# Date 2008-01-16 Time 01:15:31 PST -0800 (1200474931.37 s)
#phil __OFF__

Command line arguments: "../344.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1937
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 344

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.8686, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.97063
Completeness in resolution range: 0.949447
Completeness with d_max=infinity: 0.946557

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9494
                             d_min =   1.9706

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.97063
Completeness in resolution range: 0.949447
Completeness with d_max=infinity: 0.946557

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9498 -  4.2168 [2170/2199]  1953   217  10.0%
  bin  2:  4.2168 -  3.3595 [2079/2102]  1873   206   9.9%
  bin  3:  3.3595 -  2.9385 [2063/2088]  1851   212  10.3%
  bin  4:  2.9385 -  2.6715 [2022/2038]  1827   195   9.6%
  bin  5:  2.6715 -  2.4809 [2005/2049]  1795   210  10.5%
  bin  6:  2.4809 -  2.3352 [2024/2052]  1834   190   9.4%
  bin  7:  2.3352 -  2.2187 [2002/2038]  1795   207  10.3%
  bin  8:  2.2187 -  2.1224 [1978/2020]  1786   192   9.7%
  bin  9:  2.1224 -  2.0409 [1984/2030]  1783   201  10.1%
  bin 10:  2.0409 -  1.9706 [1262/2016]  1133   129  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 17
        2.19 -     2.87: 1212
        2.87 -     3.55: 4482
        3.55 -     4.22: 9223
        4.22 -     4.90: 13505
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.514 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.653 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.805 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.844 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28434 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_001.geo

CPU time processing inputs: 9.17


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.8686 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4957   r_free= 0.4797   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.294481                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7033 0.99   1405  158 0.4079 0.4084      6.6119      6.6599|
|  2:  4.7033 -  3.7526 0.99   1350  151 0.4281 0.4176      6.8249      6.8397|
|  3:  3.7526 -  3.2839 0.99   1330  146 0.4624 0.4294      6.7038      6.7012|
|  4:  3.2839 -  2.9863 0.99   1323  138 0.4769 0.4271      6.5299      6.4695|
|  5:  2.9863 -  2.7737 0.98   1305  149 0.5319 0.5356      6.3941       6.412|
|  6:  2.7737 -  2.6111 0.99   1305  147 0.5170 0.5109       6.278      6.1927|
|  7:  2.6111 -  2.4809 0.98   1281  151 0.5202 0.4797      6.2752      6.1977|
|  8:  2.4809 -  2.3734 0.99   1311  133 0.5348 0.5128      6.1838      6.1655|
|  9:  2.3734 -  2.2823 0.99   1298  148 0.5420 0.5517      6.1251      6.1805|
| 10:  2.2823 -  2.2038 0.98   1276  143 0.5395 0.5568       6.124      6.1326|
| 11:  2.2038 -  2.1351 0.97   1282  149 0.5481 0.5286      6.0323      6.0383|
| 12:  2.1351 -  2.0743 0.99   1272  141 0.5383 0.5125      5.9704      5.9997|
| 13:  2.0743 -  2.0198 0.94   1257  129 0.5424 0.5253      5.8903      5.8771|
| 14:  2.0198 -  1.9706 0.50    635   76 0.5648 0.5128      5.8809       5.723|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9498 -  4.7033  1405   158  0.64  39.06   0.79     0.66      86955.20|
|  2:  4.7033 -  3.7526  1350   151  0.66  38.94   0.87     0.72     119920.85|
|  3:  3.7526 -  3.2839  1330   146  0.57  46.69   0.83     0.68     124772.94|
|  4:  3.2839 -  2.9863  1323   138  0.49  52.74   0.79     0.58     104004.89|
|  5:  2.9863 -  2.7737  1305   149  0.38  61.17   0.72     0.47      88187.58|
|  6:  2.7737 -  2.6111  1305   147  0.35  63.71   0.72     0.40      74801.57|
|  7:  2.6111 -  2.4809  1281   151  0.34  64.60   0.74     0.38      68982.01|
|  8:  2.4809 -  2.3734  1311   133  0.34  64.91   0.72     0.39      60743.82|
|  9:  2.3734 -  2.2823  1298   148  0.32  66.41   0.71     0.39      57360.85|
| 10:  2.2823 -  2.2038  1276   143  0.30  67.73   0.75     0.35      52513.56|
| 11:  2.2038 -  2.1351  1282   149  0.26  70.87   0.73     0.33      50858.45|
| 12:  2.1351 -  2.0743  1272   141  0.26  70.84   0.75     0.33      47108.74|
| 13:  2.0743 -  2.0198  1257   129  0.28  68.94   0.74     0.36      39159.63|
| 14:  2.0198 -  1.9706   635    76  0.36  62.92   0.71     0.41      28041.63|
|alpha:            min =        0.33 max =            0.72 mean =         0.47|
|beta:             min =    28041.63 max =       124772.94 mean =     73847.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.58|
|phase err.(test): min =        0.00 max =           89.75 mean =        59.53|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.097466             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.378   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.468121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.207   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.984 -  1.376:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.376 -  1.767:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.767 -  2.159:       80 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.159 -  2.550:      492 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.550 -  2.942:     1309 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.942 -  3.334:     2427 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.334 -  3.725:     3950 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.725 -  4.117:     5195 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.117 -  4.508:     6832 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.508 -  4.900:     8162 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.548 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  0.984 |       2.234 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5004   r_free= 0.4866   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.295066                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4877   r_free= 0.4735   ksol= 0.33   Bsol= 8.53   scale= 0.982    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,11.49,7.39,0.00,0.00,0.00); trace/3= 8.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.287745                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.201491             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.836   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.489417              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.644   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4877      final r-factor (work) = 0.4134          |
| start r-factor (free) = 0.4735      final r-factor (free) = 0.4335          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.5358 = 16.20 * 0.50 * 6.2942 + 1.00 * 53.5483                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.5510 = 16.20 * 0.50 * 6.2208 + 1.00 * 0.1577                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4134      final r-factor (work) = 0.3701          |
| start r-factor (free) = 0.4335      final r-factor (free) = 0.4182          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2801 = 1.49 * 1.00 * 6.2208 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1871 = 1.49 * 1.00 * 6.1546 + 1.00 * 0.0202                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.76   14.25    None  None   None       |
|    all(noH): 2823   0      0.00    77.76   14.25    None  None   None       |
|    Sol.    : 438    0      0.00    77.76   24.95    None  None   None       |
|    Mac.    : 2385   0      0.00    59.71   12.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.776: 1028   |   5:    38.882 -  46.658:   82        |
|      1:     7.776 -  15.553:  773   |   6:    46.658 -  54.435:   44        |
|      2:    15.553 -  23.329:  463   |   7:    54.435 -  62.211:    8        |
|      3:    23.329 -  31.106:  262   |   8:    62.211 -  69.987:    6        |
