# Date 2008-01-16 Time 02:16:44 PST -0800 (1200478604.11 s)
#phil __OFF__

Command line arguments: "../768.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17561
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 768

-------------------------------------------------------------------------------
  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: (70.6012, 46.4607, 88.1178, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (70.6012, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 1.98283
Completeness in resolution range: 0.94674
Completeness with d_max=infinity: 0.943912

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1289
                             d_min =   1.9828

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: (70.6012, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 1.98283
Completeness in resolution range: 0.94674
Completeness with d_max=infinity: 0.943912

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1294 -  4.2434 [2171/2196]  1951   220  10.1%
  bin  2:  4.2434 -  3.3805 [2084/2104]  1879   205   9.8%
  bin  3:  3.3805 -  2.9568 [2077/2096]  1869   208  10.0%
  bin  4:  2.9568 -  2.6881 [2026/2056]  1822   204  10.1%
  bin  5:  2.6881 -  2.4963 [2032/2051]  1831   201   9.9%
  bin  6:  2.4963 -  2.3497 [2013/2038]  1810   203  10.1%
  bin  7:  2.3497 -  2.2324 [2026/2054]  1821   205  10.1%
  bin  8:  2.2324 -  2.1355 [1989/2025]  1791   198  10.0%
  bin  9:  2.1355 -  2.0535 [1997/2039]  1803   194   9.7%
  bin 10:  2.0535 -  1.9828 [1174/2032]  1053   121  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_768/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: 0.14 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:
        1.79 -     2.41: 22
        2.41 -     3.04: 2122
        3.04 -     3.66: 4639
        3.66 -     4.28: 8965
        4.28 -     4.90: 12361
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.792 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  41 " - " O   HOH Z 182 "  1.907 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.965 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.965 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28104 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_768/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_768/model_refine_001.geo

CPU time processing inputs: 9.72


============================ 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 = 70.60125 46.4607 88.1178 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: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4733   r_free= 0.4566   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.273961                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7332 0.99   1413  156 0.3941 0.3633      6.6029      6.5275|
|  2:  4.7332 -  3.7761 0.99   1363  153 0.3771 0.3859      6.7481      6.7789|
|  3:  3.7761 -  3.3044 0.99   1324  143 0.4238 0.3797      6.6502      6.6039|
|  4:  3.3044 -  3.0049 0.99   1331  152 0.4702 0.4332      6.5297       6.454|
|  5:  3.0049 -  2.7909 0.99   1313  147 0.5032 0.4475      6.3535      6.3454|
|  6:  2.7909 -  2.6273 0.99   1310  143 0.5004 0.5447       6.265      6.2165|
|  7:  2.6273 -  2.4963 0.99   1298  144 0.5146 0.5037      6.2302      6.1982|
|  8:  2.4963 -  2.3881 0.98   1294  147 0.5287 0.4943       6.184      6.1805|
|  9:  2.3881 -  2.2965 0.98   1293  137 0.5102 0.5465      6.1113      6.1607|
| 10:  2.2965 -  2.2175 1.00   1273  150 0.5226 0.4899       6.106      6.0628|
| 11:  2.2175 -  2.1484 0.98   1307  141 0.5196 0.5143      6.0283      6.0542|
| 12:  2.1484 -  2.0871 0.98   1270  145 0.5297 0.5051      5.9726      5.9843|
| 13:  2.0871 -  2.0323 0.99   1281  140 0.5251 0.4897      5.8689      5.7843|
| 14:  2.0323 -  1.9828 0.42    560   61 0.5221 0.5430       5.877      5.8226|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7332  1413   156  0.72  32.26   0.79     0.76      64706.46|
|  2:  4.7332 -  3.7761  1363   153  0.74  31.54   0.88     0.81      91243.32|
|  3:  3.7761 -  3.3044  1324   143  0.65  39.66   0.85     0.76      96161.72|
|  4:  3.3044 -  3.0049  1331   152  0.57  46.28   0.78     0.66      86321.32|
|  5:  3.0049 -  2.7909  1313   147  0.47  53.98   0.75     0.55      72785.28|
|  6:  2.7909 -  2.6273  1310   143  0.42  58.23   0.72     0.48      67805.59|
|  7:  2.6273 -  2.4963  1298   144  0.38  61.75   0.73     0.43      65110.47|
|  8:  2.4963 -  2.3881  1294   147  0.36  62.67   0.72     0.42      59128.59|
|  9:  2.3881 -  2.2965  1293   137  0.38  61.74   0.73     0.44      53199.66|
| 10:  2.2965 -  2.2175  1273   150  0.38  61.29   0.75     0.45      46815.97|
| 11:  2.2175 -  2.1484  1307   141  0.36  62.79   0.76     0.46      45288.60|
| 12:  2.1484 -  2.0871  1270   145  0.36  63.40   0.74     0.44      41383.24|
| 13:  2.0871 -  2.0323  1281   140  0.34  64.90   0.72     0.43      36497.15|
| 14:  2.0323 -  1.9828   560    61  0.38  61.44   0.75     0.42      29918.87|
|alpha:            min =        0.42 max =            0.81 mean =         0.54|
|beta:             min =    29918.87 max =        96161.72 mean =     62794.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.97 mean =        53.83|
|phase err.(test): min =        0.00 max =           89.99 mean =        54.15|
|-----------------------------------------------------------------------------|

