# Date 2008-01-16 Time 03:02:35 PST -0800 (1200481355.54 s)
#phil __OFF__

Command line arguments: "../1077.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4477
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1077

-------------------------------------------------------------------------------
  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: (71.3037, 47.8686, 88.5498, 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: 2.82, per 1000 atoms: 1.00


================================== 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: (71.3037, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.03059
Completeness in resolution range: 0.972883
Completeness with d_max=infinity: 0.9698

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   2.0306

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: (71.3037, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.03059
Completeness in resolution range: 0.972883
Completeness with d_max=infinity: 0.9698

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2595 -  4.3443 [2117/2141]  1903   214  10.1%
  bin  2:  4.3443 -  3.4614 [2037/2056]  1836   201   9.9%
  bin  3:  3.4614 -  3.0278 [2007/2026]  1808   199   9.9%
  bin  4:  3.0278 -  2.7527 [1980/2010]  1776   204  10.3%
  bin  5:  2.7527 -  2.5564 [1981/2000]  1786   195   9.8%
  bin  6:  2.5564 -  2.4063 [1960/1985]  1764   196  10.0%
  bin  7:  2.4063 -  2.2862 [1956/1984]  1762   194   9.9%
  bin  8:  2.2862 -  2.1870 [1948/1984]  1752   196  10.1%
  bin  9:  2.1870 -  2.1030 [1929/1971]  1735   194  10.1%
  bin 10:  2.1030 -  2.0306 [1674/1978]  1508   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1077/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: 0.12 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:
        1.75 -     2.38: 14
        2.38 -     3.01: 1931
        3.01 -     3.64: 4467
        3.64 -     4.27: 8835
        4.27 -     4.90: 12272
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.748 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.975 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.019 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.019 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27514 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_1077/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1077/model_refine_001.geo