|      4:    31.106 -  38.882:  155   |   9:    69.987 -  77.764:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3701 r_free = 0.4182             target_work(ml) = 6.139         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3695 r_free = 0.4169             target_work(ml) = 6.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3695   r_free= 0.4169   ksol= 0.33   Bsol= 8.53   scale= 1.105    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,11.49,7.39,0.00,0.00,0.00); trace/3= 8.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.137640                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3675   r_free= 0.4114   ksol= 0.31   Bsol= 30.82   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,7.22,4.51,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.138347                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.092117              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.027  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.571077              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.907  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3675      final r-factor (work) = 0.2932          |
| start r-factor (free) = 0.4114      final r-factor (free) = 0.3477          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1158 = 9.09 * 0.50 * 6.1502 + 1.00 * 0.1567                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.5566 = 9.09 * 0.50 * 6.0409 + 1.00 * 0.0943                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2932      final r-factor (work) = 0.2716          |
| start r-factor (free) = 0.3477      final r-factor (free) = 0.3312          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4703 = 0.57 * 1.00 * 6.0409 + 1.00 * 0.0205                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4012 = 0.57 * 1.00 * 5.9324 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.73   13.85    None  None   None       |
|    all(noH): 2823   0      0.00    87.73   13.85    None  None   None       |
|    Sol.    : 438    0      0.00    87.73   29.73    None  None   None       |
|    Mac.    : 2385   0      0.00    72.82   10.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.773: 1291   |   5:    43.864 -  52.637:   59        |
|      1:     8.773 -  17.546:  765   |   6:    52.637 -  61.410:   28        |
|      2:    17.546 -  26.319:  358   |   7:    61.410 -  70.183:    9        |
|      3:    26.319 -  35.092:  181   |   8:    70.183 -  78.956:    3        |
|      4:    35.092 -  43.864:  127   |   9:    78.956 -  87.729:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2716 r_free = 0.3312             target_work(ml) = 5.910         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2713 r_free = 0.3310             target_work(ml) = 5.909         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2713   r_free= 0.3310   ksol= 0.31   Bsol= 30.82   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,7.22,4.51,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.909376                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2697   r_free= 0.3310   ksol= 0.30   Bsol= 38.64   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.73,4.56,3.02,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.908532                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.002721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.034  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303987              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.577   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2697      final r-factor (work) = 0.1940          |
| start r-factor (free) = 0.3310      final r-factor (free) = 0.2393          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8716 = 7.00 * 0.50 * 5.9340 + 1.00 * 0.0946                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3452 = 7.00 * 0.50 * 5.7858 + 1.00 * 0.0870                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1940      final r-factor (work) = 0.1719          |
| start r-factor (free) = 0.2393      final r-factor (free) = 0.2138          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7708 = 0.30 * 1.00 * 5.7858 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6956 = 0.30 * 1.00 * 5.5421 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.10   13.78    None  None   None       |
|    all(noH): 2823   0      0.00    78.10   13.78    None  None   None       |
|    Sol.    : 438    0      2.89    78.10   34.99    None  None   None       |
|    Mac.    : 2385   0      0.00    76.75   9.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.810: 1252   |   5:    39.052 -  46.862:  101        |
|      1:     7.810 -  15.621:  846   |   6:    46.862 -  54.673:   70        |
|      2:    15.621 -  23.431:  258   |   7:    54.673 -  62.483:   30        |
|      3:    23.431 -  31.242:  131   |   8:    62.483 -  70.294:   12        |
|      4:    31.242 -  39.052:  114   |   9:    70.294 -  78.104:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1719 r_free = 0.2138             target_work(ml) = 5.493         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1716 r_free = 0.2139             target_work(ml) = 5.492         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1716   r_free= 0.2139   ksol= 0.30   Bsol= 38.64   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.73,4.56,3.02,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.491980                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1706   r_free= 0.2125   ksol= 0.32   Bsol= 38.64   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.57,2.61,1.99,0.00,0.00,0.00); trace/3= 1.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.491741                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.845746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.541  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.203407              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.687  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1706      final r-factor (work) = 0.1373          |
| start r-factor (free) = 0.2125      final r-factor (free) = 0.1787          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9861 = 2.85 * 0.50 * 5.5515 + 1.00 * 0.0870                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7438 = 2.85 * 0.50 * 5.3941 + 1.00 * 0.0687                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1373      final r-factor (work) = 0.1314          |
| start r-factor (free) = 0.1787      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1074 = 0.20 * 1.00 * 5.3941 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0829 = 0.20 * 1.00 * 5.2798 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.54   13.69    None  None   None       |
|    all(noH): 2823   0      0.00    77.54   13.69    None  None   None       |
|    Sol.    : 438    0      2.94    77.03   35.70    None  None   None       |
|    Mac.    : 2385   0      0.00    77.54   9.65     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.754: 1228   |   5:    38.770 -  46.524:   97        |
|      1:     7.754 -  15.508:  917   |   6:    46.524 -  54.278:   77        |
|      2:    15.508 -  23.262:  212   |   7:    54.278 -  62.032:   36        |
|      3:    23.262 -  31.016:  113   |   8:    62.032 -  69.786:   12        |
|      4:    31.016 -  38.770:  122   |   9:    69.786 -  77.540:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1314 r_free = 0.1717             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1313 r_free = 0.1716             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1716   ksol= 0.32   Bsol= 38.64   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.57,2.61,1.99,0.00,0.00,0.00); trace/3= 1.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.261158                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1721   ksol= 0.31   Bsol= 45.88   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.26,1.89,1.78,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.263341                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.788641              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.283  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.229216              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.034  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1314      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4325 = 2.79 * 0.50 * 5.2813 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3534 = 2.79 * 0.50 * 5.2218 + 1.00 * 0.0726                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2059 = 0.23 * 1.00 * 5.2218 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1981 = 0.23 * 1.00 * 5.1876 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.01   13.55    None  None   None       |
|    all(noH): 2823   0      0.00    78.01   13.55    None  None   None       |
|    Sol.    : 438    0      2.45    76.50   35.54    None  None   None       |