============================== 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 = 11.755025             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.035   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.027059              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.117   (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 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      173 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2617 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3879 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5058 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6512 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7642 |
|-----------------------------------------------------------------------------|
|-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 |       54.106 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.765 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    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 = 12.034)------------------------------------------|
|    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: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4799   r_free= 0.4605   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.277076                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4647   r_free= 0.4441   ksol= 0.34   Bsol= 20.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,8.18,11.33,0.00,0.00,0.00); trace/3= 8.80                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.268148                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.016736             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.407   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.952270              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.667   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4647      final r-factor (work) = 0.3737          |
| start r-factor (free) = 0.4441      final r-factor (free) = 0.3924          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.5138 = 10.02 * 0.50 * 6.2710 + 1.00 * 54.1065                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0169 = 10.02 * 0.50 * 6.1656 + 1.00 * 0.1371                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3737      final r-factor (work) = 0.3232          |
| start r-factor (free) = 0.3924      final r-factor (free) = 0.3719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8858 = 0.95 * 1.00 * 6.1656 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7846 = 0.95 * 1.00 * 6.0579 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.37   13.07    None  None   None       |
|    all(noH): 2823   0      0.00    75.37   13.07    None  None   None       |
|    Sol.    : 438    0      0.00    75.37   27.51    None  None   None       |
|    Mac.    : 2385   0      0.00    61.66   10.42    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 -   7.537: 1124   |   5:    37.684 -  45.220:   66        |
|      1:     7.537 -  15.073:  783   |   6:    45.220 -  52.757:   56        |
|      2:    15.073 -  22.610:  443   |   7:    52.757 -  60.294:   18        |
|      3:    22.610 -  30.147:  210   |   8:    60.294 -  67.830:    6        |
|      4:    30.147 -  37.684:  114   |   9:    67.830 -  75.367:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3232 r_free = 0.3719             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3227 r_free = 0.3722             target_work(ml) = 6.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3227   r_free= 0.3722   ksol= 0.34   Bsol= 20.00   scale= 1.111   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,8.18,11.33,0.00,0.00,0.00); trace/3= 8.80                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.034418                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3188   r_free= 0.3691   ksol= 0.34   Bsol= 46.23   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,4.37,7.59,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.034548                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.313556              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.715   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.406132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.344  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3188      final r-factor (work) = 0.2318          |
| start r-factor (free) = 0.3691      final r-factor (free) = 0.2889          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2228 = 5.31 * 0.50 * 6.0546 + 1.00 * 0.1371                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7380 = 5.31 * 0.50 * 5.8950 + 1.00 * 0.0762                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2318      final r-factor (work) = 0.2075          |
| start r-factor (free) = 0.2889      final r-factor (free) = 0.2625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4100 = 0.41 * 1.00 * 5.8950 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3343 = 0.41 * 1.00 * 5.7157 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.16   12.55    None  None   None       |
|    all(noH): 2823   0      0.00    81.16   12.55    None  None   None       |
|    Sol.    : 438    0      0.00    81.16   33.14    None  None   None       |
|    Mac.    : 2385   0      0.00    61.55   8.77     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 -   8.116: 1419   |   5:    40.579 -  48.695:   83        |
|      1:     8.116 -  16.232:  749   |   6:    48.695 -  56.811:   47        |
|      2:    16.232 -  24.347:  242   |   7:    56.811 -  64.926:   22        |
|      3:    24.347 -  32.463:  126   |   8:    64.926 -  73.042:    4        |
|      4:    32.463 -  40.579:  129   |   9:    73.042 -  81.158:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2075 r_free = 0.2625             target_work(ml) = 5.672         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2075 r_free = 0.2624             target_work(ml) = 5.672         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2075   r_free= 0.2624   ksol= 0.34   Bsol= 46.23   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,4.37,7.59,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.671552                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2057   r_free= 0.2613   ksol= 0.32   Bsol= 57.12   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,2.58,4.87,0.00,0.00,0.00); trace/3= 3.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.672428                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.872893              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.657  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.527816              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.422  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2057      final r-factor (work) = 0.1547          |
| start r-factor (free) = 0.2613      final r-factor (free) = 0.2034          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2993 = 2.87 * 0.50 * 5.7246 + 1.00 * 0.0762                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0443 = 2.87 * 0.50 * 5.5556 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1547      final r-factor (work) = 0.1435          |
| start r-factor (free) = 0.2034      final r-factor (free) = 0.1928          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9442 = 0.53 * 1.00 * 5.5556 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8532 = 0.53 * 1.00 * 5.3794 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.96   13.14    None  None   None       |
|    all(noH): 2823   0      0.00    81.96   13.14    None  None   None       |
|    Sol.    : 438    0      1.59    81.96   37.52    None  None   None       |
|    Mac.    : 2385   0      0.00    76.36   8.67     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 -   8.196: 1517   |   5:    40.978 -  49.173:   96        |
|      1:     8.196 -  16.391:  679   |   6:    49.173 -  57.369:   75        |
|      2:    16.391 -  24.587:  186   |   7:    57.369 -  65.564:   40        |
|      3:    24.587 -  32.782:  113   |   8:    65.564 -  73.760:   17        |
|      4:    32.782 -  40.978:   94   |   9:    73.760 -  81.955:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1435 r_free = 0.1928             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1434 r_free = 0.1929             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1434   r_free= 0.1929   ksol= 0.32   Bsol= 57.12   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,2.58,4.87,0.00,0.00,0.00); trace/3= 3.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.355115                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1432   r_free= 0.1930   ksol= 0.33   Bsol= 57.12   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.07,4.13,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.355563                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.330346              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.242  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.203826              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.833  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1432      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1930      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3333 = 2.33 * 0.50 * 5.3806 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2436 = 2.33 * 0.50 * 5.3039 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1260      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1713          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0959 = 0.20 * 1.00 * 5.3039 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0929 = 0.20 * 1.00 * 5.2502 + 1.00 * 0.0227                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.39   12.72    None  None   None       |