CPU time processing inputs: 8.18


============================ 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 = 71.30375 47.8686 88.54975 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: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5201   r_free= 0.5091   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.99 A                  |
| x-ray target function (ml) for work reflections: 6.309445                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8450 0.99   1379  153 0.4288 0.4186      6.6482      6.6127|
|  2:  4.8450 -  3.8662 0.99   1312  149 0.4642 0.5035      6.8892      7.0013|
|  3:  3.8662 -  3.3836 0.99   1306  145 0.5027 0.4657      6.7594      6.7222|
|  4:  3.3836 -  3.0770 0.99   1288  136 0.5174 0.4640      6.5895      6.5053|
|  5:  3.0770 -  2.8580 0.99   1269  144 0.5400 0.5013      6.4079      6.4326|
|  6:  2.8580 -  2.6905 0.99   1275  144 0.5404 0.5661      6.3125      6.2219|
|  7:  2.6905 -  2.5564 0.99   1280  142 0.5557 0.4876      6.2637        6.18|
|  8:  2.5564 -  2.4456 0.98   1259  137 0.5487 0.4897      6.2024      6.2104|
|  9:  2.4456 -  2.3518 0.98   1252  143 0.5475 0.6553      6.1307      6.1709|
| 10:  2.3518 -  2.2709 0.99   1266  136 0.5691 0.5568      6.1386      6.1569|
| 11:  2.2709 -  2.2001 0.98   1258  142 0.5399 0.5443      6.0502      6.0854|
| 12:  2.2001 -  2.1374 0.97   1232  139 0.5590 0.5259      5.9952      6.0519|
| 13:  2.1374 -  2.0812 1.00   1255  137 0.5463 0.5025      5.9068      5.8595|
| 14:  2.0812 -  2.0306 0.79    999  112 0.5711 0.5744       5.856      5.7913|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8450  1379   153  0.64  39.11   0.76     0.67      88943.58|
|  2:  4.8450 -  3.8662  1312   149  0.63  41.40   0.83     0.67     137433.86|
|  3:  3.8662 -  3.3836  1306   145  0.51  50.83   0.77     0.61     144051.53|
|  4:  3.3836 -  3.0770  1288   136  0.40  59.35   0.75     0.48     124603.87|
|  5:  3.0770 -  2.8580  1269   144  0.33  65.32   0.70     0.39      94657.54|
|  6:  2.8580 -  2.6905  1275   144  0.30  67.54   0.68     0.34      81559.46|
|  7:  2.6905 -  2.5564  1280   142  0.28  69.17   0.68     0.31      73004.64|
|  8:  2.5564 -  2.4456  1259   137  0.22  73.25   0.71     0.26      68620.98|
|  9:  2.4456 -  2.3518  1252   143  0.14  79.72   0.67     0.16      66468.93|
| 10:  2.3518 -  2.2709  1266   136  0.08  83.80   0.67     0.10      62031.43|
| 11:  2.2709 -  2.2001  1258   142  0.12  81.42   0.72     0.14      56803.21|
| 12:  2.2001 -  2.1374  1232   139  0.16  78.06   0.70     0.20      50183.71|
| 13:  2.1374 -  2.0812  1255   137  0.14  79.59   0.70     0.16      42486.67|
| 14:  2.0812 -  2.0306   999   112  0.15  79.15   0.67     0.16      35887.81|
|alpha:            min =        0.10 max =            0.67 mean =         0.34|
|beta:             min =    35887.81 max =       144051.53 mean =     81664.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.30|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.17|
|phase err.(test): min =        0.00 max =           89.96 mean =        67.21|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.554960             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.070   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.873991              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 86.405   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      669 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1467 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2550 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3795 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4922 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6426 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7490 |
|-----------------------------------------------------------------------------|
|-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 |       54.976 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.718 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.572)------------------------------------------|
|    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 = 12.572)------------------------------------------|
|    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: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5241   r_free= 0.5163   ksol= 0.00   Bsol= 0.00   scale= 0.718    |
|                                                                             |
| 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:   1.00 A                  |
| x-ray target function (ml) for work reflections: 6.309907                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5148   r_free= 0.5061   ksol= 0.30   Bsol= 80.00   scale= 0.922   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.22,9.35,10.27,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.02 A                  |
| x-ray target function (ml) for work reflections: 5.534352                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.883400             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.644   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.352976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.983   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5148      final r-factor (work) = 0.4615          |
| start r-factor (free) = 0.5061      final r-factor (free) = 0.4758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 123.9960 = 21.88 * 0.50 * 6.3080 + 1.00 * 54.9760                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.2507 = 21.88 * 0.50 * 5.4921 + 1.00 * 0.1581                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4615      final r-factor (work) = 0.4182          |
| start r-factor (free) = 0.4758      final r-factor (free) = 0.4638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9375 = 2.35 * 1.00 * 5.4921 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.6615 = 2.35 * 1.00 * 6.2175 + 1.00 * 0.0319                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    137.38  19.39    None  None   None       |
|    all(noH): 2823   0      0.00    137.38  19.39    None  None   None       |
|    Sol.    : 438    0      0.00    137.38  31.95    None  None   None       |
|    Mac.    : 2385   0      0.00    98.34   17.08    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 -  13.738: 1355   |   5:    68.688 -  82.426:   39        |
|      1:    13.738 -  27.475:  777   |   6:    82.426 -  96.163:   13        |
|      2:    27.475 -  41.213:  372   |   7:    96.163 - 109.901:    5        |
|      3:    41.213 -  54.950:  168   |   8:   109.901 - 123.638:    1        |
|      4:    54.950 -  68.688:   91   |   9:   123.638 - 137.376:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4182 r_free = 0.4638             target_work(ml) = 6.206         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4173 r_free = 0.4641             target_work(ml) = 6.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4173   r_free= 0.4641   ksol= 0.30   Bsol= 80.00   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.22,9.35,10.27,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.205448                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4158   r_free= 0.4600   ksol= 0.33   Bsol= 91.89   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,5.77,6.56,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.206430                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.144294             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.365  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.703930              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.914  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4158      final r-factor (work) = 0.3594          |
| start r-factor (free) = 0.4600      final r-factor (free) = 0.4267          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7716 = 11.14 * 0.50 * 6.2120 + 1.00 * 0.1577                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.3582 = 11.14 * 0.50 * 6.1487 + 1.00 * 0.0970                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3594      final r-factor (work) = 0.3506          |
| start r-factor (free) = 0.4267      final r-factor (free) = 0.4156          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3773 = 0.70 * 1.00 * 6.1487 + 1.00 * 0.0491                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3314 = 0.70 * 1.00 * 6.1090 + 1.00 * 0.0311                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    140.07  17.43    None  None   None       |
|    all(noH): 2823   0      0.00    140.07  17.43    None  None   None       |
|    Sol.    : 438    0      0.00    140.07  32.02    None  None   None       |
|    Mac.    : 2385   0      0.00    82.95   14.75    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 -  14.007: 1462   |   5:    70.034 -  84.041:   27        |
|      1:    14.007 -  28.014:  860   |   6:    84.041 -  98.048:    4        |
|      2:    28.014 -  42.021:  315   |   7:    98.048 - 112.055:    1        |
|      3:    42.021 -  56.027:  100   |   8:   112.055 - 126.062:    2        |
|      4:    56.027 -  70.034:   51   |   9:   126.062 - 140.068:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3506 r_free = 0.4156             target_work(ml) = 6.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3504 r_free = 0.4157             target_work(ml) = 6.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3504   r_free= 0.4157   ksol= 0.33   Bsol= 91.89   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,5.77,6.56,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.095175                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3495   r_free= 0.4139   ksol= 0.33   Bsol= 83.89   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,3.75,4.31,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.096044                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.672918             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.905  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.391769              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.119   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3495      final r-factor (work) = 0.2681          |
| start r-factor (free) = 0.4139      final r-factor (free) = 0.3250          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.8424 = 13.67 * 0.50 * 6.1063 + 1.00 * 0.0970                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.1543 = 13.67 * 0.50 * 6.0020 + 1.00 * 0.1216                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2681      final r-factor (work) = 0.2318          |
| start r-factor (free) = 0.3250      final r-factor (free) = 0.2981          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.3785 = 2.39 * 1.00 * 6.0020 + 1.00 * 0.0231                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.9226 = 2.39 * 1.00 * 5.8116 + 1.00 * 0.0225                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    136.51  17.73    None  None   None       |
|    all(noH): 2823   0      0.00    136.51  17.73    None  None   None       |
|    Sol.    : 438    0      0.00    136.51  43.74    None  None   None       |
|    Mac.    : 2385   0      0.00    88.90   12.96    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 -  13.651: 1607   |   5:    68.256 -  81.907:   52        |
|      1:    13.651 -  27.302:  648   |   6:    81.907 -  95.558:   20        |
|      2:    27.302 -  40.954:  246   |   7:    95.558 - 109.209:    1        |
|      3:    40.954 -  54.605:  135   |   8:   109.209 - 122.861:    3        |
