheet: -0.52 (0.51), residues: 104
  loop :  1.12 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 639 
 TYR   0.009   0.001   TYR A  52 
 PHE   0.010   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.001   0.000   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 6721)
  covalent geometry    : angle       0.43697 /  0.22 ( 9468)
  hydrogen bonds       : bond        0.03384 /  2.28 (  246)
  hydrogen bonds       : angle       3.98590 /  2.94 (  613)

********************** 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
  33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7680 (tpp80)
REVERT: A  402 GLN cc_start: 0.8844 (tt0) cc_final: 0.8542 (tm-30)
REVERT: A  651 ASP cc_start: 0.9086 (m-30) cc_final: 0.8749 (p0)
  outliers start: 2
  outliers final: 2
  residues processed: 33
  average time/residue: 0.6502
  time to fit residues: 22.6313
Evaluate side-chains
  33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  211 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 12 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0010
   chunk 9 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.3986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.123321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.066967 restraints weight = 27819.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 4.05
r_work: 0.2622 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6721  Z= 0.082
  Angle     :  0.430   8.555   9468  Z= 0.220
  Chirality :  0.036   0.130   1103
  Planarity :  0.004   0.039    934
  Dihedral  : 19.731 175.410   1851
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 10.78 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.61 (0.36), residues: 591
  helix:  2.11 (0.38), residues: 203
  sheet: -0.48 (0.51), residues: 104
  loop :  1.12 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 639 
 TYR   0.010   0.001   TYR A  52 
 PHE   0.011   0.001   PHE A  48 
 TRP   0.009   0.001   TRP A 284 
 HIS   0.002   0.000   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00183 /  0.08 ( 6721)
  covalent geometry    : angle       0.43025 /  0.22 ( 9468)
  hydrogen bonds       : bond        0.03179 /  2.15 (  246)
  hydrogen bonds       : angle       3.91697 /  2.89 (  613)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2248.43 seconds
wall clock time: 39 minutes 2.92 seconds (2342.92 seconds total)