|    all(noH): 2823   0      0.00    78.39   12.72    None  None   None       |
|    Sol.    : 438    0      2.24    78.39   35.92    None  None   None       |
|    Mac.    : 2385   0      0.00    76.61   8.46     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 -   7.839: 1496   |   5:    39.194 -  47.032:   91        |
|      1:     7.839 -  15.678:  712   |   6:    47.032 -  54.871:   76        |
|      2:    15.678 -  23.516:  181   |   7:    54.871 -  62.710:   36        |
|      3:    23.516 -  31.355:  104   |   8:    62.710 -  70.548:   19        |
|      4:    31.355 -  39.194:   97   |   9:    70.548 -  78.387:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1251 r_free = 0.1713             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1249 r_free = 0.1713             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1713   ksol= 0.33   Bsol= 57.12   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.07,4.13,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.237985                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1712   ksol= 0.33   Bsol= 57.12   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.91,1.94,3.91,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.237845                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.660422              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.672  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.013445              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.004   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1249      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1712      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0462 = 2.66 * 0.50 * 5.2492 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0035 = 2.66 * 0.50 * 5.2119 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2928 = 1.01 * 1.00 * 5.2119 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2625 = 1.01 * 1.00 * 5.1799 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.19   12.88    None  None   None       |
|    all(noH): 2823   0      0.00    80.19   12.88    None  None   None       |
|    Sol.    : 438    0      1.92    79.96   36.85    None  None   None       |
|    Mac.    : 2385   0      0.00    80.19   8.48     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 -   8.019: 1534   |   5:    40.094 -  48.113:   81        |
|      1:     8.019 -  16.038:  668   |   6:    48.113 -  56.132:   79        |
|      2:    16.038 -  24.057:  184   |   7:    56.132 -  64.151:   40        |
|      3:    24.057 -  32.075:  102   |   8:    64.151 -  72.170:   16        |
|      4:    32.075 -  40.094:  105   |   9:    72.170 -  80.189:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1634             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1634             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1634   ksol= 0.33   Bsol= 57.12   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.91,1.94,3.91,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180954                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7332 0.99   1413  156 0.0995 0.1333      5.4004       5.583|
|  2:  4.7332 -  3.7761 0.99   1363  153 0.0873 0.1209      5.4581      5.6775|
|  3:  3.7761 -  3.3044 0.99   1324  143 0.1112 0.1496      5.5148      5.8317|
|  4:  3.3044 -  3.0049 0.99   1331  152 0.1256 0.1778      5.4718      5.6582|
|  5:  3.0049 -  2.7909 0.99   1313  147 0.1375 0.1706       5.363      5.5898|
|  6:  2.7909 -  2.6273 0.99   1310  143 0.1266 0.2108      5.2315       5.527|
|  7:  2.6273 -  2.4963 0.99   1298  144 0.1353 0.1631      5.2254      5.3459|
|  8:  2.4963 -  2.3881 0.98   1294  147 0.1197 0.1661      5.1025      5.3625|
|  9:  2.3881 -  2.2965 0.98   1293  137 0.1261 0.1962      5.0889      5.3899|
| 10:  2.2965 -  2.2175 1.00   1273  150 0.1161 0.1712      4.9812      5.2146|
| 11:  2.2175 -  2.1484 0.98   1307  141 0.1170 0.1854      4.9775      5.3199|
| 12:  2.1484 -  2.0871 0.98   1270  145 0.1176 0.1786      4.9128      5.2177|
| 13:  2.0871 -  2.0323 0.99   1281  140 0.1124 0.1722      4.7925      5.0316|
| 14:  2.0323 -  1.9828 0.42    560   61 0.0940 0.1501      4.6437      4.8613|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7332  1413   156  0.94   9.40   0.97     0.95       7543.97|
|  2:  4.7332 -  3.7761  1363   153  0.95   8.43   1.01     1.00       9688.32|
|  3:  3.7761 -  3.3044  1324   143  0.93  12.05   1.02     1.02      11239.96|
|  4:  3.3044 -  3.0049  1331   152  0.91  14.35   1.01     0.99      10771.27|
|  5:  3.0049 -  2.7909  1313   147  0.90  16.37   1.00     0.98       8947.13|
|  6:  2.7909 -  2.6273  1310   143  0.89  16.74   0.97     0.94       7410.81|
|  7:  2.6273 -  2.4963  1298   144  0.90  16.47   0.99     0.95       6870.80|
|  8:  2.4963 -  2.3881  1294   147  0.90  16.29   0.99     0.97       5808.16|
|  9:  2.3881 -  2.2965  1293   137  0.90  16.70   0.99     0.95       5605.36|
| 10:  2.2965 -  2.2175  1273   150  0.90  16.11   1.00     0.96       4633.15|
| 11:  2.2175 -  2.1484  1307   141  0.89  17.10   0.98     0.93       4684.52|
| 12:  2.1484 -  2.0871  1270   145  0.90  16.43   1.00     1.00       4266.66|
| 13:  2.0871 -  2.0323  1281   140  0.90  16.91   0.99     0.97       3518.97|
| 14:  2.0323 -  1.9828   560    61  0.93  13.44   0.97     0.94       2529.83|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2529.83 max =        11239.96 mean =      6896.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.76|
|phase err.(test): min =        0.00 max =           88.89 mean =        14.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1627   ksol= 0.33   Bsol= 59.77   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.66,1.29,-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: 5.178997                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1627   ksol= 0.33   Bsol= 59.77   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.66,1.29,-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: 5.178997                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7332 0.99   1413  156 0.0992 0.1286      5.3892      5.5509|
|  2:  4.7332 -  3.7761 0.99   1363  153 0.0875 0.1179      5.4506      5.6588|
|  3:  3.7761 -  3.3044 0.99   1324  143 0.1113 0.1491      5.5102      5.8338|
|  4:  3.3044 -  3.0049 0.99   1331  152 0.1254 0.1789      5.4713      5.6596|
|  5:  3.0049 -  2.7909 0.99   1313  147 0.1374 0.1703      5.3632       5.588|
|  6:  2.7909 -  2.6273 0.99   1310  143 0.1266 0.2110      5.2315       5.527|
|  7:  2.6273 -  2.4963 0.99   1298  144 0.1353 0.1636      5.2253      5.3454|
|  8:  2.4963 -  2.3881 0.98   1294  147 0.1196 0.1663       5.102      5.3624|
|  9:  2.3881 -  2.2965 0.98   1293  137 0.1260 0.1959      5.0882       5.389|
| 10:  2.2965 -  2.2175 1.00   1273  150 0.1161 0.1713      4.9813      5.2145|
| 11:  2.2175 -  2.1484 0.98   1307  141 0.1169 0.1853      4.9774      5.3201|
| 12:  2.1484 -  2.0871 0.98   1270  145 0.1175 0.1785      4.9128      5.2176|
| 13:  2.0871 -  2.0323 0.99   1281  140 0.1123 0.1720      4.7922       5.031|
| 14:  2.0323 -  1.9828 0.42    560   61 0.0942 0.1499      4.6436       4.861|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7332  1413   156  0.94   9.17   0.97     0.94       7183.11|
|  2:  4.7332 -  3.7761  1363   153  0.95   8.15   1.01     1.00       9280.14|
|  3:  3.7761 -  3.3044  1324   143  0.93  11.88   1.02     1.02      10954.89|
|  4:  3.3044 -  3.0049  1331   152  0.91  14.35   1.01     0.99      10763.69|
|  5:  3.0049 -  2.7909  1313   147  0.90  16.39   1.00     0.98       8968.01|
|  6:  2.7909 -  2.6273  1310   143  0.89  16.73   0.98     0.95       7406.02|
|  7:  2.6273 -  2.4963  1298   144  0.90  16.45   0.99     0.95       6867.54|
|  8:  2.4963 -  2.3881  1294   147  0.90  16.28   0.99     0.97       5804.81|
|  9:  2.3881 -  2.2965  1293   137  0.90  16.70   1.00     0.96       5600.93|
| 10:  2.2965 -  2.2175  1273   150  0.90  16.11   1.00     0.96       4633.31|
| 11:  2.2175 -  2.1484  1307   141  0.89  17.10   0.99     0.93       4683.46|
| 12:  2.1484 -  2.0871  1270   145  0.90  16.44   1.00     1.01       4271.02|
| 13:  2.0871 -  2.0323  1281   140  0.90  16.90   1.00     0.97       3517.33|
| 14:  2.0323 -  1.9828   560    61  0.93  13.42   0.98     0.95       2525.86|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2525.86 max =        10954.89 mean =      6814.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.70|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.06|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.65    82.84   15.53    None  None   None       |
|    all(noH): 2823   0      2.65    82.84   15.53    None  None   None       |
|    Sol.    : 438    0      4.57    82.61   39.50    None  None   None       |
|    Mac.    : 2385   0      2.65    82.84   11.13    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:     2.649 -  10.668: 1534   |   5:    42.744 -  50.762:   81        |
|      1:    10.668 -  18.687:  668   |   6:    50.762 -  58.781:   79        |
|      2:    18.687 -  26.706:  184   |   7:    58.781 -  66.800:   40        |
|      3:    26.706 -  34.725:  102   |   8:    66.800 -  74.819:   16        |
|      4:    34.725 -  42.744:  105   |   9:    74.819 -  82.838:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.298 - 5.151
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 319
   mapped sites are within: 0.709 - 5.151

