# Date 2008-01-16 Time 00:45:57 PST -0800 (1200473157.36 s)
#phil __OFF__

Command line arguments: "../151.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7359
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 151

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.96079
Completeness in resolution range: 0.948896
Completeness with d_max=infinity: 0.946009

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8310
                             d_min =   1.9608

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: (68.845, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.96079
Completeness in resolution range: 0.948896
Completeness with d_max=infinity: 0.946009

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8314 -  4.1955 [2175/2200]  1955   220  10.1%
  bin  2:  4.1955 -  3.3426 [2079/2098]  1872   207  10.0%
  bin  3:  3.3426 -  2.9238 [2051/2070]  1848   203   9.9%
  bin  4:  2.9238 -  2.6581 [2034/2064]  1826   208  10.2%
  bin  5:  2.6581 -  2.4685 [2034/2053]  1833   201   9.9%
  bin  6:  2.4685 -  2.3236 [2008/2033]  1806   202  10.1%
  bin  7:  2.3236 -  2.2076 [2009/2037]  1815   194   9.7%
  bin  8:  2.2076 -  2.1118 [2006/2042]  1795   211  10.5%
  bin  9:  2.1118 -  2.0307 [1997/2039]  1804   193   9.7%
  bin 10:  2.0307 -  1.9608 [1196/2008]  1076   120  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_151/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.40 -     2.10: 18
        2.10 -     2.80: 777
        2.80 -     3.50: 4544
        3.50 -     4.20: 9458
        4.20 -     4.90: 13920
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.398 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.444 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.455 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.701 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.766 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28712 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_151/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_151/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 = 68.845 46.22605 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4980   r_free= 0.4906   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.293893                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6794 0.99   1409  155 0.4090 0.3936      6.6069      6.6041|
|  2:  4.6794 -  3.7337 0.99   1359  152 0.4118 0.4385      6.7897      6.8403|
|  3:  3.7337 -  3.2675 0.99   1323  151 0.4635 0.4160      6.7001      6.6694|
|  4:  3.2675 -  2.9714 0.99   1330  139 0.4967 0.5080      6.5546      6.5354|
|  5:  2.9714 -  2.7598 0.99   1303  150 0.5189 0.4778      6.3759      6.4132|
|  6:  2.7598 -  2.5980 0.99   1308  144 0.5337 0.5436      6.2968      6.2283|
|  7:  2.5980 -  2.4685 0.99   1302  148 0.5258 0.5243      6.2466      6.1713|
|  8:  2.4685 -  2.3615 0.98   1294  140 0.5507 0.5316      6.2029      6.2151|
|  9:  2.3615 -  2.2710 0.98   1296  143 0.5309 0.5537      6.1124      6.2058|
| 10:  2.2710 -  2.1928 0.99   1284  142 0.5629 0.5555      6.1193      6.1011|
| 11:  2.1928 -  2.1245 0.98   1286  148 0.5424 0.5220      6.0374      6.0305|
| 12:  2.1245 -  2.0639 0.97   1270  137 0.5390 0.5088      5.9704      6.0255|
| 13:  2.0639 -  2.0097 0.97   1257  134 0.5508 0.5040      5.8998      5.8197|
| 14:  2.0097 -  1.9608 0.47    609   76 0.5514 0.5640       5.908      5.8088|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8314 -  4.6794  1409   155  0.66  37.45   0.79     0.71      83691.24|
|  2:  4.6794 -  3.7337  1359   152  0.67  37.93   0.88     0.75     119637.48|
|  3:  3.7337 -  3.2675  1323   151  0.55  47.55   0.84     0.68     127136.44|
|  4:  3.2675 -  2.9714  1330   139  0.45  56.12   0.78     0.55     116086.04|
|  5:  2.9714 -  2.7598  1303   150  0.33  64.98   0.73     0.41      94284.59|
|  6:  2.7598 -  2.5980  1308   144  0.27  69.80   0.71     0.32      84658.99|
|  7:  2.5980 -  2.4685  1302   148  0.22  73.38   0.75     0.26      76717.36|
|  8:  2.4685 -  2.3615  1294   140  0.23  73.13   0.71     0.27      68757.59|
|  9:  2.3615 -  2.2710  1296   143  0.24  71.71   0.73     0.30      61753.20|
| 10:  2.2710 -  2.1928  1284   142  0.27  69.58   0.72     0.33      53114.37|
| 11:  2.1928 -  2.1245  1286   148  0.26  70.67   0.75     0.34      52780.68|
| 12:  2.1245 -  2.0639  1270   137  0.25  71.15   0.76     0.33      46813.11|
| 13:  2.0639 -  2.0097  1257   134  0.25  71.17   0.72     0.34      40634.27|
| 14:  2.0097 -  1.9608   609    76  0.31  66.74   0.73     0.34      31206.74|
|alpha:            min =        0.26 max =            0.75 mean =         0.43|
|beta:             min =    31206.74 max =       127136.44 mean =     77776.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.98 mean =        62.49|
|phase err.(test): min =        0.00 max =           89.98 mean =        62.84|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.881304             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.881   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.879568              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.721   (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:       43 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      179 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      713 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1535 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2682 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3990 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5131 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6652 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7777 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.206 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.196 |       2.589 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5042   r_free= 0.4917   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.294521                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4901   r_free= 0.4790   ksol= 0.38   Bsol= 20.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.30,9.00,9.55,0.00,0.00,0.00); trace/3= 8.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.286565                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.823881             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.294   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.732463              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.516   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4901      final r-factor (work) = 0.4201          |
| start r-factor (free) = 0.4790      final r-factor (free) = 0.4380          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 99.8313 = 14.82 * 0.50 * 6.2906 + 1.00 * 53.2059                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.3126 = 14.82 * 0.50 * 6.2289 + 1.00 * 0.1440                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4201      final r-factor (work) = 0.3787          |
| start r-factor (free) = 0.4380      final r-factor (free) = 0.4420          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8058 = 1.73 * 1.00 * 6.2289 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6918 = 1.73 * 1.00 * 6.1596 + 1.00 * 0.0205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.11   14.27    None  None   None       |
|    all(noH): 2823   0      0.00    65.11   14.27    None  None   None       |
|    Sol.    : 438    0      0.00    65.11   23.62    None  None   None       |
|    Mac.    : 2385   0      0.00    53.51   12.55    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 -   6.511:  805   |   5:    32.556 -  39.068:  113        |
|      1:     6.511 -  13.023:  720   |   6:    39.068 -  45.579:   63        |
|      2:    13.023 -  19.534:  548   |   7:    45.579 -  52.090:   33        |
|      3:    19.534 -  26.045:  332   |   8:    52.090 -  58.601:    8        |
|      4:    26.045 -  32.556:  197   |   9:    58.601 -  65.113:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3787 r_free = 0.4420             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3785 r_free = 0.4425             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3785   r_free= 0.4425   ksol= 0.38   Bsol= 20.00   scale= 1.120   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.30,9.00,9.55,0.00,0.00,0.00); trace/3= 8.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.151725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3758   r_free= 0.4385   ksol= 0.35   Bsol= 34.80   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.91,4.76,6.00,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.152408                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.227004             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.773   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.245  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3758      final r-factor (work) = 0.2818          |