|    Mac.    : 2385   0      0.00    78.01   9.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.801: 1279   |   5:    39.004 -  46.805:   92        |
|      1:     7.801 -  15.602:  888   |   6:    46.805 -  54.606:   75        |
|      2:    15.602 -  23.402:  201   |   7:    54.606 -  62.406:   32        |
|      3:    23.402 -  31.203:  116   |   8:    62.406 -  70.207:   12        |
|      4:    31.203 -  39.004:  118   |   9:    70.207 -  78.008:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1178 r_free = 0.1620             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1177 r_free = 0.1622             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1622   ksol= 0.31   Bsol= 45.88   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.26,1.89,1.78,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185179                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7033 0.99   1405  158 0.1010 0.1298      5.3907      5.5511|
|  2:  4.7033 -  3.7526 0.99   1350  151 0.0895 0.1080      5.4713      5.6583|
|  3:  3.7526 -  3.2839 0.99   1330  146 0.1110 0.1604      5.5204      5.9025|
|  4:  3.2839 -  2.9863 0.99   1323  138 0.1298 0.1665       5.495      5.6912|
|  5:  2.9863 -  2.7737 0.98   1305  149 0.1429 0.1642       5.389      5.4941|
|  6:  2.7737 -  2.6111 0.99   1305  147 0.1376 0.2213      5.2835      5.5656|
|  7:  2.6111 -  2.4809 0.98   1281  151 0.1267 0.1668      5.2076      5.4041|
|  8:  2.4809 -  2.3734 0.99   1311  133 0.1246 0.1829      5.1259      5.3758|
|  9:  2.3734 -  2.2823 0.99   1298  148 0.1230 0.1858      5.0562      5.3391|
| 10:  2.2823 -  2.2038 0.98   1276  143 0.1208 0.1797      5.0242      5.2613|
| 11:  2.2038 -  2.1351 0.97   1282  149 0.1203 0.1776      4.9525      5.2314|
| 12:  2.1351 -  2.0743 0.99   1272  141 0.1157 0.1649      4.8777      5.1327|
| 13:  2.0743 -  2.0198 0.94   1257  129 0.1157 0.1741      4.7961      5.0692|
| 14:  2.0198 -  1.9706 0.50    635   76 0.1055 0.1638      4.6738      4.8946|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9498 -  4.7033  1405   158  0.94   9.15   0.98     0.96       7371.32|
|  2:  4.7033 -  3.7526  1350   151  0.95   8.49   1.02     1.00       9585.78|
|  3:  3.7526 -  3.2839  1330   146  0.93  12.14   1.02     1.01      11554.01|
|  4:  3.2839 -  2.9863  1323   138  0.91  14.69   1.01     0.99      11186.74|
|  5:  2.9863 -  2.7737  1305   149  0.89  17.12   0.99     0.96       9240.69|
|  6:  2.7737 -  2.6111  1305   147  0.89  17.33   0.98     0.94       7893.06|
|  7:  2.6111 -  2.4809  1281   151  0.90  16.17   0.98     0.95       6758.95|
|  8:  2.4809 -  2.3734  1311   133  0.90  16.15   1.00     0.97       5992.55|
|  9:  2.3734 -  2.2823  1298   148  0.89  16.88   1.01     0.97       5398.92|
| 10:  2.2823 -  2.2038  1276   143  0.90  16.37   1.00     0.97       4993.11|
| 11:  2.2038 -  2.1351  1282   149  0.90  16.69   1.00     0.97       4508.11|
| 12:  2.1351 -  2.0743  1272   141  0.91  15.28   1.00     0.97       3834.66|
| 13:  2.0743 -  2.0198  1257   129  0.90  16.04   1.00     1.00       3319.47|
| 14:  2.0198 -  1.9706   635    76  0.91  15.09   0.98     0.94       2616.14|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2616.14 max =        11554.01 mean =      6931.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.75|
|phase err.(test): min =        0.00 max =           89.17 mean =        14.13|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1621   ksol= 0.32   Bsol= 47.18   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.48,0.52,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185276                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1621   ksol= 0.32   Bsol= 47.18   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.48,0.52,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185276                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7033 0.99   1405  158 0.1011 0.1299      5.3924      5.5523|
|  2:  4.7033 -  3.7526 0.99   1350  151 0.0893 0.1079      5.4706       5.657|
|  3:  3.7526 -  3.2839 0.99   1330  146 0.1111 0.1603        5.52      5.9032|
|  4:  3.2839 -  2.9863 0.99   1323  138 0.1297 0.1664      5.4951      5.6907|
|  5:  2.9863 -  2.7737 0.98   1305  149 0.1429 0.1641      5.3889      5.4939|
|  6:  2.7737 -  2.6111 0.99   1305  147 0.1376 0.2210      5.2832      5.5649|
|  7:  2.6111 -  2.4809 0.98   1281  151 0.1267 0.1669      5.2074      5.4042|
|  8:  2.4809 -  2.3734 0.99   1311  133 0.1245 0.1829      5.1261      5.3758|
|  9:  2.3734 -  2.2823 0.99   1298  148 0.1228 0.1860      5.0561      5.3401|
| 10:  2.2823 -  2.2038 0.98   1276  143 0.1208 0.1798      5.0245      5.2623|
| 11:  2.2038 -  2.1351 0.97   1282  149 0.1202 0.1774      4.9527      5.2311|
| 12:  2.1351 -  2.0743 0.99   1272  141 0.1157 0.1650      4.8777      5.1334|
| 13:  2.0743 -  2.0198 0.94   1257  129 0.1158 0.1738      4.7966      5.0684|
| 14:  2.0198 -  1.9706 0.50    635   76 0.1054 0.1638      4.6737      4.8944|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9498 -  4.7033  1405   158  0.94   9.18   0.98     0.96       7409.25|
|  2:  4.7033 -  3.7526  1350   151  0.95   8.48   1.02     1.00       9585.95|
|  3:  3.7526 -  3.2839  1330   146  0.93  12.13   1.02     1.01      11534.97|
|  4:  3.2839 -  2.9863  1323   138  0.91  14.70   1.01     0.99      11188.50|
|  5:  2.9863 -  2.7737  1305   149  0.89  17.11   0.99     0.96       9231.08|
|  6:  2.7737 -  2.6111  1305   147  0.89  17.32   0.98     0.94       7887.04|
|  7:  2.6111 -  2.4809  1281   151  0.90  16.17   0.98     0.95       6755.01|
|  8:  2.4809 -  2.3734  1311   133  0.90  16.16   1.00     0.97       5996.87|
|  9:  2.3734 -  2.2823  1298   148  0.89  16.89   1.01     0.97       5405.86|
| 10:  2.2823 -  2.2038  1276   143  0.90  16.38   1.00     0.97       4995.42|
| 11:  2.2038 -  2.1351  1282   149  0.90  16.70   1.00     0.97       4512.33|
| 12:  2.1351 -  2.0743  1272   141  0.91  15.28   1.00     0.97       3837.34|
| 13:  2.0743 -  2.0198  1257   129  0.90  16.04   1.00     1.00       3318.85|
| 14:  2.0198 -  1.9706   635    76  0.91  15.08   0.98     0.94       2611.72|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2611.72 max =        11534.97 mean =      6933.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.76|
|phase err.(test): min =        0.00 max =           89.03 mean =        14.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    79.31   14.84    None  None   None       |
|    all(noH): 2823   0      1.30    79.31   14.84    None  None   None       |
|    Sol.    : 438    0      3.74    77.80   36.84    None  None   None       |
|    Mac.    : 2385   0      1.30    79.31   10.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.297 -   9.098: 1279   |   5:    40.301 -  48.102:   92        |
|      1:     9.098 -  16.899:  888   |   6:    48.102 -  55.903:   75        |
|      2:    16.899 -  24.700:  201   |   7:    55.903 -  63.704:   32        |
|      3:    24.700 -  32.501:  116   |   8:    63.704 -  71.505:   12        |
|      4:    32.501 -  40.301:  118   |   9:    71.505 -  79.305:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.426 - 5.071
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 325
   mapped sites are within: 0.720 - 5.071

peak=    9.883 closest distance to " CB  VAL A 230 " =    1.438
peak=    6.874 closest distance to " O   HOH Z 120 " =    1.217
peak=    6.615 closest distance to " CG2 VAL A 296 " =    1.128
peak=    6.470 closest distance to " CD1AILE A 234 " =    1.317
peak=    5.912 closest distance to " O   HOH Z 402 " =    1.742
peak=    5.882 closest distance to " CG  LEU A   5 " =    1.339
peak=    5.565 closest distance to " CB  VAL A 296 " =    1.054
peak=    5.263 closest distance to " O   HOH Z 124 " =    1.672
peak=    5.221 closest distance to " O   HOH Z 403 " =    1.866
peak=    5.197 closest distance to " CB  SER A  63 " =    1.138
peak=    4.995 closest distance to " NH2 ARG A  56 " =    2.312
peak=    4.948 closest distance to " O   HOH Z 209 " =    2.312
peak=    4.909 closest distance to " O   HOH Z 154 " =    1.770
peak=    4.906 closest distance to " O   HOH Z 247 " =    1.468
peak=    4.791 closest distance to " CG  PRO A  54 " =    1.228
peak=    4.717 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.704 closest distance to " CB  PRO A  54 " =    0.903
peak=    4.669 closest distance to " CB  ARG A 275 " =    0.938