peak=   10.753 closest distance to " CB  VAL A 230 " =    1.448
peak=    8.220 closest distance to " CG2 VAL A 296 " =    1.262
peak=    6.125 closest distance to " CD2 LEU A   5 " =    1.247
peak=    5.941 closest distance to " NE2 GLN A  11 " =    1.160
peak=    5.851 closest distance to " CG  LEU A   5 " =    1.145
peak=    5.589 closest distance to " CG  PRO A  54 " =    1.338
peak=    5.581 closest distance to " NH2 ARG A  56 " =    2.129
peak=    5.524 closest distance to " O   HOH Z 142 " =    2.162
peak=    5.226 closest distance to " CG  LEU A 228 " =    1.138
peak=    4.985 closest distance to " O   HOH Z   9 " =    1.957
peak=    4.979 closest distance to " CB  GLN A 223 " =    1.485
peak=    4.904 closest distance to " CB  PRO A  54 " =    1.015
peak=    4.864 closest distance to " O   HOH Z 232 " =    2.284
peak=    4.834 closest distance to " CB  GLN A 183 " =    1.272
peak=    4.762 closest distance to " O   HOH Z 427 " =    2.700
peak=    4.648 closest distance to " CB  ASN A 148 " =    1.349
peak=    4.558 closest distance to " O   HOH Z 369 " =    2.193
peak=    4.505 closest distance to " NH1 ARG A 138 " =    1.078
peak=    4.411 closest distance to " CB  SER A  63 " =    1.237
peak=    4.349 closest distance to " O   HOH Z 346 " =    1.604
peak=    4.343 closest distance to " NH2AARG A 190 " =    1.883
peak=    4.336 closest distance to " O   HOH Z 126 " =    2.057
peak=    4.293 closest distance to " CG  LEU A 167 " =    1.289
peak=    4.271 closest distance to " O   PRO A 198 " =    1.606
peak=    4.270 closest distance to " CB  ASN A 142 " =    1.076
peak=    4.258 closest distance to " O   HOH Z 248 " =    1.510
peak=    4.258 closest distance to " CZ  PHE A 218 " =    1.093
peak=    4.223 closest distance to " CG  PRO A 213 " =    1.214
peak=    4.194 closest distance to " O   HOH Z 265 " =    1.986
peak=    4.187 closest distance to " CG  PRO A 198 " =    1.221
peak=    4.170 closest distance to " CB  ARG A  79 " =    1.528
peak=    4.161 closest distance to " ND2 ASN A 187 " =    1.672
peak=    4.156 closest distance to " CB  VAL A 265 " =    1.358
peak=    4.137 closest distance to " O   HOH Z   7 " =    1.272
peak=    4.124 closest distance to " CG  PRO A 243 " =    1.123
peak=    4.113 closest distance to " O   HOH Z 303 " =    2.122
peak=    4.110 closest distance to " O   SER A  87 " =    2.316
peak=    4.102 closest distance to " O   HOH Z 425 " =    1.416
peak=    4.092 closest distance to " O   HOH Z 287 " =    2.061
peak=    4.091 closest distance to " O   HOH Z  61 " =    1.758
peak=    4.067 closest distance to " CB  TRP A 266 " =    1.065
peak=    4.063 closest distance to " CB  ARG A 275 " =    0.937
peak=    4.057 closest distance to " O   HOH Z 380 " =    1.728
peak=    4.037 closest distance to " O   HOH Z 353 " =    2.503
peak=    4.035 closest distance to " O   HOH Z 298 " =    1.704
peak=    4.033 closest distance to " O   HOH Z 214 " =    2.138
peak=    4.019 closest distance to " CB  ARG A 190 " =    1.480
peak=    4.000 closest distance to " OG  SER A  97 " =    3.054
peak=    3.999 closest distance to " CD2 LEU A 228 " =    1.172
peak=    3.994 closest distance to " CB  VAL A 230 " =    1.219
peak=    3.978 closest distance to " CB  ASP A 124 " =    0.770
peak=    3.969 closest distance to " CA  ALA A  51 " =    1.019
peak=    3.966 closest distance to " N   PHE A 130 " =    1.311
peak=    3.946 closest distance to " CB  SER A   3 " =    1.374
peak=    3.941 closest distance to " O   HOH Z  43 " =    1.896
peak=    3.938 closest distance to " CB  GLU A 277 " =    3.652
peak=    3.926 closest distance to " O   HOH Z  78 " =    1.551
peak=    3.910 closest distance to " CB  VAL A 202 " =    1.597
peak=    3.909 closest distance to " O   HOH Z 423 " =    1.513
peak=    3.879 closest distance to " O   HOH Z 261 " =    1.575
peak=    3.878 closest distance to " CE  LYS A  76 " =    0.880
peak=    3.874 closest distance to " CH2 TRP A 266 " =    1.147
peak=    3.867 closest distance to " CG2 VAL A 257 " =    0.881
peak=    3.857 closest distance to " O   HOH Z 209 " =    2.323
peak=    3.845 closest distance to " CD  ARG A  66 " =    2.556
peak=    3.843 closest distance to " CA  VAL A 296 " =    1.085
peak=    3.831 closest distance to " O   HOH Z 193 " =    1.818
peak=    3.829 closest distance to " O   HOH Z 368 " =    2.075
peak=    3.826 closest distance to " NH1AARG A 145 " =    1.211
peak=    3.815 closest distance to " CB  TYR A 169 " =    0.719
peak=    3.814 closest distance to " CA  SER A  87 " =    0.971
peak=    3.810 closest distance to " O   HOH Z 234 " =    3.671
peak=    3.795 closest distance to " CA  VAL A 125 " =    1.182
peak=    3.793 closest distance to " CA  ARG A 195 " =    1.193
peak=    3.790 closest distance to " CB  SER A 216 " =    0.905
peak=    3.790 closest distance to " O   HOH Z 422 " =    2.663
peak=    3.785 closest distance to " O   HOH Z 359 " =    1.484
peak=    3.778 closest distance to " CB  ASN A  39 " =    0.946
peak=    3.777 closest distance to " O   HOH Z 180 " =    2.182
peak=    3.766 closest distance to " CD2 TRP A 179 " =    1.265
peak=    3.765 closest distance to " O   HOH Z 365 " =    3.017
peak=    3.765 closest distance to " O   HOH Z 272 " =    1.773
peak=    3.765 closest distance to " CB AVAL A  41 " =    1.230
peak=    3.765 closest distance to " CD  ARG A 159 " =    0.735
peak=    3.764 closest distance to " OD1 ASN A  69 " =    2.538
peak=    3.761 closest distance to " O   HOH Z 126 " =    1.528
peak=    3.744 closest distance to " O   HOH Z  40 " =    1.959
peak=    3.742 closest distance to " CA  TYR A  30 " =    0.982
peak=    3.741 closest distance to " O   HOH Z 158 " =    3.202
peak=    3.737 closest distance to " NE2 HIS A 207 " =    1.189
peak=    3.700 closest distance to " O   HOH Z  10 " =    1.761
peak=    3.698 closest distance to " CB  SER A 212 " =    1.284
peak=    3.689 closest distance to " CA  LYS A 117 " =    1.247
peak=    3.673 closest distance to " CB  GLU A 152 " =    1.228
peak=    3.673 closest distance to " CG2 ILE A 234 " =    0.895
peak=    3.673 closest distance to " O   HOH Z 406 " =    1.530
peak=    3.661 closest distance to " CE3 TRP A 150 " =    1.037
peak=    3.655 closest distance to " CD  ARG A 269 " =    0.946
peak=    3.646 closest distance to " CG1 ILE A 151 " =    1.154
peak=    3.645 closest distance to " CB  GLN A  88 " =    1.253
peak=    3.643 closest distance to " O   HOH Z 251 " =    1.505
peak=    3.638 closest distance to " N   ALA A 256 " =    1.095
peak=    3.636 closest distance to " O   HOH Z  21 " =    1.733
peak=    3.635 closest distance to " O   HOH Z 419 " =    1.960
peak=    3.629 closest distance to " O   HOH Z  68 " =    2.167
peak=    3.623 closest distance to " O   HOH Z 411 " =    3.576
peak=    3.621 closest distance to " CG2 THR A 221 " =    1.095
peak=    3.617 closest distance to " O   HOH Z  30 " =    1.577
peak=    3.616 closest distance to " CG2 ILE A  20 " =    1.539
peak=    3.613 closest distance to " CB  LYS A 117 " =    1.232
peak=    3.613 closest distance to " CB  GLU A 128 " =    0.920
peak=    3.606 closest distance to " O   HOH Z 258 " =    2.030
peak=    3.604 closest distance to " OG ASER A 258 " =    3.094
peak=    3.602 closest distance to " O  BHOH Z 338 " =    2.455
peak=    3.601 closest distance to " O   HOH Z 261 " =    1.993
peak=    3.584 closest distance to " CG AARG A 275 " =    1.237
peak=    3.582 closest distance to " CG1 VAL A 153 " =    1.035
peak=    3.574 closest distance to " CB  ASP A 140 " =    0.897
peak=    3.571 closest distance to " O   PHE A 192 " =    1.354
peak=    3.560 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.558 closest distance to " O   HOH Z  88 " =    3.094
peak=    3.553 closest distance to " O   HOH Z   1 " =    1.753
peak=    3.553 closest distance to " CB  MET A  40 " =    0.823
peak=    3.550 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.549 closest distance to " CD1 ILE A  33 " =    1.860
peak=    3.548 closest distance to " OE2 GLU A   2 " =    1.966
peak=    3.545 closest distance to " CB  ASN A 110 " =    1.155
peak=    3.544 closest distance to " O   HOH Z 218 " =    1.452
peak=    3.543 closest distance to " O   HOH Z   2 " =    1.585
peak=    3.535 closest distance to " O   HOH Z 286 " =    2.380
peak=    3.533 closest distance to " O   HOH Z 280 " =    3.012
peak=    3.527 closest distance to " O   HOH Z 211 " =    0.925
peak=    3.522 closest distance to " O   HOH Z  59 " =    1.859
peak=    3.520 closest distance to " O   HOH Z 368 " =    3.502
peak=    3.517 closest distance to " ND2 ASN A 249 " =    0.867
peak=    3.516 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.515 closest distance to " O   HOH Z 147 " =    1.667
peak=    3.502 closest distance to " CB  TRP A 179 " =    1.462
peak=    3.498 closest distance to " CD  LYS A  76 " =    1.798
peak=    3.497 closest distance to " O   HOH Z 290 " =    1.054
peak=    3.494 closest distance to " ND1 HIS A  86 " =    1.811
peak=    3.493 closest distance to " CA  ALA A 291 " =    0.853
peak=    3.488 closest distance to " CE1 TYR A 186 " =    1.314
peak=    3.487 closest distance to " CB  PRO A  90 " =    1.202
peak=    3.476 closest distance to " CA  ALA A 158 " =    1.286
peak=    3.469 closest distance to " O   HOH Z 213 " =    2.151
peak=    3.467 closest distance to " NZ  LYS A 117 " =    2.961
peak=    3.466 closest distance to " CB  TRP A 150 " =    1.319
peak=    3.462 closest distance to " CA  ASN A 215 " =    1.081
peak=    3.461 closest distance to " O   HOH Z   3 " =    2.049
peak=    3.455 closest distance to " N   SER A 135 " =    1.394
peak=    3.452 closest distance to " CA  THR A 264 " =    0.816
peak=    3.444 closest distance to " CB  SER A 210 " =    0.743
peak=    3.444 closest distance to " CG  GLN A  88 " =    1.077
peak=    3.439 closest distance to " CA  TYR A 116 " =    1.377
peak=    3.439 closest distance to " O   HOH Z 371 " =    2.848
peak=    3.433 closest distance to " CG  GLU A  37 " =    0.923
peak=    3.432 closest distance to " CA  ASN A 127 " =    1.079