| start r-factor (free) = 0.4385      final r-factor (free) = 0.3456          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.9312 = 14.23 * 0.50 * 6.1555 + 1.00 * 0.1440                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.1572 = 14.23 * 0.50 * 6.0509 + 1.00 * 0.1137                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2818      final r-factor (work) = 0.2486          |
| start r-factor (free) = 0.3456      final r-factor (free) = 0.3146          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0398 = 0.66 * 1.00 * 6.0509 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9162 = 0.66 * 1.00 * 5.8767 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.57   13.66    None  None   None       |
|    all(noH): 2823   0      0.00    74.57   13.66    None  None   None       |
|    Sol.    : 438    0      0.00    74.57   32.22    None  None   None       |
|    Mac.    : 2385   0      0.00    59.13   10.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.457: 1098   |   5:    37.287 -  44.744:   93        |
|      1:     7.457 -  14.915:  839   |   6:    44.744 -  52.201:   70        |
|      2:    14.915 -  22.372:  350   |   7:    52.201 -  59.658:   23        |
|      3:    22.372 -  29.829:  215   |   8:    59.658 -  67.116:    8        |
|      4:    29.829 -  37.287:  124   |   9:    67.116 -  74.573:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2486 r_free = 0.3146             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2481 r_free = 0.3141             target_work(ml) = 5.826         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2481   r_free= 0.3141   ksol= 0.35   Bsol= 34.80   scale= 1.071   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.91,4.76,6.00,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.826190                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2461   r_free= 0.3122   ksol= 0.33   Bsol= 44.18   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,2.77,4.05,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.822805                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.769003              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.054  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.314719              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.059  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2461      final r-factor (work) = 0.1799          |
| start r-factor (free) = 0.3122      final r-factor (free) = 0.2314          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1312 = 4.77 * 0.50 * 5.8786 + 1.00 * 0.1137                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6903 = 4.77 * 0.50 * 5.7112 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1799      final r-factor (work) = 0.1631          |
| start r-factor (free) = 0.2314      final r-factor (free) = 0.2166          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8099 = 0.31 * 1.00 * 5.7112 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7400 = 0.31 * 1.00 * 5.4944 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.40   13.59    None  None   None       |
|    all(noH): 2823   0      0.00    77.40   13.59    None  None   None       |
|    Sol.    : 438    0      1.19    77.40   35.82    None  None   None       |
|    Mac.    : 2385   0      0.00    70.25   9.50     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.740: 1303   |   5:    38.698 -  46.438:  120        |
|      1:     7.740 -  15.479:  788   |   6:    46.438 -  54.177:   77        |
|      2:    15.479 -  23.219:  241   |   7:    54.177 -  61.917:   34        |
|      3:    23.219 -  30.958:  133   |   8:    61.917 -  69.656:    6        |
|      4:    30.958 -  38.698:  117   |   9:    69.656 -  77.396:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1631 r_free = 0.2166             target_work(ml) = 5.461         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1625 r_free = 0.2153             target_work(ml) = 5.458         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1625   r_free= 0.2153   ksol= 0.33   Bsol= 44.18   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,2.77,4.05,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.458283                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1617   r_free= 0.2153   ksol= 0.32   Bsol= 44.18   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,1.49,3.18,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.456836                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.417484              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.998  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.629544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.412  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1617      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.2153      final r-factor (free) = 0.1841          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7192 = 2.42 * 0.50 * 5.4993 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5710 = 2.42 * 0.50 * 5.3861 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1357      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.1841      final r-factor (free) = 0.1819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4018 = 0.63 * 1.00 * 5.3861 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4329 = 0.63 * 1.00 * 5.2897 + 1.00 * 0.1028                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.07   13.53    None  None   None       |
|    all(noH): 2823   0      0.00    92.07   13.53    None  None   None       |
|    Sol.    : 438    0      2.47    77.64   36.17    None  None   None       |
|    Mac.    : 2385   0      0.00    92.07   9.37     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 -   9.207: 1565   |   5:    46.037 -  55.244:   89        |
|      1:     9.207 -  18.415:  656   |   6:    55.244 -  64.451:   33        |
|      2:    18.415 -  27.622:  189   |   7:    64.451 -  73.658:    6        |
|      3:    27.622 -  36.829:  137   |   8:    73.658 -  82.866:    2        |
|      4:    36.829 -  46.037:  145   |   9:    82.866 -  92.073:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1322 r_free = 0.1819             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1318 r_free = 0.1820             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1820   ksol= 0.32   Bsol= 44.18   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,1.49,3.18,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.280051                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1826   ksol= 0.32   Bsol= 44.18   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,1.49,3.18,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.280129                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.880259              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.746  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.551569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.926   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1319      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1826      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0323 = 1.88 * 0.50 * 5.2883 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9982 = 1.88 * 0.50 * 5.2551 + 1.00 * 0.0577                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1708      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4423 = 2.55 * 1.00 * 5.2551 + 1.00 * 0.0335                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3166 = 2.55 * 1.00 * 5.2137 + 1.00 * 0.0136                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.19   13.99    None  None   None       |
|    all(noH): 2823   0      0.00    92.19   13.99    None  None   None       |
|    Sol.    : 438    0      1.82    85.52   39.25    None  None   None       |
|    Mac.    : 2385   0      0.00    92.19   9.35     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 -   9.219: 1593   |   5:    46.096 -  55.315:   98        |