|      4:    54.605 -  68.256:  110   |   9:   122.861 - 136.512:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2318 r_free = 0.2981             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2313 r_free = 0.2982             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2313   r_free= 0.2982   ksol= 0.33   Bsol= 83.89   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,3.75,4.31,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.775990                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2304   r_free= 0.2970   ksol= 0.35   Bsol= 99.31   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,1.85,2.65,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.774942                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.126405              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.741  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.466408              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.006  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2304      final r-factor (work) = 0.1886          |
| start r-factor (free) = 0.2970      final r-factor (free) = 0.2454          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0264 = 5.13 * 0.50 * 5.8149 + 1.00 * 0.1216                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6866 = 5.13 * 0.50 * 5.6985 + 1.00 * 0.0802                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1886      final r-factor (work) = 0.1710          |
| start r-factor (free) = 0.2454      final r-factor (free) = 0.2295          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3789 = 1.47 * 1.00 * 5.6985 + 1.00 * 0.0226                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1631 = 1.47 * 1.00 * 5.5528 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.90  17.17    None  None   None       |
|    all(noH): 2823   0      0.00    124.90  17.17    None  None   None       |
|    Sol.    : 438    0      1.03    124.90  48.57    None  None   None       |
|    Mac.    : 2385   0      0.00    101.36  11.41    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 -  12.490: 1700   |   5:    62.450 -  74.940:   83        |
|      1:    12.490 -  24.980:  581   |   6:    74.940 -  87.429:   46        |
|      2:    24.980 -  37.470:  183   |   7:    87.429 -  99.919:   20        |
|      3:    37.470 -  49.960:  108   |   8:    99.919 - 112.409:    9        |
|      4:    49.960 -  62.450:   90   |   9:   112.409 - 124.899:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1710 r_free = 0.2295             target_work(ml) = 5.517         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1709 r_free = 0.2297             target_work(ml) = 5.517         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1709   r_free= 0.2297   ksol= 0.35   Bsol= 99.31   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,1.85,2.65,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.517076                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1710   r_free= 0.2302   ksol= 0.35   Bsol= 99.31   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,1.85,2.65,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.517592                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.511619              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.075  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.204158              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.972  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1710      final r-factor (work) = 0.1493          |
| start r-factor (free) = 0.2302      final r-factor (free) = 0.2044          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8296 = 3.51 * 0.50 * 5.5524 + 1.00 * 0.0806                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6719 = 3.51 * 0.50 * 5.4635 + 1.00 * 0.0791                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1471          |
| start r-factor (free) = 0.2044      final r-factor (free) = 0.1943          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1356 = 0.20 * 1.00 * 5.4635 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1143 = 0.20 * 1.00 * 5.3967 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.03  15.45    None  None   None       |
|    all(noH): 2823   0      0.00    117.03  15.45    None  None   None       |
|    Sol.    : 438    0      1.88    117.03  43.17    None  None   None       |
|    Mac.    : 2385   0      0.00    93.05   10.36    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 -  11.703: 1769   |   5:    58.514 -  70.216:   64        |
|      1:    11.703 -  23.406:  571   |   6:    70.216 -  81.919:   38        |
|      2:    23.406 -  35.108:  146   |   7:    81.919 -  93.622:   17        |
|      3:    35.108 -  46.811:  117   |   8:    93.622 - 105.325:    8        |
|      4:    46.811 -  58.514:   92   |   9:   105.325 - 117.027:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1471 r_free = 0.1943             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1469 r_free = 0.1944             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1469   r_free= 0.1944   ksol= 0.35   Bsol= 99.31   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,1.85,2.65,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.368670                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8450 0.99   1379  153 0.1106 0.1425      5.4837      5.6268|
|  2:  4.8450 -  3.8662 0.99   1312  149 0.1008 0.1320      5.5924      5.8422|
|  3:  3.8662 -  3.3836 0.99   1306  145 0.1325 0.1752      5.6912      5.9951|
|  4:  3.3836 -  3.0770 0.99   1288  136 0.1564 0.1936      5.6733      5.8251|
|  5:  3.0770 -  2.8580 0.99   1269  144 0.1841 0.2249      5.6142      5.7571|
|  6:  2.8580 -  2.6905 0.99   1275  144 0.1655 0.2676      5.4775      5.7377|
|  7:  2.6905 -  2.5564 0.99   1280  142 0.1685 0.2171      5.4257      5.5966|
|  8:  2.5564 -  2.4456 0.98   1259  137 0.1695 0.1981      5.3702      5.5469|
|  9:  2.4456 -  2.3518 0.98   1252  143 0.1667 0.2383      5.2918      5.5451|
| 10:  2.3518 -  2.2709 0.99   1266  136 0.1541 0.2141      5.2107      5.3849|
| 11:  2.2709 -  2.2001 0.98   1258  142 0.1581 0.2046      5.1786      5.3676|
| 12:  2.2001 -  2.1374 0.97   1232  139 0.1490 0.2141      5.0822      5.4636|
| 13:  2.1374 -  2.0812 1.00   1255  137 0.1548 0.1907      5.0153      5.1632|
| 14:  2.0812 -  2.0306 0.79    999  112 0.1481 0.2076      4.9089      5.1599|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8450  1379   153  0.93  10.85   0.95     0.93       9034.17|
|  2:  4.8450 -  3.8662  1312   149  0.94  10.29   1.00     0.97      12141.76|
|  3:  3.8662 -  3.3836  1306   145  0.91  14.52   1.02     1.01      15846.77|
|  4:  3.3836 -  3.0770  1288   136  0.89  17.35   1.00     0.97      15390.05|
|  5:  3.0770 -  2.8580  1269   144  0.85  21.66   1.01     0.99      14616.25|
|  6:  2.8580 -  2.6905  1275   144  0.85  21.25   0.98     0.93      11820.25|
|  7:  2.6905 -  2.5564  1280   142  0.85  21.36   1.00     0.96      10697.94|
|  8:  2.5564 -  2.4456  1259   137  0.86  20.39   0.99     0.95       9089.95|
|  9:  2.4456 -  2.3518  1252   143  0.86  20.87   1.01     0.95       8054.85|
| 10:  2.3518 -  2.2709  1266   136  0.86  20.37   1.00     0.94       6756.53|
| 11:  2.2709 -  2.2001  1258   142  0.87  20.07   1.00     0.94       6539.14|
| 12:  2.2001 -  2.1374  1232   139  0.88  19.22   1.01     1.00       5674.81|
| 13:  2.1374 -  2.0812  1255   137  0.87  19.36   0.98     0.96       4813.05|
| 14:  2.0812 -  2.0306   999   112  0.88  18.51   0.96     0.91       3746.54|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3746.54 max =        15846.77 mean =      9716.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.91 mean =        18.21|
|phase err.(test): min =        0.00 max =           89.67 mean =        17.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1469   r_free= 0.1943   ksol= 0.33   Bsol= 85.06   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,-0.13,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.368334                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1469   r_free= 0.1943   ksol= 0.33   Bsol= 85.06   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,-0.13,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.368334                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8450 0.99   1379  153 0.1109 0.1424      5.4769      5.6218|
|  2:  4.8450 -  3.8662 0.99   1312  149 0.1014 0.1306      5.5917      5.8311|
|  3:  3.8662 -  3.3836 0.99   1306  145 0.1325 0.1757        5.69      5.9949|
|  4:  3.3836 -  3.0770 0.99   1288  136 0.1570 0.1940      5.6758      5.8292|
|  5:  3.0770 -  2.8580 0.99   1269  144 0.1846 0.2250      5.6169      5.7578|
|  6:  2.8580 -  2.6905 0.99   1275  144 0.1656 0.2673      5.4781      5.7369|
|  7:  2.6905 -  2.5564 0.99   1280  142 0.1685 0.2174      5.4265      5.5978|
|  8:  2.5564 -  2.4456 0.98   1259  137 0.1696 0.1983      5.3703      5.5473|
|  9:  2.4456 -  2.3518 0.98   1252  143 0.1665 0.2383      5.2914      5.5452|
| 10:  2.3518 -  2.2709 0.99   1266  136 0.1539 0.2144      5.2106      5.3853|
| 11:  2.2709 -  2.2001 0.98   1258  142 0.1578 0.2051      5.1783      5.3687|
| 12:  2.2001 -  2.1374 0.97   1232  139 0.1490 0.2140      5.0821      5.4633|
| 13:  2.1374 -  2.0812 1.00   1255  137 0.1549 0.1906      5.0147      5.1634|
| 14:  2.0812 -  2.0306 0.79    999  112 0.1483 0.2063      4.9081      5.1565|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8450  1379   153  0.93  10.76   0.95     0.92       8903.46|
|  2:  4.8450 -  3.8662  1312   149  0.94  10.15   1.00     0.97      11990.59|
|  3:  3.8662 -  3.3836  1306   145  0.91  14.46   1.01     1.01      15754.99|
|  4:  3.3836 -  3.0770  1288   136  0.89  17.39   1.00     0.96      15427.20|
|  5:  3.0770 -  2.8580  1269   144  0.85  21.68   1.00     0.99      14667.51|
|  6:  2.8580 -  2.6905  1275   144  0.85  21.26   0.97     0.92      11842.75|
|  7:  2.6905 -  2.5564  1280   142  0.85  21.36   0.99     0.95      10711.83|
|  8:  2.5564 -  2.4456  1259   137  0.86  20.38   0.98     0.94       9085.34|
|  9:  2.4456 -  2.3518  1252   143  0.86  20.87   1.00     0.94       8057.39|
| 10:  2.3518 -  2.2709  1266   136  0.86  20.37   0.99     0.93       6758.19|
| 11:  2.2709 -  2.2001  1258   142  0.87  20.09   0.98     0.92       6552.83|
| 12:  2.2001 -  2.1374  1232   139  0.88  19.22   0.99     0.98       5672.76|
| 13:  2.1374 -  2.0812  1255   137  0.87  19.33   0.96     0.95       4800.93|
| 14:  2.0812 -  2.0306   999   112  0.88  18.46   0.95     0.90       3727.94|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     3727.94 max =        15754.99 mean =      9696.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.19|
|phase err.(test): min =        0.00 max =           89.65 mean =        17.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    118.55  16.97    None  None   None       |
|    all(noH): 2823   0      1.52    118.55  16.97    None  None   None       |
|    Sol.    : 438    0      3.40    118.55  44.69    None  None   None       |
|    Mac.    : 2385   0      1.52    94.57   11.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.520 -  13.223: 1769   |   5:    60.034 -  71.736:   64        |
|      1:    13.223 -  24.926:  571   |   6:    71.736 -  83.439:   38        |
|      2:    24.926 -  36.628:  146   |   7:    83.439 -  95.142:   17        |
|      3:    36.628 -  48.331:  117   |   8:    95.142 - 106.845:    8        |
|      4:    48.331 -  60.034:   92   |   9:   106.845 - 118.547:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.637 - 5.833
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 328
   mapped sites are within: 0.712 - 5.833