peak=    3.431 closest distance to " CZ  PHE A  38 " =    1.172
peak=    3.428 closest distance to " O   HOH Z 203 " =    1.764
peak=    3.428 closest distance to " O   HOH Z 294 " =    1.542
peak=    3.425 closest distance to " O   HOH Z 305 " =    3.417
peak=    3.422 closest distance to " CB  GLN A  89 " =    1.263
peak=    3.412 closest distance to " CB  LEU A 143 " =    1.182
peak=    3.411 closest distance to " CG  GLN A  77 " =    1.016
peak=    3.410 closest distance to " O   HOH Z 148 " =    2.189
peak=    3.410 closest distance to " O   HOH Z  90 " =    2.211
peak=    3.408 closest distance to " O   HOH Z 437 " =    1.520
peak=    3.405 closest distance to " O   HOH Z 409 " =    2.799
peak=    3.405 closest distance to " C   ALA A 299 " =    0.941
peak=    3.401 closest distance to " O   HOH Z 133 " =    2.674
peak=    3.386 closest distance to " O   HOH Z 148 " =    3.521
peak=    3.385 closest distance to " CG1 ILE A  49 " =    1.535
peak=    3.383 closest distance to " O   HOH Z   1 " =    1.823
peak=    3.380 closest distance to " CA  ALA A 160 " =    1.023
peak=    3.371 closest distance to " CB  ARG A  79 " =    0.928
peak=    3.371 closest distance to " CA  ARG A 159 " =    1.210
peak=    3.368 closest distance to " CG BARG A 102 " =    1.856
peak=    3.359 closest distance to " N   CYS A 260 " =    0.752
peak=    3.359 closest distance to " OE2 GLU A  53 " =    1.888
peak=    3.355 closest distance to " O   HOH Z  92 " =    2.435
peak=    3.351 closest distance to " O   ASP A 124 " =    1.199
peak=    3.350 closest distance to " CA  ARG A  36 " =    1.070
peak=    3.349 closest distance to " O   HOH Z 128 " =    2.175
peak=    3.347 closest distance to " CD BLYS A 290 " =    1.080
peak=    3.345 closest distance to " OG BSER A 134 " =    3.000
peak=    3.343 closest distance to " O   HOH Z  20 " =    1.538
peak=    3.340 closest distance to " CB  THR A  52 " =    0.884
peak=    3.334 closest distance to " O   HOH Z 299 " =    4.308
peak=    3.334 closest distance to " CA  ASP A 124 " =    0.709
peak=    3.328 closest distance to " O   HOH Z 184 " =    1.314
peak=    3.328 closest distance to " CB  HIS A 108 " =    0.848
peak=    3.327 closest distance to " CA  ALA A 233 " =    1.060
peak=    3.318 closest distance to " CB  ALA A 248 " =    1.044
peak=    3.313 closest distance to " OG  SER A  62 " =    2.817
peak=    3.312 closest distance to " OG BSER A 164 " =    2.265
peak=    3.311 closest distance to " O   ASN A  74 " =    1.526
peak=    3.306 closest distance to " CG2AVAL A  72 " =    1.606
peak=    3.303 closest distance to " O   HOH Z  97 " =    2.127
peak=    3.299 closest distance to " CB  LEU A 300 " =    0.856
peak=    3.297 closest distance to " CA  LEU A 282 " =    1.130
peak=    3.293 closest distance to " CD2 TYR A 186 " =    1.136
peak=    3.292 closest distance to " O   HOH Z 263 " =    1.709
peak=    3.292 closest distance to " O   HOH Z 403 " =    1.568
peak=    3.291 closest distance to " CG  MET A 185 " =    1.188
peak=    3.290 closest distance to " CB  SER A 273 " =    0.897
peak=    3.289 closest distance to " O   PRO A 198 " =    1.217
peak=    3.289 closest distance to " O   HOH Z  88 " =    3.232
peak=    3.287 closest distance to " CB  LEU A 228 " =    1.252
peak=    3.287 closest distance to " N   ASN A  39 " =    1.231
peak=    3.285 closest distance to " CB  ALA A 114 " =    1.298
peak=    3.285 closest distance to " O   HOH Z 285 " =    2.155
peak=    3.285 closest distance to " CA  MET A 105 " =    0.965
peak=    3.282 closest distance to " CB  ALA A   9 " =    1.609
peak=    3.280 closest distance to " N   ASN A 127 " =    1.337
peak=    3.280 closest distance to " O   ASP A 200 " =    1.546
peak=    3.278 closest distance to " CG  GLN A 278 " =    1.304
peak=    3.275 closest distance to " O   HOH Z 438 " =    2.708
peak=    3.275 closest distance to " CB  THR A  82 " =    1.274
peak=    3.271 closest distance to " O   HOH Z 329 " =    4.148
peak=    3.270 closest distance to " CB  VAL A 268 " =    0.833
peak=    3.268 closest distance to " O   HOH Z  85 " =    2.202
peak=    3.266 closest distance to " O   HOH Z 166 " =    3.986
peak=    3.264 closest distance to " CA  ASN A  74 " =    1.319
peak=    3.262 closest distance to " CB  SER A  62 " =    1.053
peak=    3.261 closest distance to " OG  SER A  62 " =    2.950
peak=    3.260 closest distance to " O   HOH Z 193 " =    1.710
peak=    3.260 closest distance to " O   HOH Z 213 " =    2.084
peak=    3.258 closest distance to " O   HOH Z 197 " =    3.220
peak=    3.253 closest distance to " O   HOH Z 260 " =    1.565
peak=    3.252 closest distance to " O   HOH Z  80 " =    1.521
peak=    3.242 closest distance to " O   HOH Z 116 " =    3.078
peak=    3.240 closest distance to " CB  ASP A 171 " =    1.158
peak=    3.239 closest distance to " O   HOH Z 196 " =    1.398
peak=    3.238 closest distance to " CD1 LEU A 300 " =    1.154
peak=    3.238 closest distance to " OG  SER A 135 " =    1.197
peak=    3.237 closest distance to " CA  ALA A 295 " =    1.151
peak=    3.232 closest distance to " O   HOH Z 325 " =    2.210
peak=    3.230 closest distance to " CZ3 TRP A  92 " =    1.270
peak=    3.223 closest distance to " CG2 ILE A 120 " =    1.346
peak=    3.221 closest distance to " N   GLN A 278 " =    1.487
peak=    3.216 closest distance to " CD1 LEU A  96 " =    0.712
peak=    3.213 closest distance to " O   THR A 251 " =    1.151
peak=    3.208 closest distance to " O   HOH Z 171 " =    4.113
peak=    3.205 closest distance to " O   HOH Z 172 " =    3.131
peak=    3.203 closest distance to " O   HOH Z 340 " =    2.051
peak=    3.203 closest distance to " O   HOH Z 154 " =    2.254
peak=    3.199 closest distance to " CB  ALA A  43 " =    0.834
peak=    3.199 closest distance to " CE3 TRP A  85 " =    1.216
peak=    3.196 closest distance to " O   HOH Z 343 " =    3.302
peak=    3.193 closest distance to " CA  GLY A 267 " =    1.032
peak=    3.193 closest distance to " O   HOH Z 145 " =    1.413
peak=    3.192 closest distance to " NE2 GLN A  73 " =    1.276
peak=    3.191 closest distance to " CG  LYS A 119 " =    1.105
peak=    3.191 closest distance to " CA  ASP A 162 " =    0.999
peak=    3.191 closest distance to " O   HOH Z   4 " =    1.494
peak=    3.189 closest distance to " CA  TYR A  30 " =    1.070
peak=    3.188 closest distance to " CA  ILE A 234 " =    0.984
peak=    3.187 closest distance to " NH2AARG A 275 " =    3.416
peak=    3.186 closest distance to " CB  THR A 157 " =    1.122
peak=    3.182 closest distance to " CD  ARG A 195 " =    3.502
peak=    3.181 closest distance to " CA  ARG A 139 " =    1.016
peak=    3.181 closest distance to " CB  ALA A 104 " =    0.722
peak=    3.177 closest distance to " NH2BARG A 190 " =    1.484
peak=    3.173 closest distance to " OG1 THR A 279 " =    1.392
peak=    3.172 closest distance to " O   HOH Z 187 " =    2.279
peak=    3.171 closest distance to " CB  ILE A 120 " =    1.401
peak=    3.171 closest distance to " CG  MET A 185 " =    1.023
peak=    3.170 closest distance to " CA  ALA A  21 " =    1.220
peak=    3.170 closest distance to " CG  GLN A  89 " =    1.538
peak=    3.170 closest distance to " NH2AARG A 145 " =    1.152
peak=    3.168 closest distance to " CB  ASN A 187 " =    1.114
peak=    3.168 closest distance to " O   HOH Z 109 " =    2.665
peak=    3.167 closest distance to " O   HOH Z 371 " =    3.322
peak=    3.166 closest distance to " CB  TYR A 116 " =    0.917
peak=    3.162 closest distance to " OG1 THR A 264 " =    0.728
peak=    3.160 closest distance to " O   HOH Z 132 " =    2.605
peak=    3.159 closest distance to " CB  ALA A   1 " =    4.885
peak=    3.158 closest distance to " CB  ALA A 160 " =    1.366
peak=    3.158 closest distance to " CB  ARG A 139 " =    1.002
peak=    3.155 closest distance to " NZ  LYS A  48 " =    1.265
peak=    3.155 closest distance to " CB  ALA A  34 " =    1.167
peak=    3.155 closest distance to " O   PHE A  61 " =    1.386
peak=    3.153 closest distance to " O   MET A 105 " =    1.768
peak=    3.153 closest distance to " CB  LEU A  83 " =    0.762
peak=    3.146 closest distance to " CA  ARG A 102 " =    1.175
peak=    3.145 closest distance to " O   HOH Z 392 " =    1.231
peak=    3.144 closest distance to " NH1 ARG A  14 " =    0.898
peak=    3.141 closest distance to " O   PRO A  90 " =    1.641
peak=    3.139 closest distance to " CB  THR A  31 " =    1.637
peak=    3.138 closest distance to " O   HOH Z 394 " =    3.707
peak=    3.133 closest distance to " O   HOH Z 227 " =    1.812
peak=    3.132 closest distance to " O   HOH Z 380 " =    5.151
peak=    3.125 closest distance to " N   ASP A 162 " =    1.168
peak=    3.124 closest distance to " CA  ASN A 217 " =    1.262
peak=    3.123 closest distance to " CB  ASN A 173 " =    1.065
peak=    3.122 closest distance to " CB  ASN A 215 " =    1.239
peak=    3.114 closest distance to " CD  ARG A 195 " =    1.198
peak=    3.109 closest distance to " CD  GLN A 194 " =    1.400
peak=    3.108 closest distance to " CA  LYS A 290 " =    1.291
peak=    3.106 closest distance to " CA  ILE A 106 " =    0.776
peak=    3.098 closest distance to " CD  GLN A 240 " =    1.550
peak=    3.095 closest distance to " CB  PRO A 243 " =    1.714
peak=    3.091 closest distance to " O   HOH Z 389 " =    1.799
peak=    3.089 closest distance to " O   HOH Z 350 " =    1.582
peak=    3.086 closest distance to " O   HOH Z  61 " =    1.630
peak=    3.084 closest distance to " OG BSER A  99 " =    2.181
peak=    3.084 closest distance to " CB  VAL A 250 " =    1.088
peak=    3.082 closest distance to " O   SER A 164 " =    1.286
peak=    3.070 closest distance to " CD1 ILE A 106 " =    0.850
peak=    3.061 closest distance to " CB  ALA A 291 " =    1.346
peak=    3.050 closest distance to " NH2BARG A 145 " =    1.985
peak=    3.048 closest distance to " CG  ARG A 159 " =    0.923
peak=    3.044 closest distance to " CB  ARG A 102 " =    0.926
peak=    3.019 closest distance to " CB  ALA A 227 " =    0.903
peak=    3.010 closest distance to " O   HOH Z  40 " =    1.418