|      1:     9.219 -  18.438:  645   |   6:    55.315 -  64.534:   50        |
|      2:    18.438 -  27.657:  176   |   7:    64.534 -  73.753:   37        |
|      3:    27.657 -  36.876:  111   |   8:    73.753 -  82.972:   13        |
|      4:    36.876 -  46.096:   97   |   9:    82.972 -  92.191:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1205 r_free = 0.1687             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1687             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1687   ksol= 0.32   Bsol= 44.18   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,1.49,3.18,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.207208                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6794 0.99   1409  155 0.1025 0.1253      5.4055      5.5512|
|  2:  4.6794 -  3.7337 0.99   1359  152 0.0898 0.1220      5.4808      5.6838|
|  3:  3.7337 -  3.2675 0.99   1323  151 0.1151 0.1571      5.5431      5.8779|
|  4:  3.2675 -  2.9714 0.99   1330  139 0.1301 0.1812      5.5022      5.6913|
|  5:  2.9714 -  2.7598 0.99   1303  150 0.1430 0.1663      5.4008      5.5569|
|  6:  2.7598 -  2.5980 0.99   1308  144 0.1337 0.2210      5.2709      5.5694|
|  7:  2.5980 -  2.4685 0.99   1302  148 0.1383 0.1770      5.2519      5.4026|
|  8:  2.4685 -  2.3615 0.98   1294  140 0.1287 0.1763      5.1585       5.385|
|  9:  2.3615 -  2.2710 0.98   1296  143 0.1289 0.1982      5.0855      5.4024|
| 10:  2.2710 -  2.1928 0.99   1284  142 0.1214 0.1691      5.0031      5.1841|
| 11:  2.1928 -  2.1245 0.98   1286  148 0.1205 0.2149      4.9955      5.3677|
| 12:  2.1245 -  2.0639 0.97   1270  137 0.1261 0.1739      4.9724      5.2745|
| 13:  2.0639 -  2.0097 0.97   1257  134 0.1139 0.1829      4.8163      5.0579|
| 14:  2.0097 -  1.9608 0.47    609   76 0.0977 0.1667      4.6541      4.9498|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8314 -  4.6794  1409   155  0.94   9.43   0.98     0.96       7564.41|
|  2:  4.6794 -  3.7337  1359   152  0.95   8.61   1.03     1.01       9798.83|
|  3:  3.7337 -  3.2675  1323   151  0.93  12.46   1.04     1.04      11761.03|
|  4:  3.2675 -  2.9714  1330   139  0.91  14.84   1.03     1.01      11423.19|
|  5:  2.9714 -  2.7598  1303   150  0.89  17.09   1.01     0.98       9615.49|
|  6:  2.7598 -  2.5980  1308   144  0.88  17.79   0.98     0.95       8014.95|
|  7:  2.5980 -  2.4685  1302   148  0.89  17.52   0.99     0.95       7337.04|
|  8:  2.4685 -  2.3615  1294   140  0.90  16.71   1.01     0.98       6376.81|
|  9:  2.3615 -  2.2710  1296   143  0.90  16.63   1.00     0.96       5515.68|
| 10:  2.2710 -  2.1928  1284   142  0.89  16.91   1.01     0.97       4875.65|
| 11:  2.1928 -  2.1245  1286   148  0.89  17.65   1.00     0.96       5086.63|
| 12:  2.1245 -  2.0639  1270   137  0.89  17.86   1.01     1.01       4875.72|
| 13:  2.0639 -  2.0097  1257   134  0.89  17.15   1.00     0.97       3636.18|
| 14:  2.0097 -  1.9608   609    76  0.93  12.88   0.99     0.96       2412.87|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2412.87 max =        11761.03 mean =      7244.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.27|
|phase err.(test): min =        0.00 max =           89.85 mean =        14.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1686   ksol= 0.31   Bsol= 46.04   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-0.43,1.41,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206882                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1686   ksol= 0.31   Bsol= 46.04   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-0.43,1.41,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206882                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6794 0.99   1409  155 0.1022 0.1254      5.4023      5.5504|
|  2:  4.6794 -  3.7337 0.99   1359  152 0.0900 0.1223      5.4825      5.6869|
|  3:  3.7337 -  3.2675 0.99   1323  151 0.1153 0.1572      5.5447      5.8793|
|  4:  3.2675 -  2.9714 0.99   1330  139 0.1300 0.1810       5.502      5.6904|
|  5:  2.9714 -  2.7598 0.99   1303  150 0.1429 0.1661      5.4003       5.556|
|  6:  2.7598 -  2.5980 0.99   1308  144 0.1335 0.2209      5.2701      5.5682|
|  7:  2.5980 -  2.4685 0.99   1302  148 0.1383 0.1772      5.2514       5.403|
|  8:  2.4685 -  2.3615 0.98   1294  140 0.1287 0.1762      5.1582      5.3849|
|  9:  2.3615 -  2.2710 0.98   1296  143 0.1289 0.1979      5.0852      5.4019|
| 10:  2.2710 -  2.1928 0.99   1284  142 0.1214 0.1691      5.0028      5.1845|
| 11:  2.1928 -  2.1245 0.98   1286  148 0.1204 0.2149      4.9955       5.368|
| 12:  2.1245 -  2.0639 0.97   1270  137 0.1261 0.1738      4.9721      5.2736|
| 13:  2.0639 -  2.0097 0.97   1257  134 0.1139 0.1824      4.8155      5.0568|
| 14:  2.0097 -  1.9608 0.47    609   76 0.0977 0.1663      4.6533      4.9477|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8314 -  4.6794  1409   155  0.94   9.42   0.98     0.95       7526.62|
|  2:  4.6794 -  3.7337  1359   152  0.95   8.62   1.03     1.01       9817.90|
|  3:  3.7337 -  3.2675  1323   151  0.93  12.49   1.05     1.04      11813.28|
|  4:  3.2675 -  2.9714  1330   139  0.91  14.85   1.03     1.01      11428.12|
|  5:  2.9714 -  2.7598  1303   150  0.89  17.07   1.01     0.98       9599.17|
|  6:  2.7598 -  2.5980  1308   144  0.88  17.78   0.98     0.95       8004.79|
|  7:  2.5980 -  2.4685  1302   148  0.89  17.52   1.00     0.96       7332.25|
|  8:  2.4685 -  2.3615  1294   140  0.90  16.71   1.01     0.98       6369.90|
|  9:  2.3615 -  2.2710  1296   143  0.90  16.62   1.00     0.96       5511.57|
| 10:  2.2710 -  2.1928  1284   142  0.89  16.91   1.01     0.98       4873.47|
| 11:  2.1928 -  2.1245  1286   148  0.89  17.65   1.01     0.96       5088.82|
| 12:  2.1245 -  2.0639  1270   137  0.89  17.86   1.02     1.01       4873.17|
| 13:  2.0639 -  2.0097  1257   134  0.89  17.13   1.00     0.97       3628.63|
| 14:  2.0097 -  1.9608   609    76  0.93  12.83   0.99     0.96       2403.17|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2403.17 max =        11813.28 mean =      7243.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.27|
|phase err.(test): min =        0.00 max =           89.99 mean =        14.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.549)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.87    94.06   15.85    None  None   None       |
|    all(noH): 2823   0      1.87    94.06   15.85    None  None   None       |
|    Sol.    : 438    0      3.68    87.39   41.12    None  None   None       |
|    Mac.    : 2385   0      1.87    94.06   11.21    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:     1.866 -  11.085: 1593   |   5:    47.962 -  57.181:   98        |
|      1:    11.085 -  20.305:  645   |   6:    57.181 -  66.400:   50        |
|      2:    20.305 -  29.524:  176   |   7:    66.400 -  75.619:   37        |
|      3:    29.524 -  38.743:  111   |   8:    75.619 -  84.838:   13        |
|      4:    38.743 -  47.962:   97   |   9:    84.838 -  94.057:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.469 - 4.161
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 317
   mapped sites are within: 0.731 - 4.161

peak=   10.392 closest distance to " CB  VAL A 230 " =    1.429
peak=    9.839 closest distance to " CB  VAL A 296 " =    1.539
peak=    8.086 closest distance to " O   HOH Z 130 " =    1.713
peak=    6.577 closest distance to " O   HOH Z 375 " =    1.594
peak=    6.283 closest distance to " CD2 LEU A   5 " =    1.254
peak=    5.868 closest distance to " CG  PRO A  54 " =    1.437
peak=    5.795 closest distance to " CG  ARG A 138 " =    1.056
peak=    5.666 closest distance to " NE2 GLN A  11 " =    1.112
peak=    5.436 closest distance to " O   HOH Z 236 " =    1.557
peak=    5.375 closest distance to " CG  LEU A   5 " =    1.140
peak=    5.314 closest distance to " O   HOH Z  65 " =    1.296
peak=    5.275 closest distance to " O   HOH Z   9 " =    2.044
peak=    5.240 closest distance to " NH1 ARG A 138 " =    0.879
peak=    5.219 closest distance to " CB  ARG A 275 " =    1.040
peak=    5.188 closest distance to " CG  LEU A 228 " =    1.163
peak=    5.153 closest distance to " O   HOH Z 427 " =    2.589
peak=    5.143 closest distance to " O   HOH Z 142 " =    1.763
peak=    5.070 closest distance to " O   HOH Z 417 " =    1.628
peak=    5.038 closest distance to " CB  VAL A 230 " =    1.188
peak=    4.880 closest distance to " O   HOH Z 369 " =    2.344