peak=    7.086 closest distance to " O   HOH Z 390 " =    1.168
peak=    7.051 closest distance to " CB  VAL A 230 " =    1.419
peak=    6.916 closest distance to " CD1AILE A 234 " =    1.492
peak=    6.427 closest distance to " O   HOH Z 120 " =    1.494
peak=    6.136 closest distance to " O  BHOH Z 338 " =    1.364
peak=    5.946 closest distance to " O   HOH Z 400 " =    1.026
peak=    5.592 closest distance to " O   HOH Z 117 " =    1.721
peak=    5.496 closest distance to " O   HOH Z 210 " =    1.617
peak=    5.356 closest distance to " O   HOH Z 102 " =    1.598
peak=    5.080 closest distance to " CA  VAL A 230 " =    1.229
peak=    5.058 closest distance to " CB  SER A  63 " =    1.271
peak=    4.971 closest distance to " O   HOH Z 107 " =    1.503
peak=    4.966 closest distance to " O   HOH Z  67 " =    1.371
peak=    4.902 closest distance to " O   HOH Z  54 " =    1.483
peak=    4.806 closest distance to " O   HOH Z  84 " =    1.022
peak=    4.764 closest distance to " O   HOH Z 411 " =    3.604
peak=    4.744 closest distance to " CB  GLN A 183 " =    1.201
peak=    4.738 closest distance to " CD2 LEU A 228 " =    1.342
peak=    4.664 closest distance to " CG1 ILE A 120 " =    1.053
peak=    4.652 closest distance to " CB  GLN A 223 " =    1.592
peak=    4.647 closest distance to " O   HOH Z  49 " =    1.798
peak=    4.615 closest distance to " CG AARG A 275 " =    1.390
peak=    4.589 closest distance to " CZ  PHE A 218 " =    1.204
peak=    4.575 closest distance to " O   HOH Z 154 " =    1.863
peak=    4.572 closest distance to " O   HOH Z 247 " =    1.630
peak=    4.557 closest distance to " N   SER A 164 " =    0.945
peak=    4.503 closest distance to " CD  GLN A  88 " =    1.080
peak=    4.474 closest distance to " O   HOH Z 128 " =    1.734
peak=    4.470 closest distance to " CB  ASP A 124 " =    0.820
peak=    4.433 closest distance to " CG1 VAL A 296 " =    1.224
peak=    4.427 closest distance to " O   HOH Z 248 " =    1.592
peak=    4.419 closest distance to " O   HOH Z 425 " =    1.857
peak=    4.401 closest distance to " NH2AARG A 145 " =    1.098
peak=    4.375 closest distance to " O   HOH Z 431 " =    1.511
peak=    4.365 closest distance to " O   HOH Z 279 " =    1.069
peak=    4.337 closest distance to " O   HOH Z  54 " =    1.610
peak=    4.335 closest distance to " CG2 VAL A 296 " =    1.125
peak=    4.298 closest distance to " CD2 LEU A   5 " =    1.183
peak=    4.283 closest distance to " O   HOH Z 394 " =    1.621
peak=    4.276 closest distance to " O   HOH Z 426 " =    1.154
peak=    4.270 closest distance to " O   HOH Z 130 " =    1.137
peak=    4.270 closest distance to " CG  LEU A   5 " =    1.337
peak=    4.212 closest distance to " CD  LYS A 166 " =    1.704
peak=    4.201 closest distance to " CA  TYR A  30 " =    1.018
peak=    4.198 closest distance to " O   HOH Z 261 " =    1.515
peak=    4.189 closest distance to " NE2 GLN A  11 " =    1.250
peak=    4.185 closest distance to " O   HOH Z  32 " =    1.147
peak=    4.173 closest distance to " CE1 HIS A 115 " =    1.085
peak=    4.159 closest distance to " CA  ALA A 100 " =    1.080
peak=    4.146 closest distance to " O   HOH Z 277 " =    1.376
peak=    4.126 closest distance to " CB  ASN A  39 " =    0.712
peak=    4.105 closest distance to " O   PRO A 198 " =    1.610
peak=    4.089 closest distance to " CD2 TRP A 179 " =    1.218
peak=    4.088 closest distance to " CG  GLN A  77 " =    0.824
peak=    4.081 closest distance to " O   HOH Z 126 " =    1.812
peak=    4.061 closest distance to " O   HOH Z   4 " =    1.844
peak=    4.023 closest distance to " O   HOH Z 343 " =    2.474
peak=    4.013 closest distance to " O   HOH Z 402 " =    1.596
peak=    4.013 closest distance to " CG  PRO A  54 " =    1.398
peak=    4.009 closest distance to " N   SER A 271 " =    1.122
peak=    3.996 closest distance to " CG2BVAL A  41 " =    1.250
peak=    3.986 closest distance to " O   GLN A  73 " =    1.233
peak=    3.957 closest distance to " O   HOH Z 417 " =    3.368
peak=    3.941 closest distance to " O   HOH Z  27 " =    1.181
peak=    3.939 closest distance to " O   HOH Z  80 " =    2.227
peak=    3.916 closest distance to " O   GLN A  11 " =    0.976
peak=    3.896 closest distance to " O   HOH Z 359 " =    1.847
peak=    3.876 closest distance to " O   HOH Z 388 " =    1.344
peak=    3.874 closest distance to " CB  GLN A  89 " =    1.041
peak=    3.873 closest distance to " CD  PRO A  54 " =    1.044
peak=    3.872 closest distance to " OE1 GLN A  11 " =    2.181
peak=    3.867 closest distance to " NH1BARG A 102 " =    1.063
peak=    3.853 closest distance to " CG  LEU A 228 " =    1.450
peak=    3.848 closest distance to " CB  PHE A 283 " =    0.923
peak=    3.836 closest distance to " O   ASN A 209 " =    1.376
peak=    3.830 closest distance to " O   HOH Z 131 " =    1.144
peak=    3.827 closest distance to " O   HOH Z 215 " =    1.461
peak=    3.824 closest distance to " CB  ARG A 275 " =    0.826
peak=    3.821 closest distance to " NH1 ARG A 138 " =    1.141
peak=    3.815 closest distance to " O   HOH Z  56 " =    2.160
peak=    3.799 closest distance to " O   HOH Z 303 " =    2.427
peak=    3.795 closest distance to " CD  ARG A 269 " =    0.821
peak=    3.794 closest distance to " O   HOH Z 207 " =    1.477
peak=    3.790 closest distance to " OE1 GLU A   2 " =    1.472
peak=    3.786 closest distance to " O   HOH Z 377 " =    1.651
peak=    3.784 closest distance to " O   HOH Z 369 " =    1.866
peak=    3.782 closest distance to " O   HOH Z  63 " =    1.619
peak=    3.761 closest distance to " O  BHOH Z  74 " =    1.238
peak=    3.757 closest distance to " CA  GLU A 152 " =    1.038
peak=    3.754 closest distance to " O   HOH Z  26 " =    1.243
peak=    3.751 closest distance to " ND2 ASN A  69 " =    1.351
peak=    3.750 closest distance to " CA  CYS A 260 " =    1.030
peak=    3.748 closest distance to " O   GLU A   2 " =    1.808
peak=    3.737 closest distance to " O   HOH Z 403 " =    1.952
peak=    3.736 closest distance to " O   HOH Z 193 " =    1.529
peak=    3.730 closest distance to " O   HOH Z 389 " =    2.003
peak=    3.722 closest distance to " O   HOH Z  47 " =    1.988
peak=    3.721 closest distance to " O   ASP A 200 " =    1.642
peak=    3.717 closest distance to " CB  TRP A 179 " =    1.269
peak=    3.714 closest distance to " CA  ILE A 106 " =    0.829
peak=    3.707 closest distance to " CB  MET A  40 " =    0.951
peak=    3.702 closest distance to " CD1 LEU A  96 " =    0.800
peak=    3.698 closest distance to " O   HOH Z 404 " =    1.561
peak=    3.695 closest distance to " O   HOH Z 146 " =    1.824
peak=    3.695 closest distance to " N   PHE A  59 " =    1.179
peak=    3.693 closest distance to " CB  VAL A 202 " =    1.412
peak=    3.676 closest distance to " CG2AVAL A 121 " =    1.784
peak=    3.676 closest distance to " CA  LEU A   5 " =    0.989
peak=    3.673 closest distance to " CA  ARG A 195 " =    1.278
peak=    3.672 closest distance to " O   HOH Z   5 " =    2.180
peak=    3.664 closest distance to " CA  ASP A 162 " =    0.895
peak=    3.658 closest distance to " O   HOH Z  95 " =    1.892
peak=    3.654 closest distance to " OD1 ASN A 301 " =    1.069
peak=    3.648 closest distance to " CG2 THR A 221 " =    0.993
peak=    3.647 closest distance to " CG  PRO A 243 " =    1.137
peak=    3.642 closest distance to " NH2 ARG A  56 " =    2.207
peak=    3.639 closest distance to " CB  SER A  62 " =    1.004
peak=    3.634 closest distance to " CG2 THR A  42 " =    0.740
peak=    3.629 closest distance to " CD  ARG A  66 " =    2.604
peak=    3.628 closest distance to " CA  SER A  87 " =    0.818
peak=    3.626 closest distance to " OG  SER A 245 " =    1.688
peak=    3.615 closest distance to " CA  ALA A 295 " =    0.978
peak=    3.614 closest distance to " O   SER A  87 " =    2.352
peak=    3.614 closest distance to " O   HOH Z 395 " =    1.443
peak=    3.608 closest distance to " CB  ASN A 285 " =    0.857
peak=    3.608 closest distance to " O   HOH Z  57 " =    2.174
peak=    3.607 closest distance to " O   HOH Z 251 " =    1.720
peak=    3.605 closest distance to " CB  PRO A  54 " =    0.899
peak=    3.599 closest distance to " CE3 TRP A  85 " =    1.136
peak=    3.599 closest distance to " CG  GLU A  37 " =    1.067
peak=    3.598 closest distance to " O   HOH Z 393 " =    3.867
peak=    3.593 closest distance to " CB  VAL A 296 " =    1.247
peak=    3.588 closest distance to " CB  ASN A 148 " =    1.507
peak=    3.584 closest distance to " OH  TYR A  68 " =    0.960
peak=    3.582 closest distance to " CB  PRO A 243 " =    1.137
peak=    3.580 closest distance to " N   ALA A 292 " =    0.991
peak=    3.568 closest distance to " OE2 GLU A   2 " =    2.242
peak=    3.568 closest distance to " CB  ASP A 140 " =    0.767
peak=    3.566 closest distance to " CA  GLY A 267 " =    1.011
peak=    3.565 closest distance to " CD1 ILE A  33 " =    1.700
peak=    3.563 closest distance to " O   HOH Z 433 " =    1.834
peak=    3.562 closest distance to " O   HOH Z 368 " =    2.277
peak=    3.561 closest distance to " CG2 ILE A 234 " =    0.975
peak=    3.553 closest distance to " O   HOH Z 232 " =    2.022
peak=    3.546 closest distance to " O   HOH Z  33 " =    2.278
peak=    3.545 closest distance to " O   THR A 182 " =    1.376
peak=    3.544 closest distance to " CZ3 TRP A 266 " =    1.148
peak=    3.543 closest distance to " CB  GLN A  88 " =    1.288
peak=    3.541 closest distance to " CG2 VAL A 197 " =    1.239
peak=    3.539 closest distance to " O   HOH Z 199 " =    1.646
peak=    3.530 closest distance to " N   CYS A 260 " =    0.894
peak=    3.523 closest distance to " CA  TYR A 116 " =    1.395
peak=    3.521 closest distance to " NE2 GLN A 278 " =    2.413
peak=    3.518 closest distance to " N   TYR A  15 " =    0.975
peak=    3.515 closest distance to " O   HOH Z 234 " =    3.809
peak=    3.513 closest distance to " O   HOH Z 285 " =    2.068
peak=    3.500 closest distance to " OD1 ASN A  69 " =    0.899
peak=    3.494 closest distance to " O   HOH Z 250 " =    1.230
peak=    3.474 closest distance to " OG ASER A 212 " =    1.886
peak=    3.473 closest distance to " O   HOH Z 261 " =    1.903
peak=    3.473 closest distance to " O   HOH Z 407 " =    2.361
peak=    3.471 closest distance to " O   HOH Z 153 " =    2.234