peak=    4.657 closest distance to " O   HOH Z 272 " =    1.962
peak=    4.645 closest distance to " CB  VAL A 230 " =    1.237
peak=    4.618 closest distance to " O   HOH Z 193 " =    1.789
peak=    4.573 closest distance to " CB  GLN A 223 " =    1.385
peak=    4.567 closest distance to " O   HOH Z 126 " =    1.627
peak=    4.558 closest distance to " O   HOH Z  80 " =    2.032
peak=    4.535 closest distance to " CG  LEU A 228 " =    1.225
peak=    4.515 closest distance to " CG2 VAL A 296 " =    1.772
peak=    4.503 closest distance to " O   HOH Z 142 " =    1.607
peak=    4.498 closest distance to " O   HOH Z 263 " =    1.596
peak=    4.483 closest distance to " CB  SER A   3 " =    1.264
peak=    4.455 closest distance to " O   SER A  87 " =    2.294
peak=    4.454 closest distance to " CB  GLN A 183 " =    1.314
peak=    4.437 closest distance to " O   HOH Z 327 " =    1.736
peak=    4.382 closest distance to " CA  TYR A  30 " =    0.978
peak=    4.350 closest distance to " NE2 GLN A  11 " =    1.037
peak=    4.344 closest distance to " O   HOH Z  67 " =    2.058
peak=    4.338 closest distance to " C   PRO A 198 " =    1.452
peak=    4.313 closest distance to " O   HOH Z 128 " =    1.599
peak=    4.304 closest distance to " O   HOH Z 433 " =    1.663
peak=    4.300 closest distance to " CG1 ILE A  33 " =    1.254
peak=    4.289 closest distance to " O   HOH Z 414 " =    2.237
peak=    4.277 closest distance to " O   HOH Z  85 " =    1.660
peak=    4.259 closest distance to " O   HOH Z 357 " =    1.972
peak=    4.232 closest distance to " CD2 LEU A   5 " =    1.192
peak=    4.201 closest distance to " O   HOH Z 102 " =    1.380
peak=    4.197 closest distance to " O   HOH Z  63 " =    2.533
peak=    4.185 closest distance to " O   HOH Z 130 " =    1.168
peak=    4.184 closest distance to " CG  PRO A 198 " =    1.228
peak=    4.175 closest distance to " O   HOH Z 130 " =    2.796
peak=    4.172 closest distance to " O   HOH Z 232 " =    2.413
peak=    4.168 closest distance to " OE1 GLU A   2 " =    2.092
peak=    4.167 closest distance to " O   HOH Z 234 " =    3.563
peak=    4.153 closest distance to " O   HOH Z 134 " =    1.985
peak=    4.149 closest distance to " CD2 LEU A 228 " =    1.155
peak=    4.137 closest distance to " O   HOH Z 346 " =    1.604
peak=    4.126 closest distance to " O   HOH Z  43 " =    1.586
peak=    4.118 closest distance to " O   HOH Z 423 " =    1.757
peak=    4.112 closest distance to " CG  ARG A  66 " =    1.015
peak=    4.102 closest distance to " O   HOH Z  40 " =    1.870
peak=    4.099 closest distance to " O   HOH Z 210 " =    1.055
peak=    4.086 closest distance to " O   HOH Z 406 " =    1.689
peak=    4.062 closest distance to " O   HOH Z 404 " =    1.503
peak=    4.057 closest distance to " CB  TRP A 179 " =    1.142
peak=    4.026 closest distance to " CD2 TRP A 179 " =    1.397
peak=    4.006 closest distance to " CB  GLU A 152 " =    1.137
peak=    3.977 closest distance to " O   ASP A 124 " =    1.531
peak=    3.972 closest distance to " O   HOH Z  49 " =    1.135
peak=    3.959 closest distance to " O   HOH Z  48 " =    1.790
peak=    3.953 closest distance to " OD1 ASN A  60 " =    1.672
peak=    3.938 closest distance to " O   HOH Z 245 " =    1.480
peak=    3.937 closest distance to " CG2 THR A 221 " =    1.198
peak=    3.937 closest distance to " O   HOH Z  47 " =    1.523
peak=    3.933 closest distance to " O   HOH Z 303 " =    2.359
peak=    3.927 closest distance to " O   HOH Z 189 " =    2.618
peak=    3.927 closest distance to " O   HOH Z  59 " =    2.276
peak=    3.906 closest distance to " CB  PRO A 198 " =    1.032
peak=    3.894 closest distance to " O   HOH Z 345 " =    2.666
peak=    3.892 closest distance to " O   HOH Z 203 " =    1.786
peak=    3.883 closest distance to " O   HOH Z 409 " =    3.364
peak=    3.883 closest distance to " NH2BARG A 145 " =    2.138
peak=    3.881 closest distance to " O   HOH Z 193 " =    2.039
peak=    3.876 closest distance to " O   HOH Z 316 " =    2.495
peak=    3.875 closest distance to " CB  ALA A 100 " =    1.322
peak=    3.875 closest distance to " O   GLY A  23 " =    2.305
peak=    3.873 closest distance to " O   HOH Z 411 " =    3.354
peak=    3.871 closest distance to " CB BVAL A  41 " =    1.048
peak=    3.845 closest distance to " O   HOH Z  15 " =    1.980
peak=    3.842 closest distance to " O   HOH Z  44 " =    1.956
peak=    3.839 closest distance to " N   ASN A  39 " =    1.251
peak=    3.825 closest distance to " O   HOH Z  54 " =    2.189
peak=    3.821 closest distance to " O   HOH Z 123 " =    2.127
peak=    3.815 closest distance to " NZ  LYS A 117 " =    3.022
peak=    3.799 closest distance to " O   HOH Z 345 " =    1.773
peak=    3.798 closest distance to " O   HOH Z 248 " =    1.660
peak=    3.783 closest distance to " OG1 THR A 294 " =    2.252
peak=    3.782 closest distance to " O   HOH Z  11 " =    1.319
peak=    3.769 closest distance to " O   HOH Z 227 " =    1.669
peak=    3.764 closest distance to " CA  VAL A  41 " =    0.821
peak=    3.763 closest distance to " O   HOH Z 389 " =    1.964
peak=    3.763 closest distance to " CG2 THR A 220 " =    0.782
peak=    3.761 closest distance to " O   HOH Z 334 " =    1.514
peak=    3.761 closest distance to " NH1BARG A 190 " =    2.128
peak=    3.760 closest distance to " O   HOH Z  97 " =    1.958
peak=    3.758 closest distance to " CD  LYS A 166 " =    1.464
peak=    3.757 closest distance to " O   HOH Z 412 " =    3.827
peak=    3.752 closest distance to " O   HOH Z  61 " =    1.575
peak=    3.752 closest distance to " O   HOH Z 250 " =    1.601
peak=    3.748 closest distance to " O   HOH Z 368 " =    2.105
peak=    3.737 closest distance to " O   HOH Z 155 " =    1.566
peak=    3.733 closest distance to " O   HOH Z 163 " =    1.419
peak=    3.732 closest distance to " O   HOH Z 380 " =    1.970
peak=    3.731 closest distance to " CB  SER A  26 " =    1.699
peak=    3.725 closest distance to " CA  ALA A  21 " =    1.206
peak=    3.724 closest distance to " O   HOH Z 156 " =    3.178
peak=    3.723 closest distance to " O   HOH Z 130 " =    2.429
peak=    3.718 closest distance to " O   HOH Z 298 " =    5.071
peak=    3.718 closest distance to " CD  ARG A 195 " =    0.986
peak=    3.715 closest distance to " O   HOH Z 425 " =    1.420
peak=    3.715 closest distance to " CA  ASP A 191 " =    0.900
peak=    3.714 closest distance to " O   HOH Z 132 " =    2.519
peak=    3.703 closest distance to " O   HOH Z 395 " =    1.423
peak=    3.703 closest distance to " CB  SER A 141 " =    0.999
peak=    3.702 closest distance to " O   GLY A  91 " =    1.344
peak=    3.692 closest distance to " O   HOH Z  54 " =    1.482
peak=    3.690 closest distance to " O   HOH Z 261 " =    2.065
peak=    3.683 closest distance to " OH  TYR A 116 " =    1.188
peak=    3.681 closest distance to " O   HOH Z  97 " =    2.346
peak=    3.677 closest distance to " CD  ARG A 159 " =    0.798
peak=    3.676 closest distance to " O   HOH Z 423 " =    3.061
peak=    3.667 closest distance to " O   HOH Z 271 " =    2.448
peak=    3.663 closest distance to " CB  THR A  31 " =    1.507
peak=    3.655 closest distance to " CB  ASN A 187 " =    1.491
peak=    3.650 closest distance to " CE1 HIS A 108 " =    1.140
peak=    3.650 closest distance to " CB  ASN A 148 " =    1.331
peak=    3.642 closest distance to " O   HOH Z 236 " =    1.773
peak=    3.640 closest distance to " O   HOH Z 394 " =    1.655
peak=    3.636 closest distance to " O   HOH Z 369 " =    2.146
peak=    3.632 closest distance to " CG  PRO A 243 " =    1.195
peak=    3.630 closest distance to " ND2 ASN A 187 " =    1.709
peak=    3.630 closest distance to " O   HOH Z 128 " =    1.806
peak=    3.630 closest distance to " O   HOH Z  46 " =    1.379
peak=    3.626 closest distance to " O   HOH Z 403 " =    1.407
peak=    3.623 closest distance to " CE1 TYR A 186 " =    1.276
peak=    3.619 closest distance to " CB  ARG A 139 " =    0.959
peak=    3.603 closest distance to " CB  TRP A 266 " =    1.136
peak=    3.598 closest distance to " CG2 ILE A  20 " =    1.419
peak=    3.597 closest distance to " O   HOH Z 126 " =    1.773
peak=    3.596 closest distance to " O   HOH Z 426 " =    1.503
peak=    3.591 closest distance to " O   HOH Z 147 " =    1.847
peak=    3.588 closest distance to " CB  TYR A 169 " =    0.734
peak=    3.586 closest distance to " O   HOH Z 408 " =    1.677
peak=    3.583 closest distance to " CA  ASN A 176 " =    1.054