peak=    4.796 closest distance to " O   HOH Z 232 " =    2.369
peak=    4.795 closest distance to " CB  PRO A  54 " =    1.049
peak=    4.795 closest distance to " O   HOH Z 403 " =    1.750
peak=    4.728 closest distance to " O   HOH Z 423 " =    1.578
peak=    4.724 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.663 closest distance to " O   HOH Z 126 " =    2.082
peak=    4.623 closest distance to " O   HOH Z 222 " =    1.308
peak=    4.575 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.567 closest distance to " O   HOH Z 112 " =    1.260
peak=    4.540 closest distance to " O   HOH Z  91 " =    2.426
peak=    4.494 closest distance to " O   HOH Z  69 " =    2.172
peak=    4.470 closest distance to " CB  GLN A 223 " =    1.513
peak=    4.468 closest distance to " O   HOH Z 124 " =    1.326
peak=    4.461 closest distance to " O   HOH Z  39 " =    1.445
peak=    4.441 closest distance to " CG  LYS A  76 " =    1.671
peak=    4.438 closest distance to " NH2 ARG A  56 " =    2.064
peak=    4.414 closest distance to " O   HOH Z 346 " =    1.597
peak=    4.402 closest distance to " O   HOH Z 425 " =    1.529
peak=    4.332 closest distance to " O   HOH Z 272 " =    1.813
peak=    4.309 closest distance to " O   HOH Z 123 " =    1.274
peak=    4.262 closest distance to " CG  PRO A 198 " =    1.247
peak=    4.232 closest distance to " CD1AILE A 234 " =    0.906
peak=    4.211 closest distance to " O   HOH Z 380 " =    2.131
peak=    4.209 closest distance to " O   HOH Z 143 " =    1.533
peak=    4.191 closest distance to " CB  ARG A 138 " =    1.185
peak=    4.181 closest distance to " O   HOH Z 402 " =    1.359
peak=    4.168 closest distance to " O   HOH Z 126 " =    1.800
peak=    4.158 closest distance to " CB  VAL A 265 " =    1.348
peak=    4.153 closest distance to " NH2AARG A 190 " =    1.981
peak=    4.133 closest distance to " CB  VAL A 202 " =    1.585
peak=    4.132 closest distance to " O   HOH Z  85 " =    1.393
peak=    4.123 closest distance to " O   HOH Z 423 " =    1.220
peak=    4.109 closest distance to " CA  ASN A 127 " =    1.030
peak=    4.102 closest distance to " OG ASER A 258 " =    3.020
peak=    4.092 closest distance to " CB AVAL A  41 " =    1.316
peak=    4.085 closest distance to " O   HOH Z 193 " =    1.578
peak=    4.074 closest distance to " CB  ASN A 148 " =    1.346
peak=    4.067 closest distance to " CB  ASN A 142 " =    1.098
peak=    4.063 closest distance to " O   HOH Z 359 " =    1.449
peak=    4.061 closest distance to " CB  GLU A 277 " =    3.490
peak=    4.050 closest distance to " O   HOH Z  11 " =    1.374
peak=    4.048 closest distance to " CB  GLN A 183 " =    1.245
peak=    4.047 closest distance to " O   HOH Z 248 " =    1.266
peak=    4.036 closest distance to " CB  SER A  26 " =    1.724
peak=    4.013 closest distance to " O   HOH Z  61 " =    1.695
peak=    4.013 closest distance to " O   HOH Z 234 " =    3.688
peak=    4.003 closest distance to " CB  ASN A  39 " =    0.959
peak=    3.996 closest distance to " CA  TYR A  30 " =    0.920
peak=    3.994 closest distance to " CG  GLN A  58 " =    0.971
peak=    3.991 closest distance to " CG  GLN A  11 " =    2.181
peak=    3.972 closest distance to " CA  PHE A 283 " =    1.167
peak=    3.968 closest distance to " O   HOH Z 422 " =    2.334
peak=    3.951 closest distance to " CG2 ILE A 234 " =    0.912
peak=    3.949 closest distance to " O   HOH Z 287 " =    1.756
peak=    3.948 closest distance to " O   HOH Z 365 " =    2.711
peak=    3.919 closest distance to " CB  GLN A  88 " =    1.336
peak=    3.916 closest distance to " CD  ARG A 269 " =    1.019
peak=    3.877 closest distance to " CG AARG A 275 " =    1.064
peak=    3.876 closest distance to " O   HOH Z 298 " =    1.619
peak=    3.872 closest distance to " O   HOH Z 303 " =    2.218
peak=    3.866 closest distance to " CG2 VAL A 257 " =    0.862
peak=    3.854 closest distance to " O   HOH Z  24 " =    1.771
peak=    3.852 closest distance to " CB  ARG A 219 " =    0.942
peak=    3.848 closest distance to " O   HOH Z  59 " =    1.602
peak=    3.847 closest distance to " CB  ALA A 114 " =    1.377
peak=    3.842 closest distance to " CB  TRP A 266 " =    1.173
peak=    3.839 closest distance to " CB  SER A   3 " =    1.268
peak=    3.825 closest distance to " O   HOH Z 188 " =    2.682
peak=    3.823 closest distance to " O   HOH Z  10 " =    1.748
peak=    3.822 closest distance to " CB  ARG A  79 " =    1.280
peak=    3.820 closest distance to " O   HOH Z 423 " =    1.735
peak=    3.819 closest distance to " O   HOH Z 362 " =    2.286
peak=    3.814 closest distance to " O   HOH Z 389 " =    1.425
peak=    3.813 closest distance to " CB  ASN A 110 " =    1.077
peak=    3.812 closest distance to " NZ  LYS A 117 " =    3.057
peak=    3.784 closest distance to " O   HOH Z 128 " =    2.033
peak=    3.783 closest distance to " CB  LEU A 300 " =    0.905
peak=    3.783 closest distance to " CG  PRO A 213 " =    1.189
peak=    3.719 closest distance to " NH2AARG A 145 " =    1.097
peak=    3.717 closest distance to " O   HOH Z  26 " =    1.285
peak=    3.707 closest distance to " O   HOH Z 425 " =    2.104
peak=    3.703 closest distance to " O   HOH Z 130 " =    1.906
peak=    3.701 closest distance to " CB  LYS A 117 " =    1.187
peak=    3.699 closest distance to " N   ASP A 162 " =    1.050
peak=    3.695 closest distance to " CB  THR A  52 " =    0.940
peak=    3.692 closest distance to " OG BSER A 212 " =    2.797
peak=    3.680 closest distance to " O   HOH Z 406 " =    1.430
peak=    3.680 closest distance to " CB  SER A  63 " =    1.283
peak=    3.678 closest distance to " O   HOH Z 344 " =    1.266
peak=    3.673 closest distance to " O   HOH Z 337 " =    1.951
peak=    3.669 closest distance to " CA  ASN A 215 " =    0.962
peak=    3.660 closest distance to " O   HOH Z 146 " =    1.582
peak=    3.650 closest distance to " CB  ARG A 190 " =    1.537
peak=    3.645 closest distance to " CB  TYR A 169 " =    0.829
peak=    3.640 closest distance to " CB  ASN A 215 " =    1.122
peak=    3.639 closest distance to " ND2 ASN A 187 " =    1.600
peak=    3.638 closest distance to " O   HOH Z 411 " =    3.960
peak=    3.637 closest distance to " CZ  PHE A 218 " =    1.128
peak=    3.635 closest distance to " CB  THR A  31 " =    1.623
peak=    3.635 closest distance to " N   GLN A 278 " =    1.486
peak=    3.634 closest distance to " O   HOH Z 368 " =    2.141
peak=    3.632 closest distance to " O   HOH Z  44 " =    1.897
peak=    3.632 closest distance to " O   HOH Z  55 " =    1.975
peak=    3.628 closest distance to " CB  ALA A 248 " =    1.314
peak=    3.619 closest distance to " O   HOH Z 258 " =    2.017
peak=    3.616 closest distance to " O   HOH Z 357 " =    1.947
peak=    3.609 closest distance to " O   HOH Z 181 " =    2.200
peak=    3.599 closest distance to " CA  ALA A 160 " =    0.920
peak=    3.598 closest distance to " CB  HIS A 108 " =    0.896
peak=    3.593 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.585 closest distance to " CA  LYS A 117 " =    1.127
peak=    3.584 closest distance to " O   PRO A 198 " =    1.553
peak=    3.582 closest distance to " O   THR A 182 " =    1.488
peak=    3.577 closest distance to " CB  ARG A  79 " =    0.916
peak=    3.576 closest distance to " O  BHOH Z 338 " =    2.401
peak=    3.571 closest distance to " CB  GLN A 278 " =    0.959
peak=    3.561 closest distance to " CB  PHE A 204 " =    0.944
peak=    3.555 closest distance to " NE  ARG A  56 " =    3.450
peak=    3.552 closest distance to " OE1 GLU A   2 " =    1.916
peak=    3.551 closest distance to " O   HOH Z 405 " =    1.419
peak=    3.549 closest distance to " CD  ARG A 138 " =    1.036
peak=    3.546 closest distance to " O   HOH Z 361 " =    3.637
peak=    3.546 closest distance to " O   HOH Z  88 " =    3.028
peak=    3.542 closest distance to " CZ  PHE A  38 " =    1.154
peak=    3.541 closest distance to " O   ASP A 124 " =    1.060
peak=    3.535 closest distance to " O   HOH Z 251 " =    1.484
peak=    3.529 closest distance to " O   HOH Z 203 " =    1.476
peak=    3.528 closest distance to " O   HOH Z 437 " =    1.819
peak=    3.528 closest distance to " O   HOH Z 371 " =    1.787
peak=    3.528 closest distance to " O   HOH Z  22 " =    2.036
peak=    3.527 closest distance to " O   HOH Z 371 " =    2.756
peak=    3.525 closest distance to " CA  ILE A 234 " =    1.067
peak=    3.524 closest distance to " ND2BASN A 224 " =    0.826
peak=    3.522 closest distance to " O   HOH Z 258 " =    1.189