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.710 - 5.673
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.710 - 5.673

peak=   -4.521 closest distance to " CG2 VAL A 230 " =    0.794
peak=   -4.427 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.327 closest distance to " CD  ARG A  14 " =    3.264
peak=   -4.318 closest distance to " O   HOH Z 211 " =    0.870
peak=   -4.241 closest distance to " OG BSER A 134 " =    1.296
peak=   -4.208 closest distance to " CD  ARG A 156 " =    2.111
peak=   -4.127 closest distance to " O   HOH Z 231 " =    1.956
peak=   -4.099 closest distance to " CZ2 TRP A  92 " =    2.883
peak=   -4.093 closest distance to " CD  GLN A  58 " =    0.923
peak=   -4.054 closest distance to " CG1 VAL A 112 " =    2.678
peak=   -4.005 closest distance to " CG2 VAL A 296 " =    1.401
peak=   -3.948 closest distance to " O   HOH Z 131 " =    4.063
peak=   -3.931 closest distance to " CB  VAL A 230 " =    1.096
peak=   -3.910 closest distance to " OG  SER A  97 " =    2.261
peak=   -3.872 closest distance to " CB  ALA A  43 " =    2.625
peak=   -3.867 closest distance to " O   HOH Z 411 " =    5.433
peak=   -3.864 closest distance to " O   PRO A 163 " =    1.982
peak=   -3.861 closest distance to " C   HIS A 108 " =    1.198
peak=   -3.857 closest distance to " CD  GLN A 223 " =    2.276
peak=   -3.844 closest distance to " CA  GLY A 241 " =    2.354
peak=   -3.831 closest distance to " CG2 VAL A 202 " =    2.734
peak=   -3.809 closest distance to " O   HOH Z 351 " =    1.482
peak=   -3.804 closest distance to " CB  PHE A 192 " =    1.938
peak=   -3.790 closest distance to " O   PRO A 198 " =    1.193
peak=   -3.743 closest distance to " O   VAL A  67 " =    2.622
peak=   -3.739 closest distance to " O   HOH Z 429 " =    1.962
peak=   -3.731 closest distance to " O   HOH Z 231 " =    1.151
peak=   -3.723 closest distance to " CE2 TYR A  30 " =    2.624
peak=   -3.712 closest distance to " CB  ALA A 161 " =    2.570
peak=   -3.704 closest distance to " N   THR A 157 " =    1.558
peak=   -3.702 closest distance to " CG2 THR A  18 " =    2.857
peak=   -3.685 closest distance to " O   HOH Z 166 " =    2.233
peak=   -3.681 closest distance to " O   HOH Z  73 " =    2.158
peak=   -3.680 closest distance to " CB  PRO A 163 " =    2.417
peak=   -3.668 closest distance to " CD1 LEU A 255 " =    2.857
peak=   -3.664 closest distance to " O   HOH Z 359 " =    3.080
peak=   -3.655 closest distance to " O   HOH Z 185 " =    2.304
peak=   -3.651 closest distance to " CD1 TYR A 247 " =    2.840
peak=   -3.648 closest distance to " O   HOH Z  44 " =    2.381
peak=   -3.636 closest distance to " O   HOH Z 389 " =    1.473
peak=   -3.631 closest distance to " CE3 TRP A 150 " =    2.399
peak=   -3.628 closest distance to " O   HOH Z 394 " =    1.560
peak=   -3.626 closest distance to " O   HOH Z 290 " =    1.247
peak=   -3.626 closest distance to " CD1 LEU A 101 " =    2.327
peak=   -3.626 closest distance to " O   HOH Z 111 " =    1.632
peak=   -3.618 closest distance to " O   VAL A 189 " =    2.584
peak=   -3.617 closest distance to " CD2 HIS A 207 " =    2.261
peak=   -3.616 closest distance to " O   HOH Z 377 " =    2.114
peak=   -3.611 closest distance to " ND2 ASN A  45 " =    2.018
peak=   -3.591 closest distance to " O   SER A  22 " =    2.257
peak=   -3.587 closest distance to " O   HOH Z  11 " =    1.881
peak=   -3.577 closest distance to " O   VAL A  67 " =    2.849
peak=   -3.572 closest distance to " ND2 ASN A 187 " =    1.506
peak=   -3.570 closest distance to " O   HOH Z 389 " =    2.148
peak=   -3.565 closest distance to " O   HOH Z 166 " =    2.028
peak=   -3.537 closest distance to " CG  TRP A 266 " =    1.895
peak=   -3.536 closest distance to " CD2 TYR A 293 " =    1.967
peak=   -3.535 closest distance to " CG1 VAL A 250 " =    2.759
peak=   -3.526 closest distance to " CA  ASP A  27 " =    2.463
peak=   -3.524 closest distance to " O   HOH Z 189 " =    2.387
peak=   -3.521 closest distance to " OG  SER A  87 " =    1.348
peak=   -3.521 closest distance to " O   HOH Z 147 " =    1.988
peak=   -3.517 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.514 closest distance to " OD1 ASP A 171 " =    1.657
peak=   -3.512 closest distance to " O   GLY A  17 " =    1.160
peak=   -3.508 closest distance to " CD1 LEU A 228 " =    2.359
peak=   -3.506 closest distance to " O   HOH Z  51 " =    0.896
peak=   -3.503 closest distance to " CE BMET A  47 " =    1.346
peak=   -3.500 closest distance to " NH2AARG A 275 " =    5.297
peak=   -3.499 closest distance to " O   HOH Z 295 " =    1.608
peak=   -3.492 closest distance to " CG1 VAL A 112 " =    2.893
peak=   -3.491 closest distance to " CZ3 TRP A 179 " =    1.203
peak=   -3.489 closest distance to " O   HOH Z 198 " =    2.023
peak=   -3.487 closest distance to " ND2 ASN A  45 " =    1.312
peak=   -3.480 closest distance to " O   HOH Z  60 " =    1.976
peak=   -3.477 closest distance to " O   HOH Z  52 " =    1.443
peak=   -3.473 closest distance to " O   HOH Z  38 " =    1.925
peak=   -3.473 closest distance to " O   HOH Z 191 " =    5.505
peak=   -3.472 closest distance to " O   HOH Z 350 " =    1.792
peak=   -3.467 closest distance to " O   HOH Z 412 " =    4.347
peak=   -3.465 closest distance to " ND2 ASN A 249 " =    2.380
peak=   -3.459 closest distance to " O   HOH Z  65 " =    1.154
peak=   -3.457 closest distance to " ND2 ASN A  60 " =    1.645
peak=   -3.455 closest distance to " CG  ASP A 231 " =    0.783
peak=   -3.444 closest distance to " O   HOH Z 103 " =    1.801
peak=   -3.444 closest distance to " OXT GLY A 302 " =    3.165
peak=   -3.441 closest distance to " O   HOH Z 149 " =    2.223
peak=   -3.441 closest distance to " CB  ALA A 114 " =    2.502
peak=   -3.436 closest distance to " CB  TRP A  85 " =    2.617
peak=   -3.434 closest distance to " N   ALA A 226 " =    2.091
peak=   -3.430 closest distance to " OG BSER A 134 " =    1.820
peak=   -3.429 closest distance to " O   HOH Z 216 " =    1.157
peak=   -3.426 closest distance to " CA  GLY A 203 " =    2.480
peak=   -3.417 closest distance to " O   HOH Z 100 " =    1.279
peak=   -3.415 closest distance to " OH  TYR A 172 " =    1.799
peak=   -3.406 closest distance to " CG  GLU A 277 " =    1.243
peak=   -3.404 closest distance to " CA  GLY A  98 " =    1.912
peak=   -3.398 closest distance to " CD2 PHE A 225 " =    1.155
peak=   -3.374 closest distance to " C   LEU A 222 " =    0.886
peak=   -3.372 closest distance to " N   ALA A  43 " =    2.566
peak=   -3.365 closest distance to " C   LEU A 143 " =    1.142