peak=    3.582 closest distance to " CG1BVAL A  72 " =    1.759
peak=    3.572 closest distance to " OD1 ASN A  69 " =    2.521
peak=    3.571 closest distance to " O   HOH Z 241 " =    1.746
peak=    3.560 closest distance to " CD  PRO A  54 " =    0.992
peak=    3.558 closest distance to " O   HOH Z 234 " =    1.847
peak=    3.544 closest distance to " CE  LYS A 119 " =    1.049
peak=    3.544 closest distance to " OE1 GLN A  11 " =    1.847
peak=    3.541 closest distance to " CB  ASN A  39 " =    0.810
peak=    3.531 closest distance to " O   HOH Z 427 " =    3.056
peak=    3.528 closest distance to " O   HOH Z 146 " =    1.361
peak=    3.528 closest distance to " NH2 ARG A  79 " =    1.277
peak=    3.524 closest distance to " O   HOH Z  39 " =    1.213
peak=    3.522 closest distance to " O   HOH Z 339 " =    1.287
peak=    3.519 closest distance to " OG  SER A 245 " =    1.478
peak=    3.509 closest distance to " O   HOH Z 136 " =    1.297
peak=    3.507 closest distance to " O   HOH Z 280 " =    2.972
peak=    3.507 closest distance to " O   HOH Z 419 " =    2.354
peak=    3.504 closest distance to " O   HOH Z 417 " =    3.248
peak=    3.501 closest distance to " O   HOH Z 236 " =    1.501
peak=    3.497 closest distance to " O   HOH Z 197 " =    2.075
peak=    3.494 closest distance to " O   HOH Z 438 " =    2.403
peak=    3.494 closest distance to " O   ALA A 158 " =    1.228
peak=    3.493 closest distance to " O   HOH Z 366 " =    2.917
peak=    3.491 closest distance to " O   HOH Z 435 " =    1.905
peak=    3.490 closest distance to " O   HOH Z 146 " =    1.465
peak=    3.489 closest distance to " O   HOH Z 128 " =    2.267
peak=    3.485 closest distance to " O   HOH Z 273 " =    2.681
peak=    3.478 closest distance to " NH2 ARG A 156 " =    1.109
peak=    3.471 closest distance to " CA  ILE A 263 " =    0.947
peak=    3.470 closest distance to " O   HOH Z   9 " =    2.344
peak=    3.465 closest distance to " CD  LYS A 119 " =    1.877
peak=    3.462 closest distance to " O   HOH Z  66 " =    2.147
peak=    3.460 closest distance to " O   HOH Z   4 " =    1.544
peak=    3.459 closest distance to " O   HOH Z 196 " =    1.733
peak=    3.458 closest distance to " O   HOH Z 315 " =    1.874
peak=    3.457 closest distance to " O   HOH Z 257 " =    2.185
peak=    3.456 closest distance to " O   HOH Z 358 " =    2.234
peak=    3.451 closest distance to " CA  ALA A  51 " =    1.061
peak=    3.450 closest distance to " NZ  LYS A 117 " =    1.496
peak=    3.448 closest distance to " O   HOH Z 251 " =    1.743
peak=    3.443 closest distance to " CB  ALA A   9 " =    1.600
peak=    3.442 closest distance to " CD1 LEU A   5 " =    1.511
peak=    3.438 closest distance to " CB  ARG A 190 " =    1.712
peak=    3.437 closest distance to " O   HOH Z 214 " =    2.565
peak=    3.432 closest distance to " CB  VAL A 202 " =    1.420
peak=    3.432 closest distance to " CB  ALA A 256 " =    0.999
peak=    3.430 closest distance to " O   HOH Z  48 " =    1.596
peak=    3.428 closest distance to " OG BSER A 164 " =    2.150
peak=    3.428 closest distance to " O   HOH Z 383 " =    2.033
peak=    3.423 closest distance to " O   HOH Z  48 " =    1.587
peak=    3.421 closest distance to " CB  GLU A 128 " =    1.150
peak=    3.415 closest distance to " O   HOH Z  19 " =    1.935
peak=    3.415 closest distance to " O   HOH Z  88 " =    3.168
peak=    3.413 closest distance to " O   HOH Z 332 " =    1.525
peak=    3.413 closest distance to " CB  VAL A 265 " =    1.333
peak=    3.413 closest distance to " O   HOH Z 298 " =    1.924
peak=    3.410 closest distance to " CB  ARG A  79 " =    1.383
peak=    3.406 closest distance to " CB  ALA A  71 " =    1.223
peak=    3.399 closest distance to " O  BHOH Z  74 " =    1.429
peak=    3.396 closest distance to " O   HOH Z 336 " =    1.839
peak=    3.392 closest distance to " CG2 VAL A 197 " =    1.090
peak=    3.391 closest distance to " CA  ASP A 162 " =    1.073
peak=    3.387 closest distance to " O   HOH Z 126 " =    1.778
peak=    3.385 closest distance to " CA  ALA A 295 " =    0.998
peak=    3.385 closest distance to " OG BSER A 210 " =    1.193
peak=    3.375 closest distance to " O   HOH Z 402 " =    2.654
peak=    3.375 closest distance to " O   HOH Z 313 " =    1.803
peak=    3.374 closest distance to " O   HOH Z 250 " =    1.401
peak=    3.372 closest distance to " O   HOH Z  35 " =    2.129
peak=    3.371 closest distance to " CG2 THR A  42 " =    0.830
peak=    3.367 closest distance to " O   TRP A 274 " =    1.918
peak=    3.364 closest distance to " O   HOH Z 361 " =    2.855
peak=    3.360 closest distance to " O   HOH Z 374 " =    2.589
peak=    3.358 closest distance to " O   HOH Z 261 " =    2.152
peak=    3.357 closest distance to " CG  ARG A  66 " =    2.930
peak=    3.357 closest distance to " O   HOH Z 420 " =    2.015
peak=    3.354 closest distance to " OG  SER A  62 " =    2.902
peak=    3.354 closest distance to " ND1 HIS A  81 " =    1.546
peak=    3.347 closest distance to " CB  ARG A  79 " =    0.898
peak=    3.346 closest distance to " CG1 ILE A  49 " =    1.587
peak=    3.343 closest distance to " CD2 LEU A 255 " =    1.212
peak=    3.341 closest distance to " CD1 LEU A 222 " =    0.720
peak=    3.339 closest distance to " NH1 ARG A  14 " =    1.155
peak=    3.337 closest distance to " O   HOH Z 162 " =    1.755
peak=    3.336 closest distance to " CD  ARG A 269 " =    1.161
peak=    3.336 closest distance to " O   HOH Z 155 " =    2.824
peak=    3.329 closest distance to " O   HOH Z 280 " =    2.527
peak=    3.324 closest distance to " CB  ARG A 259 " =    1.884
peak=    3.318 closest distance to " CA  ARG A 195 " =    1.352
peak=    3.318 closest distance to " O   ALA A 165 " =    1.265
peak=    3.304 closest distance to " OD2 ASP A 298 " =    3.946
peak=    3.304 closest distance to " O   HOH Z 112 " =    1.704
peak=    3.303 closest distance to " O   HOH Z 421 " =    1.866
peak=    3.299 closest distance to " CG1 VAL A 153 " =    1.096
peak=    3.298 closest distance to " O   HOH Z 173 " =    2.344
peak=    3.284 closest distance to " CD1 LEU A  96 " =    0.757
peak=    3.284 closest distance to " NH2AARG A 275 " =    3.779
peak=    3.282 closest distance to " O   HOH Z 387 " =    2.522
peak=    3.275 closest distance to " O   HOH Z 362 " =    3.348
peak=    3.272 closest distance to " O   HOH Z 281 " =    4.371
peak=    3.271 closest distance to " O   HOH Z 162 " =    2.010
peak=    3.266 closest distance to " C   VAL A 265 " =    1.356
peak=    3.265 closest distance to " CB  LEU A   5 " =    1.208
peak=    3.265 closest distance to " O   HOH Z 145 " =    2.865
peak=    3.255 closest distance to " CA  SER A  12 " =    1.698
peak=    3.243 closest distance to " O   HOH Z 355 " =    1.857
peak=    3.243 closest distance to " CB  ARG A 269 " =    1.794
peak=    3.242 closest distance to " CB  PHE A 204 " =    0.930
peak=    3.236 closest distance to " O   HOH Z 326 " =    1.483
peak=    3.235 closest distance to " O   HOH Z 185 " =    1.600
peak=    3.233 closest distance to " CZ  PHE A 218 " =    1.158
peak=    3.231 closest distance to " OD2 ASP A 286 " =    2.709
peak=    3.230 closest distance to " CB  MET A  47 " =    1.147
peak=    3.229 closest distance to " O   HOH Z 422 " =    2.502
peak=    3.228 closest distance to " CB  ALA A 295 " =    1.151
peak=    3.227 closest distance to " CG2 ILE A 234 " =    2.065
peak=    3.226 closest distance to " O   HOH Z 253 " =    1.633
peak=    3.225 closest distance to " O   HOH Z 255 " =    1.610
peak=    3.224 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.222 closest distance to " O   HOH Z 428 " =    3.889
peak=    3.219 closest distance to " CB  PRO A  90 " =    1.172
peak=    3.218 closest distance to " O   HOH Z  78 " =    1.608
peak=    3.217 closest distance to " CB  GLN A  58 " =    1.097
peak=    3.216 closest distance to " OD1 ASP A 286 " =    1.727
peak=    3.210 closest distance to " CG2 THR A 294 " =    1.417
peak=    3.207 closest distance to " O   HOH Z 109 " =    2.001
peak=    3.207 closest distance to " CG1 VAL A 296 " =    1.102
peak=    3.205 closest distance to " CB  ALA A 137 " =    1.342
peak=    3.202 closest distance to " CG  GLN A  58 " =    2.605
peak=    3.201 closest distance to " NE1 TRP A 274 " =    0.929
peak=    3.196 closest distance to " O   HOH Z 293 " =    1.639
peak=    3.192 closest distance to " O   HOH Z 279 " =    1.984
peak=    3.192 closest distance to " OG BSER A 212 " =    2.574
peak=    3.189 closest distance to " CZ  PHE A  38 " =    1.220