peak=    3.470 closest distance to " CA  ARG A  66 " =    0.829
peak=    3.470 closest distance to " CB  ASN A 187 " =    1.194
peak=    3.468 closest distance to " CB  GLU A  37 " =    1.017
peak=    3.466 closest distance to " CG1 VAL A 174 " =    1.121
peak=    3.465 closest distance to " CD2 LEU A 297 " =    0.866
peak=    3.463 closest distance to " CA  ASP A 191 " =    0.987
peak=    3.463 closest distance to " NH1 ARG A 269 " =    0.840
peak=    3.463 closest distance to " CB  ALA A 100 " =    1.603
peak=    3.461 closest distance to " CB  TRP A 150 " =    1.442
peak=    3.454 closest distance to " O   HOH Z 265 " =    2.233
peak=    3.454 closest distance to " CA  ALA A  21 " =    1.356
peak=    3.454 closest distance to " O   HOH Z 136 " =    1.433
peak=    3.453 closest distance to " O   HOH Z 420 " =    5.833
peak=    3.449 closest distance to " O   HOH Z 214 " =    1.681
peak=    3.449 closest distance to " O   HOH Z 148 " =    1.990
peak=    3.446 closest distance to " O   HOH Z 155 " =    3.084
peak=    3.445 closest distance to " O   HOH Z 357 " =    2.228
peak=    3.445 closest distance to " CG  PRO A 213 " =    1.343
peak=    3.445 closest distance to " O   HOH Z 324 " =    1.466
peak=    3.444 closest distance to " O   THR A 294 " =    1.732
peak=    3.443 closest distance to " CB  TRP A 266 " =    1.114
peak=    3.442 closest distance to " CA  ASP A 124 " =    0.888
peak=    3.442 closest distance to " O   HOH Z 346 " =    1.646
peak=    3.441 closest distance to " O   HOH Z 250 " =    1.326
peak=    3.441 closest distance to " OG1 THR A 279 " =    1.458
peak=    3.441 closest distance to " C   VAL A 265 " =    1.187
peak=    3.437 closest distance to " CA  ALA A 291 " =    0.902
peak=    3.435 closest distance to " CD ALYS A 290 " =    1.192
peak=    3.433 closest distance to " O   HOH Z 146 " =    1.578
peak=    3.431 closest distance to " O   HOH Z 133 " =    2.476
peak=    3.430 closest distance to " CD  ARG A 195 " =    1.039
peak=    3.427 closest distance to " NH2 ARG A  56 " =    1.222
peak=    3.425 closest distance to " CA  GLY A 196 " =    0.728
peak=    3.424 closest distance to " CA  ASP A 140 " =    1.391
peak=    3.422 closest distance to " CG1 VAL A 153 " =    1.103
peak=    3.411 closest distance to " CA  ALA A 154 " =    1.009
peak=    3.411 closest distance to " O   HOH Z 151 " =    2.058
peak=    3.411 closest distance to " O   ASN A 284 " =    1.914
peak=    3.406 closest distance to " CA  ALA A  51 " =    0.980
peak=    3.402 closest distance to " O   HOH Z 200 " =    2.174
peak=    3.401 closest distance to " O   ALA A 165 " =    1.229
peak=    3.401 closest distance to " O   HOH Z 106 " =    3.789
peak=    3.397 closest distance to " CG  PRO A  90 " =    1.681
peak=    3.396 closest distance to " O   HOH Z  40 " =    1.453
peak=    3.394 closest distance to " O   HOH Z 423 " =    1.794
peak=    3.387 closest distance to " O   HOH Z 133 " =    1.556
peak=    3.382 closest distance to " CB  SER A   3 " =    1.741
peak=    3.381 closest distance to " OD2 ASP A 298 " =    0.802
peak=    3.378 closest distance to " O   HOH Z 258 " =    2.286
peak=    3.376 closest distance to " N   VAL A 126 " =    1.853
peak=    3.370 closest distance to " O   HOH Z  63 " =    2.208
peak=    3.367 closest distance to " O   HOH Z 182 " =    1.457
peak=    3.363 closest distance to " CA  ALA A 160 " =    1.034
peak=    3.363 closest distance to " CB  GLU A 152 " =    1.160
peak=    3.361 closest distance to " CB  ARG A  79 " =    1.187
peak=    3.361 closest distance to " CB  LEU A 281 " =    0.865
peak=    3.358 closest distance to " O   HOH Z 427 " =    3.066
peak=    3.357 closest distance to " O   THR A 251 " =    1.142
peak=    3.357 closest distance to " CZ3 TRP A 274 " =    4.652
peak=    3.356 closest distance to " O   HOH Z 188 " =    3.366
peak=    3.355 closest distance to " CB  TYR A  30 " =    0.962
peak=    3.349 closest distance to " CZ  PHE A  38 " =    1.106
peak=    3.346 closest distance to " O   HOH Z 337 " =    1.911
peak=    3.343 closest distance to " CD1 LEU A 101 " =    1.015
peak=    3.342 closest distance to " O   HOH Z 213 " =    1.623
peak=    3.335 closest distance to " O   HOH Z 327 " =    2.752
peak=    3.332 closest distance to " CB  SER A 210 " =    0.977
peak=    3.328 closest distance to " CA  ILE A  33 " =    1.792
peak=    3.324 closest distance to " O   HOH Z 144 " =    1.764
peak=    3.322 closest distance to " NZ  LYS A 181 " =    0.725
peak=    3.320 closest distance to " CZ3 TRP A  85 " =    0.917
peak=    3.315 closest distance to " O   HOH Z 134 " =    2.503
peak=    3.313 closest distance to " CB  SER A  95 " =    0.834
peak=    3.308 closest distance to " O   HOH Z 406 " =    1.673
peak=    3.305 closest distance to " O   HOH Z 422 " =    2.507
peak=    3.294 closest distance to " O   HOH Z 174 " =    1.388
peak=    3.293 closest distance to " CB  ASN A 142 " =    0.994
peak=    3.287 closest distance to " O   VAL A 112 " =    1.729
peak=    3.282 closest distance to " CG  GLN A  11 " =    0.955
peak=    3.281 closest distance to " O   HOH Z 174 " =    1.910
peak=    3.280 closest distance to " O   THR A 220 " =    1.138
peak=    3.279 closest distance to " CB  SER A  26 " =    1.647
peak=    3.279 closest distance to " CB  ALA A 137 " =    1.002
peak=    3.276 closest distance to " O   HOH Z 171 " =    3.800
peak=    3.273 closest distance to " CB  ALA A 248 " =    1.406
peak=    3.271 closest distance to " O   HOH Z  88 " =    2.913
peak=    3.271 closest distance to " CB  GLU A 128 " =    1.036
peak=    3.269 closest distance to " C   ALA A 299 " =    0.850
peak=    3.267 closest distance to " O   HOH Z 332 " =    1.627
peak=    3.261 closest distance to " CD  LYS A 289 " =    1.210
peak=    3.256 closest distance to " N   TYR A 247 " =    1.168
peak=    3.253 closest distance to " O   HOH Z 316 " =    3.183
peak=    3.250 closest distance to " O   ALA A 180 " =    1.333
peak=    3.250 closest distance to " CB  THR A  52 " =    1.082
peak=    3.247 closest distance to " O   HOH Z   9 " =    2.081
peak=    3.242 closest distance to " O   HOH Z 272 " =    1.408
peak=    3.235 closest distance to " O   GLU A 152 " =    1.709
peak=    3.234 closest distance to " O   HOH Z 435 " =    3.100
peak=    3.230 closest distance to " CA  LEU A 282 " =    0.888
peak=    3.230 closest distance to " O   HOH Z 184 " =    1.634
peak=    3.230 closest distance to " ND1 HIS A  81 " =    1.793
peak=    3.223 closest distance to " CG  LYS A  76 " =    1.110
peak=    3.220 closest distance to " NH1 ARG A  56 " =    1.034
peak=    3.216 closest distance to " OE1 GLN A  55 " =    1.405
peak=    3.215 closest distance to " O   PHE A 155 " =    0.868
peak=    3.214 closest distance to " CB  SER A 288 " =    1.536
peak=    3.210 closest distance to " O   HOH Z 197 " =    1.627
peak=    3.204 closest distance to " N   GLN A 278 " =    1.335
peak=    3.204 closest distance to " CA  MET A 105 " =    0.882
peak=    3.199 closest distance to " NZ  LYS A  48 " =    1.247
peak=    3.199 closest distance to " CB  SER A 271 " =    1.097
peak=    3.197 closest distance to " NE2 HIS A 207 " =    1.112
peak=    3.197 closest distance to " O   HOH Z 368 " =    3.268
peak=    3.196 closest distance to " O   HOH Z   9 " =    1.303
peak=    3.192 closest distance to " CB  ARG A 156 " =    1.125
peak=    3.191 closest distance to " CD2 LEU A 255 " =    1.500
peak=    3.189 closest distance to " N   ASP A 132 " =    1.066
peak=    3.189 closest distance to " O   HOH Z 201 " =    2.788
peak=    3.187 closest distance to " CG  ASP A 253 " =    1.299
peak=    3.185 closest distance to " O   HOH Z 171 " =    3.386
peak=    3.180 closest distance to " CB  ALA A 226 " =    1.109
peak=    3.176 closest distance to " CG  PRO A 198 " =    1.522
peak=    3.176 closest distance to " CA  ARG A 139 " =    1.648
peak=    3.175 closest distance to " O   HOH Z  85 " =    2.193
peak=    3.173 closest distance to " CA  GLY A   6 " =    0.767
peak=    3.173 closest distance to " NZ  LYS A  76 " =    0.902
peak=    3.173 closest distance to " CA  GLY A 241 " =    0.969
peak=    3.172 closest distance to " CB  ASN A 215 " =    1.285
peak=    3.170 closest distance to " CA  PRO A  54 " =    1.038
peak=    3.154 closest distance to " CA  LYS A 181 " =    1.032
peak=    3.152 closest distance to " O   HOH Z  44 " =    1.869
peak=    3.148 closest distance to " CB  ALA A  21 " =    0.928
peak=    3.146 closest distance to " O   HOH Z 221 " =    1.377
peak=    3.144 closest distance to " CA  ARG A 156 " =    1.169
peak=    3.144 closest distance to " CB  GLU A 277 " =    3.922
peak=    3.143 closest distance to " O   PHE A 192 " =    1.397
peak=    3.143 closest distance to " N   GLY A  80 " =    1.265
peak=    3.142 closest distance to " O   HOH Z 301 " =    1.771
peak=    3.136 closest distance to " CG2 THR A 220 " =    0.817
peak=    3.118 closest distance to " N   ASN A  39 " =    1.156
peak=    3.113 closest distance to " O   HOH Z  58 " =    1.588
peak=    3.108 closest distance to " CB  TYR A 116 " =    1.354
peak=    3.108 closest distance to " CB  ALA A 299 " =    0.764
peak=    3.106 closest distance to " CG  PHE A 204 " =    1.126
peak=    3.104 closest distance to " N   GLY A  75 " =    0.815
peak=    3.101 closest distance to " CG2 VAL A 112 " =    1.511
peak=    3.099 closest distance to " O   HOH Z 422 " =    1.132
peak=    3.091 closest distance to " N   PHE A 130 " =    1.186
peak=    3.084 closest distance to " O   HOH Z 368 " =    4.245
peak=    3.081 closest distance to " CD1 LEU A   5 " =    1.341
peak=    3.080 closest distance to " O   HOH Z 379 " =    3.219
peak=    3.079 closest distance to " OG  SER A  62 " =    2.856
peak=    3.077 closest distance to " O   MET A 105 " =    1.450
peak=    3.070 closest distance to " CA  GLY A 133 " =    3.768
peak=    3.063 closest distance to " O   HOH Z 297 " =    4.390
peak=    3.062 closest distance to " O   HOH Z 150 " =    2.009
peak=    3.056 closest distance to " O   HOH Z 156 " =    4.722
peak=    3.055 closest distance to " CB  VAL A 265 " =    1.399
peak=    3.046 closest distance to " CG AARG A 102 " =    0.827
peak=    3.026 closest distance to " CG1 VAL A 257 " =    1.127
peak=    3.014 closest distance to " CA  PRO A  54 " =    1.331
peak=    3.005 closest distance to " CA  GLN A  73 " =    0.912