peak=    3.518 closest distance to " O   HOH Z 261 " =    1.839
peak=    3.514 closest distance to " O   HOH Z 193 " =    1.480
peak=    3.513 closest distance to " O   HOH Z 299 " =    4.161
peak=    3.512 closest distance to " N   ALA A 256 " =    1.023
peak=    3.507 closest distance to " OG BSER A 164 " =    2.241
peak=    3.504 closest distance to " O   THR A 220 " =    1.157
peak=    3.501 closest distance to " O   HOH Z  69 " =    1.056
peak=    3.501 closest distance to " CG2 ILE A  20 " =    1.747
peak=    3.497 closest distance to " CB  ASP A 124 " =    0.903
peak=    3.496 closest distance to " O   HOH Z 126 " =    1.544
peak=    3.496 closest distance to " OG BSER A 210 " =    1.487
peak=    3.496 closest distance to " O   HOH Z  68 " =    2.021
peak=    3.496 closest distance to " O   HOH Z 290 " =    0.969
peak=    3.489 closest distance to " CD2 TRP A 179 " =    1.335
peak=    3.482 closest distance to " O   HOH Z 427 " =    1.304
peak=    3.479 closest distance to " O   HOH Z  76 " =    0.977
peak=    3.479 closest distance to " CG  MET A 113 " =    0.953
peak=    3.478 closest distance to " O   HOH Z  40 " =    1.603
peak=    3.476 closest distance to " O   HOH Z 148 " =    2.275
peak=    3.476 closest distance to " O   HOH Z 145 " =    3.850
peak=    3.476 closest distance to " O   HOH Z 345 " =    3.088
peak=    3.475 closest distance to " CG  LEU A 167 " =    1.312
peak=    3.457 closest distance to " O   HOH Z 419 " =    1.901
peak=    3.452 closest distance to " N   SER A 135 " =    1.443
peak=    3.452 closest distance to " O   HOH Z  97 " =    2.127
peak=    3.452 closest distance to " CA  ASN A 217 " =    1.128
peak=    3.437 closest distance to " CA  ARG A 195 " =    1.211
peak=    3.433 closest distance to " O   HOH Z 337 " =    3.562
peak=    3.432 closest distance to " CB  ASP A 191 " =    1.267
peak=    3.431 closest distance to " O   HOH Z 418 " =    0.910
peak=    3.431 closest distance to " CB  GLU A 128 " =    1.094
peak=    3.430 closest distance to " CE  LYS A 119 " =    1.201
peak=    3.430 closest distance to " O   HOH Z 214 " =    2.593
peak=    3.426 closest distance to " O   HOH Z 193 " =    1.420
peak=    3.425 closest distance to " CE3 TRP A 150 " =    1.074
peak=    3.422 closest distance to " O   HOH Z 132 " =    2.730
peak=    3.412 closest distance to " CB  TRP A 179 " =    1.293
peak=    3.410 closest distance to " O   HOH Z 394 " =    1.710
peak=    3.409 closest distance to " O   HOH Z  59 " =    2.091
peak=    3.408 closest distance to " CA  ARG A  36 " =    0.931
peak=    3.407 closest distance to " N   ASN A  39 " =    1.173
peak=    3.403 closest distance to " O   HOH Z   6 " =    1.459
peak=    3.403 closest distance to " CE  LYS A  76 " =    0.905
peak=    3.400 closest distance to " CG BARG A 102 " =    1.904
peak=    3.394 closest distance to " CE AMET A  47 " =    1.403
peak=    3.390 closest distance to " CA  ASP A 124 " =    0.731
peak=    3.387 closest distance to " O   HOH Z  43 " =    1.889
peak=    3.386 closest distance to " O   HOH Z 421 " =    2.012
peak=    3.383 closest distance to " N   PHE A 130 " =    1.306
peak=    3.378 closest distance to " O   HOH Z 222 " =    2.035
peak=    3.377 closest distance to " CD2 LEU A 228 " =    1.211
peak=    3.374 closest distance to " O   HOH Z 327 " =    1.997
peak=    3.373 closest distance to " N   CYS A 260 " =    0.927
peak=    3.371 closest distance to " O   HOH Z  80 " =    1.532
peak=    3.370 closest distance to " CB  SER A 216 " =    0.892
peak=    3.370 closest distance to " O   PRO A 198 " =    1.365
peak=    3.368 closest distance to " O   HOH Z   7 " =    1.358
peak=    3.367 closest distance to " CB  TRP A 150 " =    1.253
peak=    3.367 closest distance to " O   HOH Z 188 " =    1.496
peak=    3.366 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.365 closest distance to " NE1 TRP A 274 " =    0.983
peak=    3.359 closest distance to " O   HOH Z 106 " =    2.980
peak=    3.359 closest distance to " CG2 THR A 221 " =    1.156
peak=    3.356 closest distance to " O   HOH Z 145 " =    2.219
peak=    3.351 closest distance to " CB  TYR A  30 " =    1.663
peak=    3.351 closest distance to " OG  SER A  62 " =    2.853
peak=    3.350 closest distance to " O   HOH Z 109 " =    2.453
peak=    3.348 closest distance to " O   HOH Z   1 " =    1.663
peak=    3.347 closest distance to " CB  ALA A  43 " =    0.940
peak=    3.346 closest distance to " CG  LEU A 281 " =    1.000
peak=    3.337 closest distance to " O   HOH Z 272 " =    2.082
peak=    3.328 closest distance to " O   HOH Z 352 " =    1.434
peak=    3.327 closest distance to " O   HOH Z 158 " =    3.176
peak=    3.326 closest distance to " O   HOH Z 172 " =    2.844
peak=    3.323 closest distance to " NH2BARG A 190 " =    1.498
peak=    3.319 closest distance to " NZ  LYS A  48 " =    1.119
peak=    3.318 closest distance to " CB  ALA A 114 " =    0.860
peak=    3.316 closest distance to " O   HOH Z   2 " =    1.765
peak=    3.313 closest distance to " O   HOH Z 158 " =    3.071
peak=    3.307 closest distance to " O   HOH Z 323 " =    1.489
peak=    3.302 closest distance to " O   HOH Z  85 " =    1.721
peak=    3.290 closest distance to " CG2 ILE A 120 " =    1.283
peak=    3.289 closest distance to " CA  VAL A 125 " =    1.051
peak=    3.288 closest distance to " O   HOH Z 402 " =    1.475
peak=    3.277 closest distance to " O   HOH Z 117 " =    1.905
peak=    3.266 closest distance to " O   HOH Z 303 " =    2.526
peak=    3.260 closest distance to " O   HOH Z 392 " =    1.661
peak=    3.259 closest distance to " O   HOH Z 261 " =    1.714
peak=    3.259 closest distance to " CB  SER A 210 " =    0.789
peak=    3.257 closest distance to " NE BARG A 275 " =    1.350
peak=    3.253 closest distance to " CG  GLN A  89 " =    1.445
peak=    3.249 closest distance to " CB  SER A 273 " =    0.927
peak=    3.247 closest distance to " CG1 ILE A 120 " =    1.335
peak=    3.246 closest distance to " O   HOH Z 365 " =    1.611
peak=    3.243 closest distance to " CG  LYS A 289 " =    1.357
peak=    3.243 closest distance to " O   HOH Z  41 " =    2.558
peak=    3.240 closest distance to " CG  GLN A  88 " =    1.170
peak=    3.240 closest distance to " CA  ALA A 129 " =    1.413
peak=    3.240 closest distance to " CE1 TYR A 186 " =    1.214
peak=    3.238 closest distance to " CA  SER A  87 " =    1.048
peak=    3.237 closest distance to " CE3 TRP A 274 " =    1.248
peak=    3.236 closest distance to " O   HOH Z  55 " =    1.754
peak=    3.234 closest distance to " O   HOH Z 305 " =    3.383
peak=    3.233 closest distance to " CH2 TRP A 266 " =    1.035
peak=    3.228 closest distance to " O   HOH Z 250 " =    1.418
peak=    3.224 closest distance to " C   PHE A  59 " =    0.847
peak=    3.224 closest distance to " O   HOH Z 291 " =    1.524
peak=    3.220 closest distance to " CA  ALA A  51 " =    1.013
peak=    3.218 closest distance to " O   HOH Z  40 " =    2.383
peak=    3.214 closest distance to " O   HOH Z   4 " =    1.360
peak=    3.213 closest distance to " O   HOH Z  59 " =    2.326
peak=    3.211 closest distance to " CB  LEU A 237 " =    0.831
peak=    3.207 closest distance to " CA  TRP A 150 " =    1.044
peak=    3.205 closest distance to " N   SER A 271 " =    0.995
peak=    3.201 closest distance to " CB  ASN A 187 " =    1.083
peak=    3.200 closest distance to " O   HOH Z  83 " =    1.209
peak=    3.200 closest distance to " CD1 LEU A  96 " =    0.749
peak=    3.200 closest distance to " CA  ARG A 156 " =    1.051
peak=    3.200 closest distance to " CA  SER A 210 " =    1.548
peak=    3.197 closest distance to " CA  GLY A 267 " =    1.134
peak=    3.191 closest distance to " O   HOH Z 344 " =    2.775
peak=    3.188 closest distance to " CD1 ILE A  33 " =    1.842
peak=    3.186 closest distance to " CG2 THR A 220 " =    0.863
peak=    3.186 closest distance to " O   HOH Z 184 " =    1.350
peak=    3.171 closest distance to " CB  PRO A 198 " =    1.008
peak=    3.167 closest distance to " O   HOH Z 438 " =    2.875
peak=    3.165 closest distance to " N   TYR A 116 " =    1.520
peak=    3.159 closest distance to " CA  MET A 105 " =    0.977
peak=    3.158 closest distance to " CA  SER A 146 " =    1.892
peak=    3.157 closest distance to " CB  SER A 276 " =    1.213
peak=    3.150 closest distance to " O   HOH Z 153 " =    3.705
peak=    3.150 closest distance to " O   HOH Z  85 " =    1.987
peak=    3.148 closest distance to " CD  GLN A 194 " =    1.364