peak=    3.187 closest distance to " O   HOH Z 425 " =    2.140
peak=    3.184 closest distance to " CG2AVAL A 121 " =    2.000
peak=    3.183 closest distance to " O   HOH Z 291 " =    1.576
peak=    3.180 closest distance to " CA  VAL A 126 " =    0.863
peak=    3.176 closest distance to " CD2 LEU A 297 " =    0.919
peak=    3.175 closest distance to " CB  ALA A 248 " =    1.355
peak=    3.175 closest distance to " NZ  LYS A 166 " =    2.894
peak=    3.174 closest distance to " O   HOH Z  90 " =    3.457
peak=    3.172 closest distance to " N   SER A 164 " =    1.005
peak=    3.172 closest distance to " O   HOH Z 197 " =    2.239
peak=    3.172 closest distance to " CB  ARG A 219 " =    1.474
peak=    3.170 closest distance to " O   HOH Z 227 " =    1.731
peak=    3.170 closest distance to " O   HOH Z 359 " =    1.864
peak=    3.169 closest distance to " O   HOH Z  54 " =    1.255
peak=    3.165 closest distance to " O   ILE A  33 " =    1.195
peak=    3.164 closest distance to " CG  MET A 113 " =    1.452
peak=    3.164 closest distance to " CD1 LEU A 101 " =    1.253
peak=    3.164 closest distance to " CZ3 TRP A  85 " =    1.037
peak=    3.149 closest distance to " O   HOH Z 261 " =    2.005
peak=    3.147 closest distance to " CD1 ILE A  33 " =    1.579
peak=    3.143 closest distance to " CB  TYR A 247 " =    0.991
peak=    3.142 closest distance to " O   HOH Z 163 " =    1.697
peak=    3.138 closest distance to " O   HOH Z 271 " =    1.367
peak=    3.128 closest distance to " CA  THR A 264 " =    0.774
peak=    3.123 closest distance to " NH1AARG A 145 " =    1.158
peak=    3.094 closest distance to " NH2BARG A 190 " =    1.713
peak=    3.094 closest distance to " CA  ARG A  66 " =    0.925
peak=    3.092 closest distance to " N   ASP A 162 " =    1.381
peak=    3.080 closest distance to " O   HOH Z 404 " =    2.001
peak=    3.080 closest distance to " CG2 ILE A 106 " =    0.740
peak=    3.075 closest distance to " NZ  LYS A  76 " =    1.832
peak=    3.058 closest distance to " CB  PHE A 283 " =    0.806
peak=    3.055 closest distance to " O   HOH Z 214 " =    1.829
peak=    3.051 closest distance to " CB  GLN A 278 " =    0.860
peak=    3.040 closest distance to " OG BSER A 258 " =    3.273
peak=    3.022 closest distance to " CA  GLU A  46 " =    0.737

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.479 - 5.950
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.727 - 5.950

peak=   -5.520 closest distance to " CG2 VAL A 230 " =    0.755
peak=   -4.759 closest distance to " O   HOH Z 210 " =    0.765
peak=   -4.703 closest distance to " O   PRO A 163 " =    2.028
peak=   -4.547 closest distance to " O   HOH Z 290 " =    0.859
peak=   -4.531 closest distance to " CG2BVAL A  41 " =    2.676
peak=   -4.494 closest distance to " O   HOH Z 155 " =    1.689
peak=   -4.399 closest distance to " CD  ARG A 156 " =    1.994
peak=   -4.195 closest distance to " O   HOH Z 166 " =    1.668
peak=   -4.096 closest distance to " O   HOH Z 266 " =    4.573
peak=   -4.081 closest distance to " OXT GLY A 302 " =    2.736
peak=   -4.081 closest distance to " C   THR A 279 " =    1.180
peak=   -4.057 closest distance to " CG1 VAL A 112 " =    2.531
peak=   -4.040 closest distance to " O   HOH Z 151 " =    0.956
peak=   -4.032 closest distance to " SG  CYS A 254 " =    3.156
peak=   -4.005 closest distance to " CD  GLN A  58 " =    1.201
peak=   -3.992 closest distance to " CD2 TYR A  30 " =    2.753
peak=   -3.959 closest distance to " O   HOH Z 165 " =    2.032
peak=   -3.953 closest distance to " O   HOH Z 136 " =    2.310
peak=   -3.947 closest distance to " C   HIS A 108 " =    1.226
peak=   -3.944 closest distance to " O   VAL A  67 " =    2.627
peak=   -3.929 closest distance to " CG  MET A  93 " =    2.498
peak=   -3.915 closest distance to " O   HOH Z 109 " =    5.950
peak=   -3.910 closest distance to " CD1 PHE A  59 " =    1.950
peak=   -3.891 closest distance to " CG  ASP A 231 " =    0.823
peak=   -3.890 closest distance to " CZ  TYR A 169 " =    1.828
peak=   -3.886 closest distance to " CD2 LEU A 300 " =    2.622
peak=   -3.878 closest distance to " O   HOH Z 426 " =    1.796
peak=   -3.844 closest distance to " O   HOH Z  71 " =    1.511
peak=   -3.843 closest distance to " N   THR A 235 " =    1.349
peak=   -3.842 closest distance to " O   ALA A   1 " =    2.020
peak=   -3.834 closest distance to " OG  SER A  97 " =    2.333
peak=   -3.762 closest distance to " CD2 LEU A 237 " =    2.713
peak=   -3.759 closest distance to " O   HOH Z 351 " =    1.584
peak=   -3.754 closest distance to " O   HOH Z   6 " =    2.028
peak=   -3.752 closest distance to " O   HOH Z 166 " =    1.282
peak=   -3.737 closest distance to " CG2 THR A 182 " =    2.203
peak=   -3.730 closest distance to " CG2 THR A   4 " =    1.873
peak=   -3.722 closest distance to " OG BSER A 134 " =    1.468
peak=   -3.712 closest distance to " OG BSER A 210 " =    1.368
peak=   -3.706 closest distance to " O   HOH Z 196 " =    2.303
peak=   -3.704 closest distance to " NH2 ARG A  66 " =    1.358
peak=   -3.700 closest distance to " CH2 TRP A 179 " =    1.252
peak=   -3.674 closest distance to " N   ALA A 226 " =    1.954
peak=   -3.673 closest distance to " O   HOH Z  15 " =    1.430
peak=   -3.667 closest distance to " O   HOH Z 103 " =    1.931
peak=   -3.663 closest distance to " CB  PHE A 208 " =    2.317
peak=   -3.659 closest distance to " OG BSER A 134 " =    1.717
peak=   -3.657 closest distance to " O   HOH Z 312 " =    1.561
peak=   -3.637 closest distance to " CB  ALA A 248 " =    1.968
peak=   -3.631 closest distance to " O   HOH Z 423 " =    2.219
peak=   -3.622 closest distance to " OG  SER A  26 " =    1.252
peak=   -3.617 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.613 closest distance to " CB  ALA A 248 " =    2.203
peak=   -3.612 closest distance to " O   TRP A  92 " =    1.995
peak=   -3.610 closest distance to " O   ALA A 256 " =    1.518
peak=   -3.609 closest distance to " O   HOH Z 174 " =    2.011
peak=   -3.608 closest distance to " ND2 ASN A  69 " =    1.545
peak=   -3.582 closest distance to " O   HOH Z 126 " =    1.899
peak=   -3.568 closest distance to " OG  SER A   3 " =    1.540
peak=   -3.559 closest distance to " CG  ASP A  50 " =    2.265
peak=   -3.547 closest distance to " N   GLN A  58 " =    1.804
peak=   -3.546 closest distance to " CB  ALA A 161 " =    2.466
peak=   -3.541 closest distance to " O   HOH Z 120 " =    1.243
peak=   -3.540 closest distance to " O   HOH Z 407 " =    1.345
peak=   -3.537 closest distance to " O   VAL A 174 " =    2.145
peak=   -3.536 closest distance to " CB  SER A 210 " =    1.188
peak=   -3.530 closest distance to " O   HOH Z 407 " =    3.144
peak=   -3.523 closest distance to " O   HOH Z  78 " =    1.602
peak=   -3.515 closest distance to " CG2 VAL A 296 " =    0.997
peak=   -3.513 closest distance to " NE2 GLN A 194 " =    1.696
peak=   -3.503 closest distance to " OD1 ASN A 148 " =    1.573
peak=   -3.498 closest distance to " O   HOH Z 377 " =    1.980
peak=   -3.496 closest distance to " O   HOH Z 231 " =    2.219
peak=   -3.488 closest distance to " O   ASN A  45 " =    1.879
peak=   -3.476 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.473 closest distance to " O   HOH Z 340 " =    1.055
peak=   -3.472 closest distance to " OD1 ASN A 249 " =    2.202
peak=   -3.463 closest distance to " C   GLY A  91 " =    1.407
peak=   -3.463 closest distance to " O   HOH Z 422 " =    1.490
peak=   -3.462 closest distance to " C   LEU A 143 " =    1.088
peak=   -3.457 closest distance to " CD2 LEU A 143 " =    2.396
peak=   -3.446 closest distance to " NH1 ARG A 195 " =    2.284
peak=   -3.445 closest distance to " OG BSER A 212 " =    1.720
peak=   -3.444 closest distance to " O   HOH Z  92 " =    1.452
peak=   -3.442 closest distance to " CD1 LEU A 228 " =    2.240
peak=   -3.441 closest distance to " CD  GLN A 223 " =    0.816
peak=   -3.440 closest distance to " CA  GLY A 203 " =    2.263
peak=   -3.435 closest distance to " CD2 TYR A 293 " =    2.010
peak=   -3.434 closest distance to " CD  ARG A 139 " =    1.570
peak=   -3.431 closest distance to " N   LEU A 281 " =    1.875
peak=   -3.426 closest distance to " O   HOH Z 234 " =    4.055
peak=   -3.418 closest distance to " OG ASER A 134 " =    1.351
peak=   -3.417 closest distance to " O   HOH Z  52 " =    2.122
peak=   -3.415 closest distance to " CB  PRO A 163 " =    2.732
peak=   -3.414 closest distance to " CD1 TYR A 247 " =    2.294