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 231         
Filter by distance & map next to the model:
   mapped sites are within: 0.366 - 5.214
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 225 from: 231
   mapped sites are within: 0.722 - 5.214

peak=   -5.270 closest distance to " CG2 VAL A 230 " =    0.789
peak=   -4.594 closest distance to " CD1 PHE A  59 " =    2.011
peak=   -4.593 closest distance to " O   HOH Z 400 " =    1.116
peak=   -4.565 closest distance to " O   HOH Z 377 " =    0.722
peak=   -4.553 closest distance to " CB  ALA A 291 " =    2.523
peak=   -4.540 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -4.538 closest distance to " O   GLN A  73 " =    0.723
peak=   -4.461 closest distance to " O   HOH Z 166 " =    1.414
peak=   -4.352 closest distance to " CZ  ARG A 259 " =    0.820
peak=   -4.275 closest distance to " CA  ASP A 298 " =    1.095
peak=   -4.268 closest distance to " CD  GLN A  55 " =    0.855
peak=   -4.230 closest distance to " O   HOH Z 411 " =    5.210
peak=   -4.226 closest distance to " O   HOH Z 216 " =    0.923
peak=   -4.196 closest distance to " N   SER A 134 " =    1.165
peak=   -4.100 closest distance to " CG1 VAL A 296 " =    1.096
peak=   -4.078 closest distance to " O   PRO A 198 " =    1.182
peak=   -4.072 closest distance to " CG  GLN A 103 " =    2.348
peak=   -4.061 closest distance to " O   HOH Z 103 " =    2.379
peak=   -4.053 closest distance to " CD  GLN A 223 " =    1.227
peak=   -4.033 closest distance to " OD2 ASP A 171 " =    1.913
peak=   -4.003 closest distance to " CG  ARG A 269 " =    2.510
peak=   -3.989 closest distance to " CD  GLN A  58 " =    0.811
peak=   -3.968 closest distance to " O   HOH Z  54 " =    1.201
peak=   -3.939 closest distance to " O   HOH Z 351 " =    1.868
peak=   -3.896 closest distance to " CG1 VAL A 112 " =    2.649
peak=   -3.892 closest distance to " OG  SER A  63 " =    0.783
peak=   -3.873 closest distance to " O   HOH Z 155 " =    1.765
peak=   -3.866 closest distance to " O   HOH Z 250 " =    1.482
peak=   -3.859 closest distance to " CG  PRO A 243 " =    1.783
peak=   -3.854 closest distance to " CG  LEU A   5 " =    0.821
peak=   -3.838 closest distance to " CG  ASP A 231 " =    0.791
peak=   -3.831 closest distance to " O   HOH Z 100 " =    0.729
peak=   -3.822 closest distance to " O   VAL A  67 " =    2.866
peak=   -3.806 closest distance to " O   HOH Z 257 " =    1.167
peak=   -3.802 closest distance to " N   ARG A 275 " =    1.318
peak=   -3.788 closest distance to " O   HOH Z 120 " =    1.063
peak=   -3.778 closest distance to " O   HOH Z  82 " =    0.917
peak=   -3.772 closest distance to " O   HOH Z 255 " =    0.826
peak=   -3.765 closest distance to " OE1 GLU A  44 " =    0.826
peak=   -3.751 closest distance to " CD2 TYR A 293 " =    1.806
peak=   -3.719 closest distance to " O   HOH Z 231 " =    1.237
peak=   -3.713 closest distance to " O   HOH Z  10 " =    1.662
peak=   -3.709 closest distance to " OD2 ASP A  50 " =    2.191
peak=   -3.708 closest distance to " OD2 ASP A 298 " =    1.072
peak=   -3.705 closest distance to " O   VAL A 121 " =    0.847
peak=   -3.694 closest distance to " O   HOH Z 368 " =    2.115
peak=   -3.689 closest distance to " OG1 THR A  82 " =    2.155
peak=   -3.679 closest distance to " O   HOH Z 340 " =    1.316
peak=   -3.650 closest distance to " O   SER A 276 " =    1.656
peak=   -3.646 closest distance to " CG  GLN A  55 " =    1.041
peak=   -3.644 closest distance to " O   HOH Z 183 " =    1.197
peak=   -3.642 closest distance to " O   HOH Z 221 " =    0.949
peak=   -3.636 closest distance to " O   GLN A  11 " =    1.111
peak=   -3.630 closest distance to " N   ILE A 120 " =    1.243
peak=   -3.628 closest distance to " CD  ARG A  14 " =    3.162
peak=   -3.626 closest distance to " O   HOH Z 424 " =    1.330
peak=   -3.623 closest distance to " CE3 TRP A  70 " =    1.989
peak=   -3.614 closest distance to " CA  TRP A 274 " =    0.946
peak=   -3.611 closest distance to " O   HOH Z 150 " =    1.387
peak=   -3.602 closest distance to " NH1 ARG A 195 " =    0.944
peak=   -3.600 closest distance to " O   HOH Z 151 " =    0.880
peak=   -3.587 closest distance to " CD2 TYR A  15 " =    2.349
peak=   -3.586 closest distance to " CZ2 TRP A  92 " =    2.847
peak=   -3.583 closest distance to " CD2 LEU A 237 " =    2.644
peak=   -3.569 closest distance to " CD1 PHE A  59 " =    2.009
peak=   -3.565 closest distance to " O   SER A 135 " =    2.076
peak=   -3.559 closest distance to " CA  GLY A  98 " =    2.238
peak=   -3.553 closest distance to " O   HOH Z  52 " =    1.995
peak=   -3.548 closest distance to " CD2 PHE A  61 " =    2.583
peak=   -3.548 closest distance to " CD  GLN A  11 " =    1.052
peak=   -3.538 closest distance to " CA  GLY A 229 " =    2.543
peak=   -3.534 closest distance to " CD2 PHE A  61 " =    2.129
peak=   -3.534 closest distance to " O   HOH Z 120 " =    4.869
peak=   -3.531 closest distance to " OD1 ASP A 298 " =    2.123
peak=   -3.528 closest distance to " O   HOH Z 407 " =    1.237
peak=   -3.515 closest distance to " CH2 TRP A 179 " =    1.054
peak=   -3.508 closest distance to " CA  PRO A 198 " =    0.932
peak=   -3.499 closest distance to " O   HOH Z 259 " =    0.762
peak=   -3.482 closest distance to " OD1 ASP A 107 " =    1.641
peak=   -3.482 closest distance to " CG2 VAL A 189 " =    2.237
peak=   -3.482 closest distance to " CE  MET A 105 " =    2.311
peak=   -3.478 closest distance to " O   HOH Z 137 " =    1.628
peak=   -3.472 closest distance to " CA  GLY A 241 " =    2.279
peak=   -3.469 closest distance to " NH2 ARG A  79 " =    1.662
peak=   -3.466 closest distance to " CD2 PHE A 225 " =    2.688
peak=   -3.466 closest distance to " CG  ARG A 259 " =    2.525
peak=   -3.459 closest distance to " O   HOH Z 361 " =    4.626
peak=   -3.452 closest distance to " O   HOH Z 394 " =    1.591
peak=   -3.448 closest distance to " O   HOH Z 106 " =    2.207
peak=   -3.446 closest distance to " O   HOH Z 313 " =    0.923
peak=   -3.446 closest distance to " CA  GLU A 277 " =    1.282
peak=   -3.439 closest distance to " CG  GLN A  58 " =    1.344
peak=   -3.435 closest distance to " CE3 TRP A 150 " =    2.399
peak=   -3.432 closest distance to " O   HOH Z 136 " =    1.377
peak=   -3.426 closest distance to " O   HOH Z  19 " =    2.189
peak=   -3.425 closest distance to " O   HOH Z 117 " =    0.872
peak=   -3.419 closest distance to " CE2 TYR A  30 " =    2.681
peak=   -3.413 closest distance to " O   HOH Z  37 " =    1.335
peak=   -3.412 closest distance to " CG1 VAL A 232 " =    2.280
peak=   -3.403 closest distance to " O   VAL A  67 " =    2.442
peak=   -3.396 closest distance to " O   HOH Z 109 " =    1.105
peak=   -3.394 closest distance to " O   HOH Z 215 " =    1.259
peak=   -3.392 closest distance to " O   HOH Z 222 " =    1.067
peak=   -3.392 closest distance to " CB  ALA A 256 " =    2.735
peak=   -3.392 closest distance to " O   HOH Z 390 " =    1.169
peak=   -3.390 closest distance to " CD1 LEU A   5 " =    2.436
peak=   -3.390 closest distance to " O   HOH Z 403 " =    1.020
peak=   -3.390 closest distance to " O   HOH Z 205 " =    0.730
peak=   -3.378 closest distance to " CB  PRO A 243 " =    3.008
peak=   -3.378 closest distance to " OD1 ASP A 107 " =    0.924