peak=    3.147 closest distance to " NH1BARG A 145 " =    1.659
peak=    3.146 closest distance to " CA  LYS A 290 " =    1.203
peak=    3.144 closest distance to " O   HOH Z  95 " =    1.089
peak=    3.139 closest distance to " O   HOH Z 227 " =    1.860
peak=    3.123 closest distance to " CB  ASN A 215 " =    1.757
peak=    3.120 closest distance to " O   HOH Z 375 " =    1.961
peak=    3.116 closest distance to " O   HOH Z 183 " =    1.798
peak=    3.110 closest distance to " CD2 TYR A 186 " =    1.098
peak=    3.106 closest distance to " CG1 ILE A 151 " =    1.288
peak=    3.099 closest distance to " CE  LYS A 119 " =    3.548
peak=    3.098 closest distance to " O   HOH Z 128 " =    1.844
peak=    3.098 closest distance to " O   HOH Z 325 " =    1.969
peak=    3.098 closest distance to " CG  LYS A 119 " =    1.029
peak=    3.097 closest distance to " CB  GLU A 152 " =    1.241
peak=    3.095 closest distance to " O   HOH Z 162 " =    1.380
peak=    3.091 closest distance to " O   HOH Z 180 " =    2.148
peak=    3.081 closest distance to " O   HOH Z 156 " =    3.113
peak=    3.073 closest distance to " O   HOH Z 361 " =    2.974
peak=    3.069 closest distance to " N   GLU A   2 " =    1.461
peak=    3.069 closest distance to " O   HOH Z 389 " =    1.473
peak=    3.063 closest distance to " OG BSER A  99 " =    2.272
peak=    3.057 closest distance to " O   HOH Z  51 " =    1.304
peak=    3.037 closest distance to " O   HOH Z  40 " =    1.367
peak=    3.036 closest distance to " OE2 GLU A   2 " =    1.774
peak=    3.032 closest distance to " O   HOH Z 392 " =    1.050

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.742 - 5.665
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 207
   mapped sites are within: 0.742 - 5.665

peak=   -4.472 closest distance to " OG BSER A 134 " =    1.262
peak=   -4.443 closest distance to " CD  ARG A 156 " =    1.936
peak=   -4.371 closest distance to " O   HOH Z 131 " =    4.105
peak=   -4.317 closest distance to " CB  ALA A  43 " =    2.440
peak=   -4.253 closest distance to " C   HIS A 108 " =    1.239
peak=   -4.248 closest distance to " CD  ARG A 138 " =    1.250
peak=   -4.218 closest distance to " CG  GLN A  58 " =    1.045
peak=   -4.208 closest distance to " O   HOH Z 211 " =    1.159
peak=   -4.104 closest distance to " O   VAL A  67 " =    2.435
peak=   -4.086 closest distance to " O   HOH Z 266 " =    5.294
peak=   -4.078 closest distance to " O   PRO A 198 " =    1.204
peak=   -4.078 closest distance to " CD1 LEU A 255 " =    2.780
peak=   -4.023 closest distance to " O   HOH Z 185 " =    1.845
peak=   -4.009 closest distance to " O   HOH Z  69 " =    1.908
peak=   -3.978 closest distance to " CG2 VAL A 230 " =    0.785
peak=   -3.975 closest distance to " CB  ALA A 248 " =    2.070
peak=   -3.941 closest distance to " O   HOH Z 193 " =    1.273
peak=   -3.893 closest distance to " CB  ALA A 114 " =    2.429
peak=   -3.876 closest distance to " CG  GLN A 223 " =    2.282
peak=   -3.874 closest distance to " CG2 ILE A  20 " =    2.847
peak=   -3.868 closest distance to " O   HOH Z 394 " =    1.486
peak=   -3.854 closest distance to " O   ALA A 292 " =    2.171
peak=   -3.845 closest distance to " CD  ARG A  14 " =    3.318
peak=   -3.845 closest distance to " CB  VAL A 230 " =    0.943
peak=   -3.837 closest distance to " CD2 TYR A 293 " =    1.929
peak=   -3.800 closest distance to " CZ2 TRP A 274 " =    0.934
peak=   -3.789 closest distance to " O   HOH Z 107 " =    0.909
peak=   -3.784 closest distance to " O   HOH Z  11 " =    1.810
peak=   -3.775 closest distance to " CB  PHE A 192 " =    1.941
peak=   -3.769 closest distance to " CG  ARG A 138 " =    0.945
peak=   -3.764 closest distance to " O   SER A  22 " =    2.445
peak=   -3.763 closest distance to " O   SER A 135 " =    1.403
peak=   -3.759 closest distance to " N   ASN A 127 " =    1.361
peak=   -3.743 closest distance to " O   HOH Z 100 " =    0.961
peak=   -3.740 closest distance to " CB  SER A 210 " =    1.068
peak=   -3.710 closest distance to " N   ALA A 248 " =    1.544
peak=   -3.708 closest distance to " O   PRO A 163 " =    1.930
peak=   -3.704 closest distance to " CG2 VAL A 202 " =    2.681
peak=   -3.697 closest distance to " CE2 TYR A  30 " =    2.781
peak=   -3.695 closest distance to " OE1 GLN A 183 " =    1.803
peak=   -3.672 closest distance to " CA  GLY A  35 " =    2.047
peak=   -3.654 closest distance to " O   SER A 271 " =    2.169
peak=   -3.648 closest distance to " CB  GLN A  55 " =    1.155
peak=   -3.636 closest distance to " O   HOH Z 281 " =    2.716
peak=   -3.632 closest distance to " CE BMET A  47 " =    1.074
peak=   -3.632 closest distance to " CD2 HIS A 207 " =    2.214
peak=   -3.632 closest distance to " OE2 GLU A 152 " =    1.262
peak=   -3.619 closest distance to " O   HOH Z 238 " =    0.907
peak=   -3.609 closest distance to " NE2 GLN A  55 " =    0.926
peak=   -3.584 closest distance to " O   HOH Z 165 " =    2.103
peak=   -3.579 closest distance to " CD2 PHE A 225 " =    1.029
peak=   -3.575 closest distance to " CA  GLY A 203 " =    2.502
peak=   -3.563 closest distance to " CE  MET A 105 " =    2.447
peak=   -3.559 closest distance to " O   HOH Z 423 " =    2.495
peak=   -3.558 closest distance to " CG1 VAL A 112 " =    2.962
peak=   -3.557 closest distance to " O   HOH Z 208 " =    2.132
peak=   -3.550 closest distance to " O   SER A  95 " =    1.474
peak=   -3.545 closest distance to " CD1 ILE A 239 " =    2.573
peak=   -3.538 closest distance to " CD  GLN A  88 " =    1.231
peak=   -3.533 closest distance to " O   HOH Z 231 " =    2.100
peak=   -3.526 closest distance to " ND2 ASN A 249 " =    2.134
peak=   -3.524 closest distance to " OD2 ASP A 191 " =    1.323
peak=   -3.512 closest distance to " OG  SER A  97 " =    2.264
peak=   -3.510 closest distance to " N   ASP A 286 " =    2.092
peak=   -3.491 closest distance to " O   HOH Z 406 " =    0.910
peak=   -3.491 closest distance to " O   GLN A 240 " =    1.987
peak=   -3.491 closest distance to " OE1 GLN A  88 " =    1.243
peak=   -3.489 closest distance to " CD1 LEU A 101 " =    2.229
peak=   -3.482 closest distance to " O   HOH Z 166 " =    2.075
peak=   -3.478 closest distance to " CA  ASP A 298 " =    1.051
peak=   -3.474 closest distance to " O   HOH Z 235 " =    1.108
peak=   -3.469 closest distance to " O   HOH Z 377 " =    1.226
peak=   -3.468 closest distance to " ND2 ASN A 187 " =    1.486
peak=   -3.466 closest distance to " CB  ASP A  27 " =    2.338
peak=   -3.458 closest distance to " O   HOH Z 134 " =    4.097
peak=   -3.456 closest distance to " NE2 GLN A  11 " =    1.921
peak=   -3.456 closest distance to " O   HOH Z 371 " =    2.434
peak=   -3.454 closest distance to " CA  GLY A 133 " =    1.895
peak=   -3.449 closest distance to " O   MET A  40 " =    2.832
peak=   -3.449 closest distance to " CD2 LEU A 237 " =    2.614
peak=   -3.446 closest distance to " O   HOH Z 236 " =    1.540
peak=   -3.445 closest distance to " O   TRP A  70 " =    1.421
peak=   -3.432 closest distance to " CG  TRP A 266 " =    1.932
peak=   -3.425 closest distance to " CD  GLN A  77 " =    1.220
peak=   -3.421 closest distance to " O   HOH Z  26 " =    1.004
peak=   -3.417 closest distance to " O   HOH Z 298 " =    2.796
peak=   -3.416 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.416 closest distance to " OG  SER A  87 " =    1.414
peak=   -3.414 closest distance to " O   HOH Z 256 " =    1.344
peak=   -3.411 closest distance to " O   LEU A 300 " =    2.299
peak=   -3.406 closest distance to " O   HOH Z 286 " =    1.646
peak=   -3.404 closest distance to " NH2 ARG A  79 " =    2.105
peak=   -3.399 closest distance to " N   ALA A 226 " =    1.922
peak=   -3.399 closest distance to " O   HOH Z 385 " =    1.652
peak=   -3.384 closest distance to " CD  LYS A 289 " =    2.415
peak=   -3.383 closest distance to " CD  PRO A 213 " =    1.963
peak=   -3.380 closest distance to " C   LEU A 222 " =    1.365
peak=   -3.380 closest distance to " OXT GLY A 302 " =    3.034
peak=   -3.378 closest distance to " N   THR A 157 " =    1.420
peak=   -3.377 closest distance to " OH  TYR A 172 " =    1.751
peak=   -3.373 closest distance to " CE3 TRP A 274 " =    2.205
peak=   -3.370 closest distance to " O   ASN A 187 " =    1.508
peak=   -3.369 closest distance to " CG  LEU A 228 " =    1.023
peak=   -3.368 closest distance to " O   HOH Z 283 " =    2.365
peak=   -3.366 closest distance to " O   HOH Z 389 " =    1.412
peak=   -3.364 closest distance to " CZ  PHE A  38 " =    2.409