peak=   -3.363 closest distance to " O   GLU A  53 " =    1.854
peak=   -3.356 closest distance to " OE1 GLN A  88 " =    1.007
peak=   -3.356 closest distance to " CG  MET A 105 " =    0.976
peak=   -3.355 closest distance to " O   HOH Z 140 " =    1.543
peak=   -3.355 closest distance to " O   HOH Z 193 " =    1.346
peak=   -3.355 closest distance to " CE  MET A 105 " =    2.397
peak=   -3.354 closest distance to " O   GLY A 203 " =    2.404
peak=   -3.341 closest distance to " O   HOH Z 292 " =    1.574
peak=   -3.338 closest distance to " CA  ALA A 158 " =    1.313
peak=   -3.337 closest distance to " CD2 LEU A   5 " =    1.117
peak=   -3.331 closest distance to " O   ASP A  27 " =    1.887
peak=   -3.325 closest distance to " O   HOH Z 134 " =    3.973
peak=   -3.324 closest distance to " CA  GLY A 241 " =    3.200
peak=   -3.321 closest distance to " O   HOH Z 250 " =    1.685
peak=   -3.320 closest distance to " N   ALA A 248 " =    1.576
peak=   -3.316 closest distance to " O   HOH Z 102 " =    1.576
peak=   -3.314 closest distance to " CD  LYS A 166 " =    2.612
peak=   -3.307 closest distance to " O   ARG A 145 " =    1.354
peak=   -3.303 closest distance to " O   HOH Z 176 " =    0.710
peak=   -3.295 closest distance to " O   HOH Z  43 " =    1.770
peak=   -3.292 closest distance to " CZ2 TRP A 274 " =    0.925
peak=   -3.288 closest distance to " O   HOH Z 285 " =    2.159
peak=   -3.284 closest distance to " O   HOH Z 318 " =    2.016
peak=   -3.282 closest distance to " O   GLY A  80 " =    2.489
peak=   -3.281 closest distance to " OG  SER A  62 " =    4.391
peak=   -3.279 closest distance to " C   ARG A 269 " =    1.462
peak=   -3.278 closest distance to " O   HOH Z 276 " =    1.813
peak=   -3.276 closest distance to " O   PRO A 198 " =    1.401
peak=   -3.275 closest distance to " C   MET A 188 " =    1.453
peak=   -3.273 closest distance to " O   HOH Z  63 " =    1.819
peak=   -3.268 closest distance to " O   HOH Z 106 " =    1.805
peak=   -3.265 closest distance to " CG  PHE A 283 " =    2.582
peak=   -3.259 closest distance to " CB  ALA A 248 " =    2.343
peak=   -3.259 closest distance to " C   GLU A 236 " =    0.931
peak=   -3.252 closest distance to " CD2 TYR A 247 " =    2.467
peak=   -3.246 closest distance to " NH2 ARG A 219 " =    1.680
peak=   -3.244 closest distance to " O   HOH Z 108 " =    1.399
peak=   -3.242 closest distance to " NE2 GLN A 278 " =    1.862
peak=   -3.237 closest distance to " O   HOH Z  68 " =    1.381
peak=   -3.235 closest distance to " O   HOH Z 179 " =    2.226
peak=   -3.234 closest distance to " O   HOH Z 252 " =    3.827
peak=   -3.232 closest distance to " O   HOH Z 138 " =    1.336
peak=   -3.231 closest distance to " CZ  PHE A 192 " =    2.678
peak=   -3.228 closest distance to " NE2 GLN A 194 " =    1.874
peak=   -3.226 closest distance to " O   HOH Z 313 " =    1.655
peak=   -3.220 closest distance to " O   ILE A  49 " =    1.745
peak=   -3.214 closest distance to " CB  TYR A  15 " =    2.242
peak=   -3.211 closest distance to " CE1 PHE A  59 " =    2.021
peak=   -3.208 closest distance to " O   PHE A 218 " =    1.610
peak=   -3.205 closest distance to " O   HOH Z 275 " =    1.481
peak=   -3.205 closest distance to " O   HOH Z 323 " =    1.792
peak=   -3.205 closest distance to " CG1 VAL A 296 " =    1.408
peak=   -3.204 closest distance to " CA  GLY A 302 " =    2.884
peak=   -3.197 closest distance to " O   HOH Z 275 " =    1.881
peak=   -3.195 closest distance to " CG2 ILE A 263 " =    2.398
peak=   -3.190 closest distance to " CB  HIS A  81 " =    0.949
peak=   -3.188 closest distance to " O   HOH Z 238 " =    0.992
peak=   -3.183 closest distance to " O   HOH Z 336 " =    5.673
peak=   -3.183 closest distance to " CG  GLN A  88 " =    0.867
peak=   -3.181 closest distance to " CB  GLN A  11 " =    1.713
peak=   -3.180 closest distance to " OH  TYR A 214 " =    1.206
peak=   -3.178 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.177 closest distance to " O   GLY A 229 " =    1.860
peak=   -3.175 closest distance to " CD2 PHE A  61 " =    1.962
peak=   -3.172 closest distance to " O   HOH Z 390 " =    2.215
peak=   -3.170 closest distance to " O   HOH Z   9 " =    3.148
peak=   -3.169 closest distance to " O   SER A 210 " =    1.913
peak=   -3.164 closest distance to " NH2 ARG A  79 " =    2.143
peak=   -3.160 closest distance to " CD  LYS A 289 " =    2.393
peak=   -3.159 closest distance to " NE2 GLN A 240 " =    1.644
peak=   -3.155 closest distance to " CB  ASP A 132 " =    2.389
peak=   -3.153 closest distance to " O   HOH Z 165 " =    2.114
peak=   -3.152 closest distance to " ND2 ASN A  69 " =    1.843
peak=   -3.149 closest distance to " CD1 ILE A 199 " =    2.549
peak=   -3.143 closest distance to " O   HOH Z 281 " =    2.661
peak=   -3.139 closest distance to " O   GLY A 211 " =    1.248
peak=   -3.138 closest distance to " OE2 GLU A 152 " =    1.273
peak=   -3.135 closest distance to " OH  TYR A 247 " =    1.876
peak=   -3.133 closest distance to " CG2 ILE A 151 " =    2.592
peak=   -3.129 closest distance to " CB  SER A 210 " =    1.076
peak=   -3.121 closest distance to " N   SER A 276 " =    1.439
peak=   -3.118 closest distance to " CA  GLY A 133 " =    1.951
peak=   -3.117 closest distance to " O   HOH Z 144 " =    1.251
peak=   -3.116 closest distance to " NZ  LYS A 166 " =    1.227
peak=   -3.113 closest distance to " O   HOH Z  10 " =    1.499
peak=   -3.109 closest distance to " CB  ALA A 129 " =    2.503
peak=   -3.108 closest distance to " CB  ALA A 291 " =    2.376
peak=   -3.106 closest distance to " CG2 VAL A 189 " =    1.822
peak=   -3.106 closest distance to " O   HOH Z 111 " =    4.437
peak=   -3.104 closest distance to " O   SER A 135 " =    1.434
peak=   -3.098 closest distance to " O   HOH Z 357 " =    2.080
peak=   -3.094 closest distance to " O   THR A 178 " =    1.029
peak=   -3.073 closest distance to " O   GLN A 240 " =    2.108
peak=   -3.073 closest distance to " O   TYR A 186 " =    1.687
peak=   -3.070 closest distance to " O   GLN A 240 " =    2.521
peak=   -3.068 closest distance to " CG  GLU A 152 " =    1.463
peak=   -3.055 closest distance to " O   HOH Z 166 " =    1.526
peak=   -3.054 closest distance to " CA  GLY A 133 " =    2.257
peak=   -3.047 closest distance to " O   ALA A  51 " =    1.326
peak=   -3.047 closest distance to " OE1 GLN A 183 " =    1.603
peak=   -3.045 closest distance to " N   ALA A 248 " =    1.872
peak=   -3.032 closest distance to " O   HOH Z 407 " =    3.002