peak=   -3.410 closest distance to " CB  PHE A 192 " =    2.054
peak=   -3.409 closest distance to " CB  ALA A 291 " =    2.325
peak=   -3.406 closest distance to " ND2 ASN A  39 " =    1.104
peak=   -3.406 closest distance to " O   HOH Z  20 " =    1.378
peak=   -3.402 closest distance to " CE2 TYR A 186 " =    2.236
peak=   -3.392 closest distance to " O   SER A 210 " =    1.932
peak=   -3.389 closest distance to " O   SER A 273 " =    1.195
peak=   -3.386 closest distance to " CG  ARG A 219 " =    2.428
peak=   -3.384 closest distance to " O   PHE A 218 " =    1.524
peak=   -3.379 closest distance to " NH1 ARG A 195 " =    2.484
peak=   -3.375 closest distance to " NH2 ARG A  79 " =    1.964
peak=   -3.371 closest distance to " NE1 TRP A 266 " =    2.368
peak=   -3.370 closest distance to " O   HOH Z  60 " =    2.202
peak=   -3.361 closest distance to " O  BHOH Z 338 " =    1.547
peak=   -3.360 closest distance to " CG1 VAL A 296 " =    1.210
peak=   -3.360 closest distance to " CG  ARG A 269 " =    2.215
peak=   -3.354 closest distance to " N   ALA A 248 " =    1.820
peak=   -3.352 closest distance to " CD1 TYR A 169 " =    2.330
peak=   -3.343 closest distance to " O   HOH Z 150 " =    1.752
peak=   -3.340 closest distance to " N   ARG A  66 " =    1.757
peak=   -3.338 closest distance to " O   HOH Z 139 " =    3.394
peak=   -3.336 closest distance to " CA  SER A 276 " =    1.469
peak=   -3.330 closest distance to " CE BMET A  47 " =    1.464
peak=   -3.329 closest distance to " CD2 LEU A 237 " =    2.745
peak=   -3.328 closest distance to " OD1 ASN A  39 " =    2.241
peak=   -3.326 closest distance to " CD1 TRP A 179 " =    1.134
peak=   -3.322 closest distance to " OE2 GLU A   2 " =    1.579
peak=   -3.321 closest distance to " O   HOH Z 388 " =    2.016
peak=   -3.316 closest distance to " CE  LYS A 166 " =    2.976
peak=   -3.313 closest distance to " NE2 GLN A  88 " =    1.043
peak=   -3.307 closest distance to " O   HOH Z 313 " =    1.165
peak=   -3.300 closest distance to " CG2 VAL A 189 " =    1.957
peak=   -3.294 closest distance to " O   HOH Z 124 " =    1.525
peak=   -3.291 closest distance to " O   HOH Z  97 " =    1.128
peak=   -3.290 closest distance to " O   HOH Z  10 " =    1.588
peak=   -3.286 closest distance to " O   SER A 146 " =    0.938
peak=   -3.281 closest distance to " O   HOH Z  49 " =    0.906
peak=   -3.277 closest distance to " O   VAL A 125 " =    2.278
peak=   -3.277 closest distance to " O   HOH Z  17 " =    1.075
peak=   -3.277 closest distance to " NH2 ARG A  66 " =    5.133
peak=   -3.273 closest distance to " CE  MET A 105 " =    1.947
peak=   -3.272 closest distance to " O   HOH Z 171 " =    2.225
peak=   -3.269 closest distance to " O   HOH Z 196 " =    2.057
peak=   -3.267 closest distance to " CG1 VAL A  78 " =    2.516
peak=   -3.267 closest distance to " O   HOH Z  56 " =    2.070
peak=   -3.264 closest distance to " O   HOH Z 411 " =    1.615
peak=   -3.259 closest distance to " O   GLY A 196 " =    1.039
peak=   -3.259 closest distance to " CG  MET A 105 " =    0.793
peak=   -3.257 closest distance to " CD  GLN A  11 " =    0.891
peak=   -3.256 closest distance to " O   TYR A  15 " =    1.759
peak=   -3.254 closest distance to " O   HOH Z  39 " =    1.660
peak=   -3.250 closest distance to " SG  CYS A 260 " =    2.543
peak=   -3.249 closest distance to " ND2 ASN A 187 " =    1.644
peak=   -3.248 closest distance to " CA  GLY A 133 " =    2.042
peak=   -3.245 closest distance to " N   THR A 157 " =    1.618
peak=   -3.244 closest distance to " O   HOH Z 424 " =    2.781
peak=   -3.241 closest distance to " CB  ALA A 291 " =    2.241
peak=   -3.241 closest distance to " CE2 TRP A 274 " =    1.280
peak=   -3.231 closest distance to " CD1 PHE A  59 " =    2.125
peak=   -3.227 closest distance to " O   HOH Z 174 " =    4.051
peak=   -3.224 closest distance to " O   HOH Z 414 " =    2.671
peak=   -3.220 closest distance to " C   ALA A 158 " =    1.342
peak=   -3.220 closest distance to " C   ASP A 270 " =    1.461
peak=   -3.219 closest distance to " OG1 THR A  82 " =    1.300
peak=   -3.214 closest distance to " N   VAL A 189 " =    1.613
peak=   -3.214 closest distance to " CA  VAL A 197 " =    0.965
peak=   -3.208 closest distance to " CD  LYS A 289 " =    2.511
peak=   -3.208 closest distance to " NE2 GLN A 103 " =    1.653
peak=   -3.195 closest distance to " CD  GLN A 223 " =    1.793
peak=   -3.193 closest distance to " CA  GLY A 241 " =    2.358
peak=   -3.192 closest distance to " O   HOH Z 377 " =    1.367
peak=   -3.187 closest distance to " N   ALA A 242 " =    1.970
peak=   -3.183 closest distance to " OXT GLY A 302 " =    3.436
peak=   -3.183 closest distance to " C   ASN A 285 " =    2.268
peak=   -3.181 closest distance to " O   HOH Z 368 " =    1.848
peak=   -3.181 closest distance to " CG  ASP A 132 " =    2.298
peak=   -3.179 closest distance to " O   HOH Z 397 " =    1.222
peak=   -3.177 closest distance to " C   SER A 206 " =    1.655
peak=   -3.172 closest distance to " CG2 VAL A 112 " =    2.555
peak=   -3.169 closest distance to " ND2 ASN A  45 " =    1.085
peak=   -3.165 closest distance to " ND2 ASN A  45 " =    1.835
peak=   -3.165 closest distance to " CH2 TRP A 150 " =    1.079
peak=   -3.164 closest distance to " OD2 ASP A 171 " =    2.379
peak=   -3.163 closest distance to " O   HOH Z 120 " =    0.925
peak=   -3.162 closest distance to " CG  GLN A  11 " =    1.590
peak=   -3.161 closest distance to " CA  ALA A 137 " =    2.497
peak=   -3.159 closest distance to " O   HOH Z 119 " =    2.122
peak=   -3.143 closest distance to " CB  LEU A 167 " =    2.187
peak=   -3.140 closest distance to " CG  GLU A  53 " =    1.519
peak=   -3.134 closest distance to " O   HOH Z 244 " =    1.469
peak=   -3.128 closest distance to " O   HOH Z 360 " =    2.475
peak=   -3.126 closest distance to " NE  ARG A 259 " =    1.176
peak=   -3.125 closest distance to " O   GLY A  80 " =    2.516
peak=   -3.121 closest distance to " CD  ARG A 195 " =    5.063
peak=   -3.119 closest distance to " O   HOH Z 372 " =    2.507
peak=   -3.118 closest distance to " CA  LYS A 166 " =    2.179
peak=   -3.115 closest distance to " O   MET A  40 " =    2.832
peak=   -3.110 closest distance to " ND2 ASN A  60 " =    1.493
peak=   -3.103 closest distance to " N   VAL A 230 " =    1.088
peak=   -3.079 closest distance to " CD  GLN A  73 " =    0.727
peak=   -3.076 closest distance to " O   HOH Z 185 " =    2.353
peak=   -3.058 closest distance to " O   HOH Z   1 " =    4.543
peak=   -3.048 closest distance to " O   ILE A 234 " =    1.298
peak=   -3.047 closest distance to " CB  CYS A 254 " =    2.576
peak=   -3.031 closest distance to " CG2BVAL A  41 " =    1.573

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4957 0.4797   6.294481e+00   6.282916e+00
   1_bss:  0.4877 0.4735   6.287745e+00   6.277704e+00
   1_xyz:  0.4134 0.4335   6.202308e+00   6.226730e+00
   1_adp:  0.3701 0.4182   6.138829e+00   6.209339e+00
   1_occ:  0.3695 0.4169   6.137640e+00   6.209049e+00
   2_bss:  0.3675 0.4114   6.138347e+00   6.208428e+00
   2_xyz:  0.2932 0.3477   5.960993e+00   6.093032e+00
   2_adp:  0.2716 0.3312   5.909773e+00   6.052175e+00
   2_occ:  0.2713 0.3310   5.909376e+00   6.051814e+00
   3_bss:  0.2697 0.3310   5.908532e+00   6.050243e+00
   3_xyz:  0.1940 0.2393   5.604160e+00   5.774958e+00
   3_adp:  0.1719 0.2138   5.492855e+00   5.672010e+00
   3_occ:  0.1716 0.2139   5.491980e+00   5.671988e+00
   4_bss:  0.1706 0.2125   5.491741e+00   5.669002e+00
   4_xyz:  0.1373 0.1787   5.299683e+00   5.506417e+00
   4_adp:  0.1314 0.1717   5.261449e+00   5.470161e+00
   4_occ:  0.1313 0.1716   5.261158e+00   5.470652e+00
   5_bss:  0.1314 0.1721   5.263341e+00   5.473368e+00
   5_xyz:  0.1193 0.1630   5.194232e+00   5.424594e+00
   5_adp:  0.1178 0.1620   5.185286e+00   5.419779e+00
   5_occ:  0.1177 0.1622   5.185179e+00   5.420135e+00
   5_bss:  0.1177 0.1621   5.185276e+00   5.420212e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.329   8.528   7.040  11.485   7.394   0.000   0.000   0.000
   1_xyz:  0.329   8.528   7.040  11.485   7.394   0.000   0.000   0.000
   1_adp:  0.329   8.528   7.040  11.485   7.394   0.000   0.000   0.000
   1_occ:  0.329   8.528   7.040  11.485   7.394   0.000   0.000   0.000
   2_bss:  0.306  30.817   3.496   7.223   4.512   0.000   0.000   0.000
   2_xyz:  0.306  30.817   3.496   7.223   4.512   0.000   0.000   0.000
   2_adp:  0.306  30.817   3.496   7.223   4.512   0.000   0.000   0.000