peak=   -3.362 closest distance to " CE1 TYR A 247 " =    2.537
peak=   -3.354 closest distance to " O   HOH Z  64 " =    1.473
peak=   -3.352 closest distance to " O   HOH Z 201 " =    2.098
peak=   -3.345 closest distance to " O   ILE A  49 " =    1.664
peak=   -3.342 closest distance to " O   HOH Z 351 " =    1.546
peak=   -3.338 closest distance to " CB  ASP A 132 " =    2.403
peak=   -3.337 closest distance to " N   ALA A 244 " =    1.314
peak=   -3.332 closest distance to " O   HOH Z 346 " =    1.712
peak=   -3.329 closest distance to " CA  HIS A 207 " =    1.247
peak=   -3.328 closest distance to " CG  PHE A 283 " =    2.571
peak=   -3.326 closest distance to " OE1 GLN A 183 " =    1.576
peak=   -3.324 closest distance to " O   HOH Z 359 " =    1.707
peak=   -3.322 closest distance to " CZ3 TRP A 179 " =    1.271
peak=   -3.307 closest distance to " O   HOH Z 392 " =    0.850
peak=   -3.303 closest distance to " O   HOH Z 359 " =    3.325
peak=   -3.300 closest distance to " CA  TYR A  68 " =    1.058
peak=   -3.297 closest distance to " O   HOH Z 126 " =    1.706
peak=   -3.294 closest distance to " CB  ALA A   7 " =    2.087
peak=   -3.293 closest distance to " O   HOH Z 231 " =    1.374
peak=   -3.287 closest distance to " O   HOH Z 111 " =    4.718
peak=   -3.287 closest distance to " O   HOH Z 114 " =    3.213
peak=   -3.287 closest distance to " C   ARG A 269 " =    1.299
peak=   -3.284 closest distance to " OE1 GLU A 277 " =    2.195
peak=   -3.279 closest distance to " O   VAL A 189 " =    2.526
peak=   -3.279 closest distance to " CZ  ARG A 259 " =    0.974
peak=   -3.278 closest distance to " O   HOH Z 372 " =    2.184
peak=   -3.269 closest distance to " CA  GLY A 241 " =    2.264
peak=   -3.267 closest distance to " NE1 TRP A  70 " =    1.629
peak=   -3.263 closest distance to " O   HOH Z 430 " =    2.075
peak=   -3.262 closest distance to " O   HOH Z 387 " =    2.333
peak=   -3.262 closest distance to " O   HOH Z 364 " =    2.724
peak=   -3.261 closest distance to " O   HOH Z 352 " =    1.579
peak=   -3.260 closest distance to " OG  SER A  63 " =    1.245
peak=   -3.259 closest distance to " CZ2 TRP A  70 " =    2.227
peak=   -3.257 closest distance to " ND2 ASN A 285 " =    1.997
peak=   -3.257 closest distance to " N   VAL A  72 " =    1.814
peak=   -3.255 closest distance to " O   HOH Z 111 " =    2.025
peak=   -3.255 closest distance to " O   SER A 276 " =    1.565
peak=   -3.254 closest distance to " O   HOH Z 244 " =    1.740
peak=   -3.253 closest distance to " O   HOH Z 191 " =    5.665
peak=   -3.251 closest distance to " O   ASP A  27 " =    1.959
peak=   -3.243 closest distance to " O   VAL A 125 " =    2.135
peak=   -3.240 closest distance to " O   ALA A 227 " =    1.444
peak=   -3.238 closest distance to " N   MET A 188 " =    1.936
peak=   -3.237 closest distance to " NZ  LYS A 166 " =    1.397
peak=   -3.235 closest distance to " O   HOH Z 345 " =    1.911
peak=   -3.233 closest distance to " OG  SER A  62 " =    4.188
peak=   -3.233 closest distance to " O   HOH Z 298 " =    3.762
peak=   -3.226 closest distance to " O   HOH Z 216 " =    1.523
peak=   -3.224 closest distance to " O   HOH Z 155 " =    1.279
peak=   -3.224 closest distance to " NE2 GLN A 223 " =    1.677
peak=   -3.223 closest distance to " O   HOH Z 427 " =    1.807
peak=   -3.223 closest distance to " ND2 ASN A 252 " =    2.060
peak=   -3.222 closest distance to " N   GLN A  58 " =    1.306
peak=   -3.210 closest distance to " NH2 ARG A 219 " =    1.661
peak=   -3.210 closest distance to " O   HOH Z 415 " =    1.466
peak=   -3.203 closest distance to " NE2 GLN A 278 " =    1.647
peak=   -3.202 closest distance to " O   LEU A 297 " =    0.742
peak=   -3.202 closest distance to " O   PHE A 218 " =    1.559
peak=   -3.198 closest distance to " O   HOH Z 103 " =    1.721
peak=   -3.191 closest distance to " O   LYS A  76 " =    1.735
peak=   -3.186 closest distance to " O   GLU A 152 " =    1.517
peak=   -3.186 closest distance to " O   SER A 210 " =    1.714
peak=   -3.185 closest distance to " CE2 PHE A 218 " =    2.377
peak=   -3.184 closest distance to " CB  PRO A 163 " =    2.397
peak=   -3.180 closest distance to " O   HOH Z 295 " =    1.811
peak=   -3.177 closest distance to " O   GLN A  11 " =    1.369
peak=   -3.173 closest distance to " O   HOH Z 404 " =    1.527
peak=   -3.170 closest distance to " OD1 ASN A 301 " =    1.945
peak=   -3.169 closest distance to " C   MET A 188 " =    1.462
peak=   -3.168 closest distance to " CD2 LEU A   5 " =    1.132
peak=   -3.167 closest distance to " CG  GLN A 103 " =    2.393
peak=   -3.157 closest distance to " CZ2 TRP A  92 " =    2.794
peak=   -3.157 closest distance to " O   HOH Z  15 " =    1.393
peak=   -3.150 closest distance to " ND2 ASN A 173 " =    1.499
peak=   -3.146 closest distance to " CB  ASN A  39 " =    2.323
peak=   -3.142 closest distance to " O   ALA A 180 " =    1.236
peak=   -3.141 closest distance to " O   HOH Z 158 " =    1.904
peak=   -3.135 closest distance to " CG2 ILE A 151 " =    2.489
peak=   -3.135 closest distance to " OG  SER A  63 " =    1.178
peak=   -3.133 closest distance to " O   HOH Z  24 " =    1.391
peak=   -3.133 closest distance to " CG2 ILE A 263 " =    2.306
peak=   -3.130 closest distance to " OD1 ASN A  39 " =    2.216
peak=   -3.127 closest distance to " O   HOH Z 368 " =    1.523
peak=   -3.120 closest distance to " O   HOH Z 139 " =    4.820
peak=   -3.120 closest distance to " O   ALA A   1 " =    1.537
peak=   -3.118 closest distance to " N   PHE A  59 " =    2.126
peak=   -3.117 closest distance to " OH  TYR A 169 " =    0.857
peak=   -3.113 closest distance to " CG1 ILE A 109 " =    2.802
peak=   -3.111 closest distance to " CZ  TYR A 169 " =    1.802
peak=   -3.094 closest distance to " CB  ALA A  51 " =    1.865
peak=   -3.091 closest distance to " O   HOH Z 313 " =    1.576
peak=   -3.088 closest distance to " C   LEU A 222 " =    0.868
peak=   -3.083 closest distance to " O   HOH Z 407 " =    2.510
peak=   -3.083 closest distance to " CA  GLN A  58 " =    1.223
peak=   -3.083 closest distance to " O   HOH Z 130 " =    1.920
peak=   -3.077 closest distance to " O   HOH Z 166 " =    1.818
peak=   -3.070 closest distance to " CG  GLU A 152 " =    1.498
peak=   -3.065 closest distance to " CE1 HIS A  81 " =    1.725
peak=   -3.031 closest distance to " CG  GLN A 278 " =    1.881
peak=   -3.009 closest distance to " O   PRO A 163 " =    1.271

================= 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    :  0.4980 0.4906   6.293893e+00   6.286006e+00
   1_bss:  0.4901 0.4790   6.286565e+00   6.277069e+00
   1_xyz:  0.4201 0.4380   6.206322e+00   6.231479e+00
   1_adp:  0.3787 0.4420   6.152259e+00   6.227942e+00
   1_occ:  0.3785 0.4425   6.151725e+00   6.228788e+00
   2_bss:  0.3758 0.4385   6.152408e+00   6.228536e+00
   2_xyz:  0.2818 0.3456   5.927554e+00   6.074924e+00
   2_adp:  0.2486 0.3146   5.826856e+00   5.993035e+00
   2_occ:  0.2481 0.3141   5.826190e+00   5.992127e+00
   3_bss:  0.2461 0.3122   5.822805e+00   5.988721e+00
   3_xyz:  0.1799 0.2314   5.542275e+00   5.738240e+00
   3_adp:  0.1631 0.2166   5.460585e+00   5.670176e+00
   3_occ:  0.1625 0.2153   5.458283e+00   5.667861e+00
   4_bss:  0.1617 0.2153   5.456836e+00   5.668297e+00
   4_xyz:  0.1357 0.1841   5.303736e+00   5.523643e+00
   4_adp:  0.1322 0.1819   5.281635e+00   5.507313e+00
   4_occ:  0.1318 0.1820   5.280051e+00   5.505914e+00
   5_bss:  0.1319 0.1826   5.280129e+00   5.505733e+00
   5_xyz:  0.1242 0.1708   5.228713e+00   5.461822e+00
   5_adp:  0.1205 0.1687   5.207306e+00   5.447607e+00
   5_occ:  0.1205 0.1687   5.207208e+00   5.447535e+00
   5_bss:  0.1204 0.1686   5.206882e+00   5.447422e+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:  0.380  20.000   7.301   9.002   9.547   0.000   0.000   0.000
   1_xyz:  0.380  20.000   7.301   9.002   9.547   0.000   0.000   0.000
   1_adp:  0.380  20.000   7.301   9.002   9.547   0.000   0.000   0.000
   1_occ:  0.380  20.000   7.301   9.002   9.547   0.000   0.000   0.000
   2_bss:  0.353  34.800   3.913   4.759   5.995   0.000   0.000   0.000
   2_xyz:  0.353  34.800   3.913   4.759   5.995   0.000   0.000   0.000
   2_adp:  0.353  34.800   3.913   4.759   5.995   0.000   0.000   0.000
   2_occ:  0.353  34.800   3.913   4.759   5.995   0.000   0.000   0.000
   3_bss:  0.327  44.175   1.899   2.765   4.053   0.000   0.000   0.000
   3_xyz:  0.327  44.175   1.899   2.765   4.053   0.000   0.000   0.000