peak=   -3.370 closest distance to " OD1 ASN A 148 " =    1.381
peak=   -3.368 closest distance to " O   HOH Z 407 " =    3.673
peak=   -3.364 closest distance to " CA  SER A 271 " =    2.256
peak=   -3.360 closest distance to " O   HOH Z 410 " =    1.288
peak=   -3.358 closest distance to " O   HOH Z 156 " =    2.946
peak=   -3.345 closest distance to " CG2 THR A 221 " =    2.375
peak=   -3.345 closest distance to " O   HOH Z 177 " =    1.478
peak=   -3.345 closest distance to " O   HOH Z 428 " =    1.177
peak=   -3.339 closest distance to " CE  LYS A  76 " =    0.851
peak=   -3.338 closest distance to " O   TYR A  15 " =    1.855
peak=   -3.336 closest distance to " CD  GLN A  73 " =    0.753
peak=   -3.336 closest distance to " N   ASP A 191 " =    1.401
peak=   -3.336 closest distance to " CD  LYS A 289 " =    2.230
peak=   -3.335 closest distance to " ND2 ASN A  45 " =    2.587
peak=   -3.334 closest distance to " CA  GLY A  98 " =    2.267
peak=   -3.334 closest distance to " O   HOH Z 265 " =    1.127
peak=   -3.334 closest distance to " CG1BVAL A  72 " =    2.674
peak=   -3.327 closest distance to " O   SER A   3 " =    0.988
peak=   -3.325 closest distance to " NE2 GLN A  55 " =    2.374
peak=   -3.320 closest distance to " O   HOH Z 103 " =    1.079
peak=   -3.320 closest distance to " C   GLU A 236 " =    1.005
peak=   -3.316 closest distance to " O   HOH Z 295 " =    1.576
peak=   -3.315 closest distance to " CB  SER A 276 " =    1.047
peak=   -3.312 closest distance to " NE2 HIS A  86 " =    0.923
peak=   -3.310 closest distance to " O   HOH Z 200 " =    1.455
peak=   -3.303 closest distance to " O   HOH Z  41 " =    2.236
peak=   -3.302 closest distance to " NE2 GLN A 194 " =    2.123
peak=   -3.302 closest distance to " O   HOH Z 396 " =    2.011
peak=   -3.297 closest distance to " O   HOH Z 400 " =    0.754
peak=   -3.294 closest distance to " CB  ILE A 120 " =    0.983
peak=   -3.292 closest distance to " CA  TYR A  68 " =    2.921
peak=   -3.286 closest distance to " CB  ALA A  10 " =    2.207
peak=   -3.281 closest distance to " O   HOH Z  94 " =    4.020
peak=   -3.275 closest distance to " O   HOH Z  43 " =    1.753
peak=   -3.274 closest distance to " O   HOH Z 214 " =    0.888
peak=   -3.274 closest distance to " O   HOH Z 132 " =    4.141
peak=   -3.272 closest distance to " CG  LEU A   5 " =    1.379
peak=   -3.265 closest distance to " SG  CYS A 254 " =    3.259
peak=   -3.261 closest distance to " CZ  TYR A  68 " =    1.190
peak=   -3.255 closest distance to " CD2 TYR A 169 " =    2.460
peak=   -3.254 closest distance to " OE2 GLU A 277 " =    2.837
peak=   -3.253 closest distance to " CD1 TYR A 247 " =    2.430
peak=   -3.252 closest distance to " O   HOH Z 194 " =    1.374
peak=   -3.250 closest distance to " O   HOH Z  99 " =    4.637
peak=   -3.247 closest distance to " O   HOH Z 401 " =    0.898
peak=   -3.246 closest distance to " O   HOH Z  73 " =    2.746
peak=   -3.242 closest distance to " CG  MET A 105 " =    0.911
peak=   -3.237 closest distance to " O   HOH Z 290 " =    1.120
peak=   -3.236 closest distance to " O   HOH Z 379 " =    0.968
peak=   -3.236 closest distance to " O   HOH Z  60 " =    1.799
peak=   -3.231 closest distance to " CG  TRP A 266 " =    1.751
peak=   -3.231 closest distance to " N   ALA A  43 " =    2.697
peak=   -3.230 closest distance to " CZ  PHE A 283 " =    2.013
peak=   -3.230 closest distance to " C   ASP A  50 " =    1.258
peak=   -3.228 closest distance to " CD2 HIS A 115 " =    1.097
peak=   -3.227 closest distance to " O   HOH Z 251 " =    4.459
peak=   -3.226 closest distance to " OG  SER A  32 " =    1.222
peak=   -3.223 closest distance to " O   HOH Z 166 " =    1.618
peak=   -3.223 closest distance to " O   HOH Z 287 " =    1.830
peak=   -3.220 closest distance to " CD1 ILE A 263 " =    2.334
peak=   -3.213 closest distance to " O   HOH Z 193 " =    1.805
peak=   -3.210 closest distance to " O   HOH Z 189 " =    2.415
peak=   -3.210 closest distance to " O   GLY A 203 " =    2.735
peak=   -3.203 closest distance to " C   LEU A 228 " =    2.047
peak=   -3.202 closest distance to " CB  PHE A  16 " =    2.411
peak=   -3.195 closest distance to " O   HOH Z 171 " =    2.461
peak=   -3.195 closest distance to " O   HOH Z 345 " =    2.794
peak=   -3.195 closest distance to " O   ASP A 253 " =    1.902
peak=   -3.194 closest distance to " O   HOH Z   5 " =    1.572
peak=   -3.193 closest distance to " CA  ASN A 110 " =    1.068
peak=   -3.188 closest distance to " CB  ALA A 161 " =    2.637
peak=   -3.185 closest distance to " CD  GLN A  77 " =    0.960
peak=   -3.178 closest distance to " OG  SER A  62 " =    0.995
peak=   -3.178 closest distance to " CD1 ILE A 109 " =    2.287
peak=   -3.178 closest distance to " O   HOH Z 102 " =    1.277
peak=   -3.177 closest distance to " O   HOH Z 275 " =    1.729
peak=   -3.177 closest distance to " O   HOH Z 378 " =    1.347
peak=   -3.175 closest distance to " CA  GLY A 241 " =    3.419
peak=   -3.175 closest distance to " OD1 ASN A 173 " =    1.383
peak=   -3.172 closest distance to " O   HOH Z  31 " =    2.275
peak=   -3.170 closest distance to " O   HOH Z 174 " =    1.737
peak=   -3.169 closest distance to " O   HOH Z 144 " =    1.502
peak=   -3.168 closest distance to " CE2 TYR A 116 " =    1.553
peak=   -3.164 closest distance to " O   HOH Z   6 " =    1.599
peak=   -3.164 closest distance to " SG  CYS A 260 " =    2.493
peak=   -3.160 closest distance to " CD2 LEU A  25 " =    1.115
peak=   -3.156 closest distance to " O   HOH Z 114 " =    1.307
peak=   -3.156 closest distance to " N   ALA A  51 " =    1.725
peak=   -3.152 closest distance to " CG2BVAL A  41 " =    1.554
peak=   -3.151 closest distance to " CG  ARG A 259 " =    1.579
peak=   -3.151 closest distance to " O   HOH Z 133 " =    1.011
peak=   -3.145 closest distance to " O   HOH Z 193 " =    1.094
peak=   -3.142 closest distance to " O   HOH Z 402 " =    1.223
peak=   -3.142 closest distance to " O   HOH Z  30 " =    1.071
peak=   -3.142 closest distance to " O   HOH Z  60 " =    1.515
peak=   -3.140 closest distance to " O   HOH Z 175 " =    3.544
peak=   -3.136 closest distance to " CG  ASP A 298 " =    0.880
peak=   -3.128 closest distance to " CA  VAL A 268 " =    2.897
peak=   -3.121 closest distance to " O   SER A 210 " =    1.940
peak=   -3.118 closest distance to " CD1 ILE A 151 " =    2.548
peak=   -3.117 closest distance to " O   HOH Z 198 " =    1.425
peak=   -3.108 closest distance to " O   ASN A  74 " =    2.068
peak=   -3.105 closest distance to " CB  ASP A 171 " =    2.342
peak=   -3.102 closest distance to " O   HOH Z 165 " =    1.571
peak=   -3.101 closest distance to " CD  PRO A 243 " =    1.700
peak=   -3.100 closest distance to " O   HOH Z 329 " =    0.922
peak=   -3.100 closest distance to " ND2 ASN A 249 " =    1.243
peak=   -3.091 closest distance to " O   HOH Z 100 " =    1.146
peak=   -3.089 closest distance to " OG  SER A  97 " =    2.055
peak=   -3.069 closest distance to " O   HOH Z 139 " =    5.214
peak=   -3.064 closest distance to " O   HOH Z  32 " =    2.175
peak=   -3.063 closest distance to " N   VAL A 230 " =    0.969
peak=   -3.055 closest distance to " CB  ALA A   9 " =    2.495
peak=   -3.038 closest distance to " O   LYS A 289 " =    2.895
peak=   -3.032 closest distance to " O   HOH Z 109 " =    1.075