   2_occ:  0.306  30.817   3.496   7.223   4.512   0.000   0.000   0.000
   3_bss:  0.300  38.639   1.726   4.557   3.019   0.000   0.000   0.000
   3_xyz:  0.300  38.639   1.726   4.557   3.019   0.000   0.000   0.000
   3_adp:  0.300  38.639   1.726   4.557   3.019   0.000   0.000   0.000
   3_occ:  0.300  38.639   1.726   4.557   3.019   0.000   0.000   0.000
   4_bss:  0.318  38.639   0.567   2.606   1.991   0.000   0.000   0.000
   4_xyz:  0.318  38.639   0.567   2.606   1.991   0.000   0.000   0.000
   4_adp:  0.318  38.639   0.567   2.606   1.991   0.000   0.000   0.000
   4_occ:  0.318  38.639   0.567   2.606   1.991   0.000   0.000   0.000
   5_bss:  0.315  45.884   0.255   1.895   1.780   0.000   0.000   0.000
   5_xyz:  0.315  45.884   0.255   1.895   1.780   0.000   0.000   0.000
   5_adp:  0.315  45.884   0.255   1.895   1.780   0.000   0.000   0.000
   5_occ:  0.315  45.884   0.255   1.895   1.780   0.000   0.000   0.000
   5_bss:  0.322  47.181  -0.999   0.481   0.518   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.572 0.4000  0.4663    73836.212
   1_bss:  60.010 0.3926  0.5860    72368.073
   1_xyz:  52.326 0.4893  0.7152    56739.139
   1_adp:  48.487 0.5381  0.8484    51890.238
   1_occ:  48.353 0.5398  0.8491    51616.547
   2_bss:  47.918 0.5452  0.7614    50954.097
   2_xyz:  38.704 0.6568  0.9087    34666.023
   2_adp:  35.702 0.6929  0.9438    30770.218
   2_occ:  35.691 0.6930  0.9436    30772.712
   3_bss:  35.509 0.6950  0.8820    30492.119
   3_xyz:  23.899 0.8224  0.9962    14876.679
   3_adp:  20.775 0.8544  1.0150    11960.636
   3_occ:  20.763 0.8545  1.0154    11961.812
   4_bss:  20.674 0.8554  0.9673    11867.186
   4_xyz:  16.689 0.8919  0.9871     8131.765
   4_adp:  15.830 0.8998  0.9899     7626.114
   4_occ:  15.840 0.8998  0.9899     7639.424
   5_bss:  15.886 0.8994  0.9755     7719.597
   5_xyz:  14.825 0.9085  0.9772     6989.614
   5_adp:  14.690 0.9097  0.9735     6922.329
   5_occ:  14.692 0.9097  0.9733     6930.334
   5_bss:  14.692 0.9097  0.9732     6931.917
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3548e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3548e+01
   1_xyz:   1.791  0.014  0.112 18.286  0.007  4.119   1.5767e-01
   1_adp:   1.791  0.014  0.112 18.286  0.007  4.119   1.5767e-01
   1_occ:   1.791  0.014  0.112 18.286  0.007  4.119   1.5767e-01
   2_bss:   1.791  0.014  0.112 18.286  0.007  4.119   1.5767e-01
   2_xyz:   1.279  0.009  0.086 16.616  0.005  4.126   9.4269e-02
   2_adp:   1.279  0.009  0.086 16.616  0.005  4.126   9.4269e-02
   2_occ:   1.279  0.009  0.086 16.616  0.005  4.126   9.4269e-02
   3_bss:   1.279  0.009  0.086 16.616  0.005  4.126   9.4269e-02
   3_xyz:   1.269  0.009  0.088 16.049  0.005  4.108   8.7027e-02
   3_adp:   1.269  0.009  0.088 16.049  0.005  4.108   8.7027e-02
   3_occ:   1.269  0.009  0.088 16.049  0.005  4.108   8.7027e-02
   4_bss:   1.269  0.009  0.088 16.049  0.005  4.108   8.7027e-02
   4_xyz:   1.048  0.008  0.080 15.512  0.004  4.118   6.8668e-02
   4_adp:   1.048  0.008  0.080 15.512  0.004  4.118   6.8668e-02
   4_occ:   1.048  0.008  0.080 15.512  0.004  4.118   6.8668e-02
   5_bss:   1.048  0.008  0.080 15.512  0.004  4.118   6.8668e-02
   5_xyz:   1.124  0.008  0.087 15.618  0.004  4.111   7.2578e-02
   5_adp:   1.124  0.008  0.087 15.618  0.004  4.111   7.2578e-02
   5_occ:   1.124  0.008  0.087 15.618  0.004  4.111   7.2578e-02
   5_bss:   1.124  0.008  0.087 15.618  0.004  4.111   7.2578e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.984   6.9389e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.984   6.9389e+00
   1_xyz:  16.460  0.174  0.563 86.779  0.048  2.236   1.0963e-01
   1_adp:  16.460  0.174  0.563 86.779  0.048  2.236   1.0963e-01
   1_occ:  16.460  0.174  0.563 86.779  0.048  2.236   1.0963e-01
   2_bss:  16.460  0.174  0.563 86.779  0.048  2.236   1.0963e-01
   2_xyz:   8.837  0.115  0.289 89.168  0.043  2.053   7.3298e-02
   2_adp:   8.837  0.115  0.289 89.168  0.043  2.053   7.3298e-02
   2_occ:   8.837  0.115  0.289 89.168  0.043  2.053   7.3298e-02
   3_bss:   8.837  0.115  0.289 89.168  0.043  2.053   7.3298e-02
   3_xyz:   6.996  0.066  0.345 84.930  0.042  2.091   6.1481e-02
   3_adp:   6.996  0.066  0.345 84.930  0.042  2.091   6.1481e-02
   3_occ:   6.996  0.066  0.345 84.930  0.042  2.091   6.1481e-02
   4_bss:   6.996  0.066  0.345 84.930  0.042  2.091   6.1481e-02
   4_xyz:   7.025  0.046  0.493 82.743  0.034  2.244   1.0891e-01
   4_adp:   7.025  0.046  0.493 82.743  0.034  2.244   1.0891e-01
   4_occ:   7.025  0.046  0.493 82.743  0.034  2.244   1.0891e-01
   5_bss:   7.025  0.046  0.493 82.743  0.034  2.244   1.0891e-01
   5_xyz:   7.801  0.050  0.641 83.348  0.038  2.273   5.1398e-02
   5_adp:   7.801  0.050  0.641 83.348  0.038  2.273   5.1398e-02
   5_occ:   7.801  0.050  0.641 83.348  0.038  2.273   5.1398e-02
   5_bss:   7.801  0.050  0.641 83.348  0.038  2.273   5.1398e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  77.76   0.00  14.25  59.71   0.00  12.28  77.76   0.00  24.95
   1_occ:  77.76   0.00  14.25  59.71   0.00  12.28  77.76   0.00  24.95
   2_bss:  77.76   0.00  14.25  59.71   0.00  12.28  77.76   0.00  24.95
   2_xyz:  77.76   0.00  14.25  59.71   0.00  12.28  77.76   0.00  24.95
   2_adp:  87.73   0.00  13.85  72.82   0.00  10.93  87.73   0.00  29.73
   2_occ:  87.73   0.00  13.85  72.82   0.00  10.93  87.73   0.00  29.73
   3_bss:  87.73   0.00  13.85  72.82   0.00  10.93  87.73   0.00  29.73
   3_xyz:  87.73   0.00  13.85  72.82   0.00  10.93  87.73   0.00  29.73
   3_adp:  78.10   0.00  13.78  76.75   0.00   9.89  78.10   2.89  34.99
   3_occ:  78.10   0.00  13.78  76.75   0.00   9.89  78.10   2.89  34.99
   4_bss:  78.10   0.00  13.78  76.75   0.00   9.89  78.10   2.89  34.99
   4_xyz:  78.10   0.00  13.78  76.75   0.00   9.89  78.10   2.89  34.99
   4_adp:  77.54   0.00  13.69  77.54   0.00   9.65  77.03   2.94  35.70
   4_occ:  77.54   0.00  13.69  77.54   0.00   9.65  77.03   2.94  35.70
   5_bss:  77.54   0.00  13.69  77.54   0.00   9.65  77.03   2.94  35.70
   5_xyz:  77.54   0.00  13.69  77.54   0.00   9.65  77.03   2.94  35.70
   5_adp:  78.01   0.00  13.55  78.01   0.00   9.51  76.50   2.45  35.54
   5_occ:  78.01   0.00  13.55  78.01   0.00   9.51  76.50   2.45  35.54
   5_bss:  79.31   1.30  14.84  79.31   1.30  10.80  77.80   3.74  36.84
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.146    0.010    0.418
   1_adp:    1.146    0.010    0.418
   1_occ:    1.146    0.010    0.418
   2_bss:    1.146    0.010    0.418
   2_xyz:    1.736    0.034    0.604
   2_adp:    1.736    0.034    0.604
   2_occ:    1.736    0.034    0.604
   3_bss:    1.736    0.034    0.604
   3_xyz:    1.683    0.039    0.743
   3_adp:    1.683    0.039    0.743
   3_occ:    1.683    0.039    0.743
   4_bss:    1.683    0.039    0.743
   4_xyz:    1.808    0.063    0.803
   4_adp:    1.808    0.063    0.803
   4_occ:    1.808    0.063    0.803
   5_bss:    1.808    0.063    0.803
   5_xyz:    1.872    0.054    0.828
   5_adp:    1.872    0.054    0.828
   5_occ:    1.872    0.054    0.828
   5_bss:    1.872    0.054    0.828
------------------------------------------------------------------------

CPU time actual refinement: 347.64


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_344/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 347.49 
  Macro-tasks:
    bulk solvent and scale       = 40.87  
    individual site refinement   = 149.59 
    weights calculation          = 33.07  
    collect and process          = 6.48   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 230.14 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 108.34 
    alpha_beta                      = 8.38   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 120.17 
    fmodel                         = 7.49   
    r_factors                      = 0.26   
    phase_errors                   = 10.33  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 258.86 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.824 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    650 calls, 108.05 s
gradients_fft:          594 calls, 106.33 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 01:21:33 PST -0800 (1200475293.57 s)
Start R-work = 0.4957, R-free = 0.4797 (no bulk solvent and anisotropic scale)
Final R-work = 0.1354, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.4877, R-free = 0.4735
Final R-work = 0.1177, R-free = 0.1621