================= 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    :  0.4733 0.4566   6.273961e+00   6.249821e+00
   1_bss:  0.4647 0.4441   6.268148e+00   6.240076e+00
   1_xyz:  0.3737 0.3924   6.135101e+00   6.158335e+00
   1_adp:  0.3232 0.3719   6.035152e+00   6.123432e+00
   1_occ:  0.3227 0.3722   6.034418e+00   6.124222e+00
   2_bss:  0.3188 0.3691   6.034548e+00   6.122978e+00
   2_xyz:  0.2318 0.2889   5.764951e+00   5.924251e+00
   2_adp:  0.2075 0.2625   5.671784e+00   5.843077e+00
   2_occ:  0.2075 0.2624   5.671552e+00   5.843332e+00
   3_bss:  0.2057 0.2613   5.672428e+00   5.844681e+00
   3_xyz:  0.1547 0.2034   5.415831e+00   5.620502e+00
   3_adp:  0.1435 0.1928   5.355374e+00   5.571740e+00
   3_occ:  0.1434 0.1929   5.355115e+00   5.571734e+00
   4_bss:  0.1432 0.1930   5.355563e+00   5.572505e+00
   4_xyz:  0.1260 0.1751   5.251667e+00   5.482918e+00
   4_adp:  0.1251 0.1713   5.238306e+00   5.461566e+00
   4_occ:  0.1249 0.1713   5.237985e+00   5.461588e+00
   5_bss:  0.1249 0.1712   5.237845e+00   5.461591e+00
   5_xyz:  0.1178 0.1634   5.189730e+00   5.426169e+00
   5_adp:  0.1155 0.1634   5.181110e+00   5.427448e+00
   5_occ:  0.1154 0.1634   5.180954e+00   5.427257e+00
   5_bss:  0.1154 0.1627   5.178997e+00   5.423204e+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:  0.344  20.000   6.903   8.179  11.327   0.000   0.000   0.000
   1_xyz:  0.344  20.000   6.903   8.179  11.327   0.000   0.000   0.000
   1_adp:  0.344  20.000   6.903   8.179  11.327   0.000   0.000   0.000
   1_occ:  0.344  20.000   6.903   8.179  11.327   0.000   0.000   0.000
   2_bss:  0.335  46.234   3.788   4.367   7.593   0.000   0.000   0.000
   2_xyz:  0.335  46.234   3.788   4.367   7.593   0.000   0.000   0.000
   2_adp:  0.335  46.234   3.788   4.367   7.593   0.000   0.000   0.000
   2_occ:  0.335  46.234   3.788   4.367   7.593   0.000   0.000   0.000
   3_bss:  0.318  57.121   2.354   2.577   4.873   0.000   0.000   0.000
   3_xyz:  0.318  57.121   2.354   2.577   4.873   0.000   0.000   0.000
   3_adp:  0.318  57.121   2.354   2.577   4.873   0.000   0.000   0.000
   3_occ:  0.318  57.121   2.354   2.577   4.873   0.000   0.000   0.000
   4_bss:  0.327  57.121   1.935   2.066   4.131   0.000   0.000   0.000
   4_xyz:  0.327  57.121   1.935   2.066   4.131   0.000   0.000   0.000
   4_adp:  0.327  57.121   1.935   2.066   4.131   0.000   0.000   0.000
   4_occ:  0.327  57.121   1.935   2.066   4.131   0.000   0.000   0.000
   5_bss:  0.327  57.121   1.912   1.941   3.906   0.000   0.000   0.000
   5_xyz:  0.327  57.121   1.912   1.941   3.906   0.000   0.000   0.000
   5_adp:  0.327  57.121   1.912   1.941   3.906   0.000   0.000   0.000
   5_occ:  0.327  57.121   1.912   1.941   3.906   0.000   0.000   0.000
   5_bss:  0.327  59.770  -0.629  -0.656   1.285  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.865 0.4721  0.5444    62794.762
   1_bss:  53.606 0.4742  0.7075    60833.896
   1_xyz:  43.916 0.5945  0.8588    43289.429
   1_adp:  40.138 0.6407  0.9628    38367.110
   1_occ:  40.208 0.6398  0.9609    38455.185
   2_bss:  39.933 0.6430  0.8526    38070.808
   2_xyz:  29.633 0.7608  0.9769    21607.723
   2_adp:  25.954 0.8017  0.9982    17561.151
   2_occ:  25.973 0.8014  0.9973    17542.728
   3_bss:  25.923 0.8021  0.9302    17611.791
   3_xyz:  19.323 0.8680  0.9815    10449.438
   3_adp:  18.051 0.8802  0.9851     9496.443
   3_occ:  18.052 0.8801  0.9852     9495.970
   4_bss:  18.070 0.8801  0.9657     9538.394
   4_xyz:  16.060 0.8978  0.9730     7814.317
   4_adp:  15.528 0.9027  0.9729     7509.078
   4_occ:  15.545 0.9025  0.9726     7514.344
   5_bss:  15.540 0.9025  0.9685     7515.131
   5_xyz:  14.723 0.9093  0.9730     6930.647
   5_adp:  14.696 0.9097  0.9684     6898.202
   5_occ:  14.695 0.9097  0.9684     6896.492
   5_bss:  14.639 0.9101  0.9705     6814.473
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4106e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4106e+01
   1_xyz:   1.667  0.013  0.107 18.332  0.006  4.111   1.3712e-01
   1_adp:   1.667  0.013  0.107 18.332  0.006  4.111   1.3712e-01
   1_occ:   1.667  0.013  0.107 18.332  0.006  4.111   1.3712e-01
   2_bss:   1.667  0.013  0.107 18.332  0.006  4.111   1.3712e-01
   2_xyz:   1.127  0.008  0.081 16.436  0.005  4.111   7.6205e-02
   2_adp:   1.127  0.008  0.081 16.436  0.005  4.111   7.6205e-02
   2_occ:   1.127  0.008  0.081 16.436  0.005  4.111   7.6205e-02
   3_bss:   1.127  0.008  0.081 16.436  0.005  4.111   7.6205e-02
   3_xyz:   1.033  0.007  0.079 15.989  0.003  4.126   6.3922e-02
   3_adp:   1.033  0.007  0.079 15.989  0.003  4.126   6.3922e-02
   3_occ:   1.033  0.007  0.079 15.989  0.003  4.126   6.3922e-02
   4_bss:   1.033  0.007  0.079 15.989  0.003  4.126   6.3922e-02
   4_xyz:   1.009  0.008  0.078 15.802  0.003  4.133   6.3654e-02
   4_adp:   1.009  0.008  0.078 15.802  0.003  4.133   6.3654e-02
   4_occ:   1.009  0.008  0.078 15.802  0.003  4.133   6.3654e-02
   5_bss:   1.009  0.008  0.078 15.802  0.003  4.133   6.3654e-02
   5_xyz:   1.077  0.009  0.085 15.580  0.004  4.113   7.0482e-02
   5_adp:   1.077  0.009  0.085 15.580  0.004  4.113   7.0482e-02
   5_occ:   1.077  0.009  0.085 15.580  0.004  4.113   7.0482e-02
   5_bss:   1.077  0.009  0.085 15.580  0.004  4.113   7.0482e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0147e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0147e+00
   1_xyz:  13.723  0.169  0.411 85.200  0.029  2.162   9.9665e-02
   1_adp:  13.723  0.169  0.411 85.200  0.029  2.162   9.9665e-02
   1_occ:  13.723  0.169  0.411 85.200  0.029  2.162   9.9665e-02
   2_bss:  13.723  0.169  0.411 85.200  0.029  2.162   9.9665e-02
   2_xyz:   6.366  0.067  0.249 89.992  0.044  2.279   5.0784e-02
   2_adp:   6.366  0.067  0.249 89.992  0.044  2.279   5.0784e-02
   2_occ:   6.366  0.067  0.249 89.992  0.044  2.279   5.0784e-02
   3_bss:   6.366  0.067  0.249 89.992  0.044  2.279   5.0784e-02
   3_xyz:   7.304  0.057  0.368 89.645  0.029  2.309   4.9388e-02
   3_adp:   7.304  0.057  0.368 89.645  0.029  2.309   4.9388e-02
   3_occ:   7.304  0.057  0.368 89.645  0.029  2.309   4.9388e-02
   4_bss:   7.304  0.057  0.368 89.645  0.029  2.309   4.9388e-02
   4_xyz:   8.344  0.053  0.408 81.767  0.038  2.354   4.2132e-02
   4_adp:   8.344  0.053  0.408 81.767  0.038  2.354   4.2132e-02
   4_occ:   8.344  0.053  0.408 81.767  0.038  2.354   4.2132e-02
   5_bss:   8.344  0.053  0.408 81.767  0.038  2.354   4.2132e-02
   5_xyz:   7.093  0.047  0.488 89.797  0.040  2.289   4.7729e-02
   5_adp:   7.093  0.047  0.488 89.797  0.040  2.289   4.7729e-02
   5_occ:   7.093  0.047  0.488 89.797  0.040  2.289   4.7729e-02
   5_bss:   7.093  0.047  0.488 89.797  0.040  2.289   4.7729e-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:  75.37   0.00  13.07  61.66   0.00  10.42  75.37   0.00  27.51
   1_occ:  75.37   0.00  13.07  61.66   0.00  10.42  75.37   0.00  27.51
   2_bss:  75.37   0.00  13.07  61.66   0.00  10.42  75.37   0.00  27.51
   2_xyz:  75.37   0.00  13.07  61.66   0.00  10.42  75.37   0.00  27.51
   2_adp:  81.16   0.00  12.55  61.55   0.00   8.77  81.16   0.00  33.14
   2_occ:  81.16   0.00  12.55  61.55   0.00   8.77  81.16   0.00  33.14
   3_bss:  81.16   0.00  12.55  61.55   0.00   8.77  81.16   0.00  33.14
   3_xyz:  81.16   0.00  12.55  61.55   0.00   8.77  81.16   0.00  33.14
   3_adp:  81.96   0.00  13.14  76.36   0.00   8.67  81.96   1.59  37.52
   3_occ:  81.96   0.00  13.14  76.36   0.00   8.67  81.96   1.59  37.52
   4_bss:  81.96   0.00  13.14  76.36   0.00   8.67  81.96   1.59  37.52
   4_xyz:  81.96   0.00  13.14  76.36   0.00   8.67  81.96   1.59  37.52
   4_adp:  78.39   0.00  12.72  76.61   0.00   8.46  78.39   2.24  35.92
   4_occ:  78.39   0.00  12.72  76.61   0.00   8.46  78.39   2.24  35.92
   5_bss:  78.39   0.00  12.72  76.61   0.00   8.46  78.39   2.24  35.92
   5_xyz:  78.39   0.00  12.72  76.61   0.00   8.46  78.39   2.24  35.92
   5_adp:  80.19   0.00  12.88  80.19   0.00   8.48  79.96   1.92  36.85
   5_occ:  80.19   0.00  12.88  80.19   0.00   8.48  79.96   1.92  36.85
   5_bss:  82.84   2.65  15.53  82.84   2.65  11.13  82.61   4.57  39.50
------------------------------------------------------------------------
 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:    1.255    0.020    0.409
   1_adp:    1.255    0.020    0.409
   1_occ:    1.255    0.020    0.409
   2_bss:    1.255    0.020    0.409
   2_xyz:    1.652    0.026    0.563
   2_adp:    1.652    0.026    0.563
   2_occ:    1.652    0.026    0.563
   3_bss:    1.652    0.026    0.563
   3_xyz:    1.598    0.051    0.629
   3_adp:    1.598    0.051    0.629
   3_occ:    1.598    0.051    0.629
   4_bss:    1.598    0.051    0.629
   4_xyz:    1.724    0.023    0.661
   4_adp:    1.724    0.023    0.661
   4_occ:    1.724    0.023    0.661
   5_bss:    1.724    0.023    0.661
   5_xyz:    1.823    0.037    0.678
   5_adp:    1.823    0.037    0.678
   5_occ:    1.823    0.037    0.678
   5_bss:    1.823    0.037    0.678
------------------------------------------------------------------------

CPU time actual refinement: 328.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_768/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_768/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_768/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_768/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_768/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.85 
  Macro-tasks:
    bulk solvent and scale       = 40.97  
    individual site refinement   = 133.62 
    weights calculation          = 31.05  
    collect and process          = 6.38   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 212.13 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 100.46 
    alpha_beta                      = 8.07   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 110.75 
    fmodel                         = 7.13   
    r_factors                      = 0.26   
    phase_errors                   = 10.37  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 240.80 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.617 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    656 calls, 100.19 s
gradients_fft:          601 calls,  97.50 s

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

# Date 2008-01-16 Time 02:22:24 PST -0800 (1200478944.94 s)
Start R-work = 0.4733, R-free = 0.4566 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1798 (no bulk solvent and anisotropic scale)

Start R-work = 0.4647, R-free = 0.4441
Final R-work = 0.1154, R-free = 0.1627