================= 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    :  0.5201 0.5091   6.309445e+00   6.299914e+00
   1_bss:  0.5148 0.5061   5.534352e+00   5.536376e+00
   1_xyz:  0.4615 0.4758   6.256215e+00   6.264689e+00
   1_adp:  0.4182 0.4638   6.205564e+00   6.252139e+00
   1_occ:  0.4173 0.4641   6.205448e+00   6.253309e+00
   2_bss:  0.4158 0.4600   6.206430e+00   6.253615e+00
   2_xyz:  0.3594 0.4267   6.112539e+00   6.206984e+00
   2_adp:  0.3506 0.4156   6.095376e+00   6.189162e+00
   2_occ:  0.3504 0.4157   6.095175e+00   6.189360e+00
   3_bss:  0.3495 0.4139   6.096044e+00   6.189201e+00
   3_xyz:  0.2681 0.3250   5.879845e+00   6.020642e+00
   3_adp:  0.2318 0.2981   5.776261e+00   5.957843e+00
   3_occ:  0.2313 0.2982   5.775990e+00   5.957925e+00
   4_bss:  0.2304 0.2970   5.774942e+00   5.957015e+00
   4_xyz:  0.1886 0.2454   5.593893e+00   5.800620e+00
   4_adp:  0.1710 0.2295   5.517150e+00   5.738073e+00
   4_occ:  0.1709 0.2297   5.517076e+00   5.738470e+00
   5_bss:  0.1710 0.2302   5.517592e+00   5.738670e+00
   5_xyz:  0.1493 0.2044   5.398545e+00   5.630713e+00
   5_adp:  0.1471 0.1943   5.369131e+00   5.581605e+00
   5_occ:  0.1469 0.1944   5.368670e+00   5.581911e+00
   5_bss:  0.1469 0.1943   5.368334e+00   5.580987e+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:  0.300  80.000   6.223   9.348  10.274   0.000   0.000   0.000
   1_xyz:  0.300  80.000   6.223   9.348  10.274   0.000   0.000   0.000
   1_adp:  0.300  80.000   6.223   9.348  10.274   0.000   0.000   0.000
   1_occ:  0.300  80.000   6.223   9.348  10.274   0.000   0.000   0.000
   2_bss:  0.330  91.886   3.524   5.775   6.558   0.000   0.000   0.000
   2_xyz:  0.330  91.886   3.524   5.775   6.558   0.000   0.000   0.000
   2_adp:  0.330  91.886   3.524   5.775   6.558   0.000   0.000   0.000
   2_occ:  0.330  91.886   3.524   5.775   6.558   0.000   0.000   0.000
   3_bss:  0.334  83.888   1.960   3.749   4.309   0.000   0.000   0.000
   3_xyz:  0.334  83.888   1.960   3.749   4.309   0.000   0.000   0.000
   3_adp:  0.334  83.888   1.960   3.749   4.309   0.000   0.000   0.000
   3_occ:  0.334  83.888   1.960   3.749   4.309   0.000   0.000   0.000
   4_bss:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   4_xyz:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   4_adp:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   4_occ:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   5_bss:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   5_xyz:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   5_adp:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   5_occ:  0.346  99.309   0.799   1.850   2.652   0.000   0.000   0.000
   5_bss:  0.335  85.055  -0.882  -0.131   1.014   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.178 0.2995  0.3392    81659.603
   1_bss:  67.312 0.2970  0.4220    81231.995
   1_xyz:  58.244 0.4147  0.5882    67511.656
   1_adp:  55.593 0.4492  0.7153    64266.363
   1_occ:  55.839 0.4460  0.7086    64725.569
   2_bss:  55.771 0.4468  0.6388    64559.004
   2_xyz:  49.740 0.5225  0.7497    53318.082
   2_adp:  46.792 0.5599  0.8076    49292.220
   2_occ:  46.823 0.5595  0.8065    49275.804
   3_bss:  46.786 0.5599  0.7566    49246.123
   3_xyz:  34.090 0.7120  0.9374    28516.191
   3_adp:  30.828 0.7489  0.9458    23824.034
   3_occ:  30.863 0.7484  0.9447    23823.206
   4_bss:  30.753 0.7496  0.8959    23657.000
   4_xyz:  24.799 0.8130  0.9444    15806.604
   4_adp:  22.426 0.8379  0.9410    13649.780
   4_occ:  22.443 0.8377  0.9405    13658.422
   5_bss:  22.448 0.8377  0.9400    13670.617
   5_xyz:  19.571 0.8655  0.9595    10682.733
   5_adp:  18.104 0.8801  0.9578     9710.438
   5_occ:  18.109 0.8801  0.9577     9715.789
   5_bss:  18.092 0.8802  0.9498     9695.420
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4976e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4976e+01
   1_xyz:   1.789  0.014  0.112 18.436  0.007  4.125   1.5808e-01
   1_adp:   1.789  0.014  0.112 18.436  0.007  4.125   1.5808e-01
   1_occ:   1.789  0.014  0.112 18.436  0.007  4.125   1.5808e-01
   2_bss:   1.789  0.014  0.112 18.436  0.007  4.125   1.5808e-01
   2_xyz:   1.297  0.009  0.085 16.979  0.005  4.111   9.6956e-02
   2_adp:   1.297  0.009  0.085 16.979  0.005  4.111   9.6956e-02
   2_occ:   1.297  0.009  0.085 16.979  0.005  4.111   9.6956e-02
   3_bss:   1.297  0.009  0.085 16.979  0.005  4.111   9.6956e-02
   3_xyz:   1.453  0.012  0.102 16.838  0.005  4.112   1.2164e-01
   3_adp:   1.453  0.012  0.102 16.838  0.005  4.112   1.2164e-01
   3_occ:   1.453  0.012  0.102 16.838  0.005  4.112   1.2164e-01
   4_bss:   1.453  0.012  0.102 16.838  0.005  4.112   1.2164e-01
   4_xyz:   1.139  0.009  0.081 15.979  0.004  4.139   8.0215e-02
   4_adp:   1.139  0.009  0.081 15.979  0.004  4.139   8.0215e-02
   4_occ:   1.139  0.009  0.081 15.979  0.004  4.139   8.0215e-02
   5_bss:   1.139  0.009  0.081 15.979  0.004  4.139   8.0215e-02
   5_xyz:   1.138  0.010  0.086 15.511  0.004  4.116   7.9147e-02
   5_adp:   1.138  0.010  0.086 15.511  0.004  4.116   7.9147e-02
   5_occ:   1.138  0.010  0.086 15.511  0.004  4.116   7.9147e-02
   5_bss:   1.138  0.010  0.086 15.511  0.004  4.116   7.9147e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1277e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1277e+00
   1_xyz:  14.845  0.132  0.461 86.999  0.049  2.168   1.1059e-01
   1_adp:  14.845  0.132  0.461 86.999  0.049  2.168   1.1059e-01
   1_occ:  14.845  0.132  0.461 86.999  0.049  2.168   1.1059e-01
   2_bss:  14.845  0.132  0.461 86.999  0.049  2.168   1.1059e-01
   2_xyz:   8.702  0.066  0.296 86.498  0.031  2.154   6.4695e-02
   2_adp:   8.702  0.066  0.296 86.498  0.031  2.154   6.4695e-02
   2_occ:   8.702  0.066  0.296 86.498  0.031  2.154   6.4695e-02
   3_bss:   8.702  0.066  0.296 86.498  0.031  2.154   6.4695e-02
   3_xyz:  11.483  0.068  0.346 86.558  0.030  2.077   8.7570e-02
   3_adp:  11.483  0.068  0.346 86.558  0.030  2.077   8.7570e-02
   3_occ:  11.483  0.068  0.346 86.558  0.030  2.077   8.7570e-02
   4_bss:  11.483  0.068  0.346 86.558  0.030  2.077   8.7570e-02
   4_xyz:   8.790  0.057  0.307 88.697  0.046  2.214   6.5438e-02
   4_adp:   8.790  0.057  0.307 88.697  0.046  2.214   6.5438e-02
   4_occ:   8.790  0.057  0.307 88.697  0.046  2.214   6.5438e-02
   5_bss:   8.790  0.057  0.307 88.697  0.046  2.214   6.5438e-02
   5_xyz:   7.621  0.053  0.343 80.945  0.041  2.235   6.9623e-02
   5_adp:   7.621  0.053  0.343 80.945  0.041  2.235   6.9623e-02
   5_occ:   7.621  0.053  0.343 80.945  0.041  2.235   6.9623e-02
   5_bss:   7.621  0.053  0.343 80.945  0.041  2.235   6.9623e-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: 137.38   0.00  19.39  98.34   0.00  17.08 137.38   0.00  31.95
   1_occ: 137.38   0.00  19.39  98.34   0.00  17.08 137.38   0.00  31.95
   2_bss: 137.38   0.00  19.39  98.34   0.00  17.08 137.38   0.00  31.95
   2_xyz: 137.38   0.00  19.39  98.34   0.00  17.08 137.38   0.00  31.95
   2_adp: 140.07   0.00  17.43  82.95   0.00  14.75 140.07   0.00  32.02
   2_occ: 140.07   0.00  17.43  82.95   0.00  14.75 140.07   0.00  32.02
   3_bss: 140.07   0.00  17.43  82.95   0.00  14.75 140.07   0.00  32.02
   3_xyz: 140.07   0.00  17.43  82.95   0.00  14.75 140.07   0.00  32.02
   3_adp: 136.51   0.00  17.73  88.90   0.00  12.96 136.51   0.00  43.74
   3_occ: 136.51   0.00  17.73  88.90   0.00  12.96 136.51   0.00  43.74
   4_bss: 136.51   0.00  17.73  88.90   0.00  12.96 136.51   0.00  43.74
   4_xyz: 136.51   0.00  17.73  88.90   0.00  12.96 136.51   0.00  43.74
   4_adp: 124.90   0.00  17.17 101.36   0.00  11.41 124.90   1.03  48.57
   4_occ: 124.90   0.00  17.17 101.36   0.00  11.41 124.90   1.03  48.57
   5_bss: 124.90   0.00  17.17 101.36   0.00  11.41 124.90   1.03  48.57
   5_xyz: 124.90   0.00  17.17 101.36   0.00  11.41 124.90   1.03  48.57
   5_adp: 117.03   0.00  15.45  93.05   0.00  10.36 117.03   1.88  43.17
   5_occ: 117.03   0.00  15.45  93.05   0.00  10.36 117.03   1.88  43.17
   5_bss: 118.55   1.52  16.97  94.57   1.52  11.88 118.55   3.40  44.69
------------------------------------------------------------------------
 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:    1.208    0.010    0.412
   1_adp:    1.208    0.010    0.412
   1_occ:    1.208    0.010    0.412
   2_bss:    1.208    0.010    0.412
   2_xyz:    1.702    0.038    0.562
   2_adp:    1.702    0.038    0.562
   2_occ:    1.702    0.038    0.562
   3_bss:    1.702    0.038    0.562
   3_xyz:    1.972    0.068    0.788
   3_adp:    1.972    0.068    0.788
   3_occ:    1.972    0.068    0.788
   4_bss:    1.972    0.068    0.788
   4_xyz:    1.808    0.097    0.874
   4_adp:    1.808    0.097    0.874
   4_occ:    1.808    0.097    0.874
   5_bss:    1.808    0.097    0.874
   5_xyz:    1.941    0.062    0.919
   5_adp:    1.941    0.062    0.919
   5_occ:    1.941    0.062    0.919
   5_bss:    1.941    0.062    0.919
------------------------------------------------------------------------

CPU time actual refinement: 296.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1077/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_1077/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1077/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1077/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1077/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 296.33 
  Macro-tasks:
    bulk solvent and scale       = 51.59  
    individual site refinement   = 113.78 
    weights calculation          = 27.07  
    collect and process          = 5.22   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 197.76 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 86.52  
    alpha_beta                      = 6.73   
    target                          = 0.94   
    gradients_wrt_atomic_parameters = 94.56  
    fmodel                         = 8.37   
    r_factors                      = 0.43   
    phase_errors                   = 8.11   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 208.33 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.182 micro seconds
Total CPU time: 5.14 minutes
from_scatterers_fft:    630 calls, 86.16 s
gradients_fft:          576 calls, 83.76 s

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

# Date 2008-01-16 Time 03:07:43 PST -0800 (1200481663.56 s)
Start R-work = 0.5201, R-free = 0.5091 (no bulk solvent and anisotropic scale)
Final R-work = 0.1619, R-free = 0.2097 (no bulk solvent and anisotropic scale)

Start R-work = 0.5148, R-free = 0.5061
Final R-work = 0.1469, R-free = 0.1943