   3_adp:  0.327  44.175   1.899   2.765   4.053   0.000   0.000   0.000
   3_occ:  0.327  44.175   1.899   2.765   4.053   0.000   0.000   0.000
   4_bss:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   4_xyz:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   4_adp:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   4_occ:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   5_bss:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   5_xyz:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   5_adp:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   5_occ:  0.323  44.175   0.814   1.491   3.185   0.000   0.000   0.000
   5_bss:  0.309  46.041  -0.975  -0.430   1.405  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.522 0.3608  0.4310    77768.654
   1_bss:  62.252 0.3629  0.5549    75240.981
   1_xyz:  52.205 0.4914  0.7371    58227.507
   1_adp:  51.118 0.5052  0.8160    57411.758
   1_occ:  51.185 0.5043  0.8126    57508.438
   2_bss:  50.891 0.5079  0.7201    56988.149
   2_xyz:  37.549 0.6707  0.9354    33192.232
   2_adp:  32.565 0.7290  0.9830    26280.050
   2_occ:  32.541 0.7293  0.9829    26206.422
   3_bss:  32.288 0.7319  0.9172    25817.684
   3_xyz:  22.545 0.8362  1.0007    13603.992
   3_adp:  20.494 0.8572  1.0082    11839.279
   3_occ:  20.448 0.8576  1.0083    11770.364
   4_bss:  20.412 0.8580  0.9693    11759.189
   4_xyz:  16.990 0.8897  0.9841     8606.069
   4_adp:  16.580 0.8935  0.9804     8360.599
   4_occ:  16.568 0.8935  0.9800     8331.318
   5_bss:  16.580 0.8935  0.9798     8347.442
   5_xyz:  15.540 0.9023  0.9851     7476.847
   5_adp:  15.220 0.9052  0.9804     7246.045
   5_occ:  15.219 0.9052  0.9804     7243.868
   5_bss:  15.215 0.9052  0.9816     7242.439
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3206e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3206e+01
   1_xyz:   1.714  0.013  0.106 18.241  0.006  4.104   1.4404e-01
   1_adp:   1.714  0.013  0.106 18.241  0.006  4.104   1.4404e-01
   1_occ:   1.714  0.013  0.106 18.241  0.006  4.104   1.4404e-01
   2_bss:   1.714  0.013  0.106 18.241  0.006  4.104   1.4404e-01
   2_xyz:   1.378  0.011  0.095 16.552  0.006  4.105   1.1372e-01
   2_adp:   1.378  0.011  0.095 16.552  0.006  4.105   1.1372e-01
   2_occ:   1.378  0.011  0.095 16.552  0.006  4.105   1.1372e-01
   3_bss:   1.378  0.011  0.095 16.552  0.006  4.105   1.1372e-01
   3_xyz:   1.067  0.008  0.074 15.907  0.005  4.111   7.1911e-02
   3_adp:   1.067  0.008  0.074 15.907  0.005  4.111   7.1911e-02
   3_occ:   1.067  0.008  0.074 15.907  0.005  4.111   7.1911e-02
   4_bss:   1.067  0.008  0.074 15.907  0.005  4.111   7.1911e-02
   4_xyz:   0.991  0.006  0.071 15.736  0.004  4.115   6.0647e-02
   4_adp:   0.991  0.006  0.071 15.736  0.004  4.115   6.0647e-02
   4_occ:   0.991  0.006  0.071 15.736  0.004  4.115   6.0647e-02
   5_bss:   0.991  0.006  0.071 15.736  0.004  4.115   6.0647e-02
   5_xyz:   0.959  0.006  0.071 15.673  0.004  4.119   5.7714e-02
   5_adp:   0.959  0.006  0.071 15.673  0.004  4.119   5.7714e-02
   5_occ:   0.959  0.006  0.071 15.673  0.004  4.119   5.7714e-02
   5_bss:   0.959  0.006  0.071 15.673  0.004  4.119   5.7714e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8916e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8916e+00
   1_xyz:  13.755  0.170  0.418 85.510  0.031  2.203   9.7787e-02
   1_adp:  13.755  0.170  0.418 85.510  0.031  2.203   9.7787e-02
   1_occ:  13.755  0.170  0.418 85.510  0.031  2.203   9.7787e-02
   2_bss:  13.755  0.170  0.418 85.510  0.031  2.203   9.7787e-02
   2_xyz:   9.673  0.160  0.326 83.342  0.056  2.088   1.0898e-01
   2_adp:   9.673  0.160  0.326 83.342  0.056  2.088   1.0898e-01
   2_occ:   9.673  0.160  0.326 83.342  0.056  2.088   1.0898e-01
   3_bss:   9.673  0.160  0.326 83.342  0.056  2.088   1.0898e-01
   3_xyz:   8.298  0.049  0.294 86.164  0.046  2.308   7.4213e-02
   3_adp:   8.298  0.049  0.294 86.164  0.046  2.308   7.4213e-02
   3_occ:   8.298  0.049  0.294 86.164  0.046  2.308   7.4213e-02
   4_bss:   8.298  0.049  0.294 86.164  0.046  2.308   7.4213e-02
   4_xyz:   7.294  0.047  0.242 84.898  0.031  2.384   4.5435e-02
   4_adp:   7.294  0.047  0.242 84.898  0.031  2.384   4.5435e-02
   4_occ:   7.294  0.047  0.242 84.898  0.031  2.384   4.5435e-02
   5_bss:   7.294  0.047  0.242 84.898  0.031  2.384   4.5435e-02
   5_xyz:   7.691  0.045  0.262 84.317  0.033  2.365   3.6491e-02
   5_adp:   7.691  0.045  0.262 84.317  0.033  2.365   3.6491e-02
   5_occ:   7.691  0.045  0.262 84.317  0.033  2.365   3.6491e-02
   5_bss:   7.691  0.045  0.262 84.317  0.033  2.365   3.6491e-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:  65.11   0.00  14.27  53.51   0.00  12.55  65.11   0.00  23.62
   1_occ:  65.11   0.00  14.27  53.51   0.00  12.55  65.11   0.00  23.62
   2_bss:  65.11   0.00  14.27  53.51   0.00  12.55  65.11   0.00  23.62
   2_xyz:  65.11   0.00  14.27  53.51   0.00  12.55  65.11   0.00  23.62
   2_adp:  74.57   0.00  13.66  59.13   0.00  10.26  74.57   0.00  32.22
   2_occ:  74.57   0.00  13.66  59.13   0.00  10.26  74.57   0.00  32.22
   3_bss:  74.57   0.00  13.66  59.13   0.00  10.26  74.57   0.00  32.22
   3_xyz:  74.57   0.00  13.66  59.13   0.00  10.26  74.57   0.00  32.22
   3_adp:  77.40   0.00  13.59  70.25   0.00   9.50  77.40   1.19  35.82
   3_occ:  77.40   0.00  13.59  70.25   0.00   9.50  77.40   1.19  35.82
   4_bss:  77.40   0.00  13.59  70.25   0.00   9.50  77.40   1.19  35.82
   4_xyz:  77.40   0.00  13.59  70.25   0.00   9.50  77.40   1.19  35.82
   4_adp:  92.07   0.00  13.53  92.07   0.00   9.37  77.64   2.47  36.17
   4_occ:  92.07   0.00  13.53  92.07   0.00   9.37  77.64   2.47  36.17
   5_bss:  92.07   0.00  13.53  92.07   0.00   9.37  77.64   2.47  36.17
   5_xyz:  92.07   0.00  13.53  92.07   0.00   9.37  77.64   2.47  36.17
   5_adp:  92.19   0.00  13.99  92.19   0.00   9.35  85.52   1.82  39.25
   5_occ:  92.19   0.00  13.99  92.19   0.00   9.35  85.52   1.82  39.25
   5_bss:  94.06   1.87  15.85  94.06   1.87  11.21  87.39   3.68  41.12
------------------------------------------------------------------------
 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:    1.278    0.017    0.410
   1_adp:    1.278    0.017    0.410
   1_occ:    1.278    0.017    0.410
   2_bss:    1.278    0.017    0.410
   2_xyz:    1.690    0.036    0.625
   2_adp:    1.690    0.036    0.625
   2_occ:    1.690    0.036    0.625
   3_bss:    1.690    0.036    0.625
   3_xyz:    1.553    0.045    0.720
   3_adp:    1.553    0.045    0.720
   3_occ:    1.553    0.045    0.720
   4_bss:    1.553    0.045    0.720
   4_xyz:    1.598    0.028    0.765
   4_adp:    1.598    0.028    0.765
   4_occ:    1.598    0.028    0.765
   5_bss:    1.598    0.028    0.765
   5_xyz:    1.795    0.051    0.782
   5_adp:    1.795    0.051    0.782
   5_occ:    1.795    0.051    0.782
   5_bss:    1.795    0.051    0.782
------------------------------------------------------------------------

CPU time actual refinement: 342.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_151/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_151/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_151/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_151/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_151/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.60 
  Macro-tasks:
    bulk solvent and scale       = 41.68  
    individual site refinement   = 144.07 
    weights calculation          = 31.17  
    collect and process          = 6.51   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.56 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 106.62 
    alpha_beta                      = 8.28   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 117.92 
    fmodel                         = 7.43   
    r_factors                      = 0.26   
    phase_errors                   = 10.33  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 254.66 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.792 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    658 calls, 106.20 s
gradients_fft:          602 calls, 104.62 s

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

# Date 2008-01-16 Time 00:51:54 PST -0800 (1200473514.89 s)
Start R-work = 0.4980, R-free = 0.4906 (no bulk solvent and anisotropic scale)
Final R-work = 0.1376, R-free = 0.1837 (no bulk solvent and anisotropic scale)

Start R-work = 0.4901, R-free = 0.4790
Final R-work = 0.1204, R-free = 0.1686