# Date 2008-01-16 Time 04:19:22 PST -0800 (1200485962.23 s)
#phil __OFF__

Command line arguments: "../264.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18294
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 264

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.2261, 84.2302, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95107
Completeness in resolution range: 0.967645
Completeness with d_max=infinity: 0.964595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7280
                             d_min =   1.9511

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95107
Completeness in resolution range: 0.967645
Completeness with d_max=infinity: 0.964595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7284 -  4.1745 [2117/2144]  1906   211  10.0%
  bin  2:  4.1745 -  3.3260 [2042/2058]  1837   205  10.0%
  bin  3:  3.3260 -  2.9093 [2019/2038]  1815   204  10.1%
  bin  4:  2.9093 -  2.6449 [2005/2035]  1810   195   9.7%
  bin  5:  2.6449 -  2.4563 [1982/2001]  1782   200  10.1%
  bin  6:  2.4563 -  2.3121 [1957/1982]  1763   194   9.9%
  bin  7:  2.3121 -  2.1967 [1970/2004]  1771   199  10.1%
  bin  8:  2.1967 -  2.1013 [1956/1986]  1760   196  10.0%
  bin  9:  2.1013 -  2.0206 [1961/2003]  1765   196  10.0%
  bin 10:  2.0206 -  1.9511 [1580/1993]  1421   159  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_264/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:
        1.08 -     1.84: 12
        1.84 -     2.61: 109
        2.61 -     3.37: 4334
        3.37 -     4.14: 9644
        4.14 -     4.90: 15046
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.076 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.380 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.391 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.482 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.575 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29140 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 =====================


==================== 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/noshake/run_264/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_264/model_refine_001.geo

CPU time processing inputs: 9.23


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.22605 84.23025 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4720   r_free= 0.4743   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.275136                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6559 0.99   1378  154 0.3792 0.3793      6.5569      6.5493|
|  2:  4.6559 -  3.7151 0.99   1336  145 0.4067 0.3911      6.7981      6.7726|
|  3:  3.7151 -  3.2512 0.99   1300  147 0.4447 0.4694      6.6782      6.7942|
|  4:  3.2512 -  2.9566 0.99   1294  144 0.4488 0.4580      6.5272      6.5133|
|  5:  2.9566 -  2.7461 0.99   1281  141 0.4954 0.4810      6.3743      6.3401|
|  6:  2.7461 -  2.5851 0.99   1282  145 0.5063 0.5421      6.2821      6.2798|
|  7:  2.5851 -  2.4563 0.99   1279  139 0.5060 0.4749      6.2472      6.2022|
|  8:  2.4563 -  2.3498 0.98   1264  145 0.5106 0.5094      6.1863      6.1828|
|  9:  2.3498 -  2.2597 0.98   1273  139 0.5317 0.4972      6.1303      6.1366|
| 10:  2.2597 -  2.1820 0.99   1249  141 0.5092 0.5293      6.0984      6.1155|
| 11:  2.1820 -  2.1139 0.99   1274  139 0.5320 0.5731        6.05        6.08|
| 12:  2.1139 -  2.0537 0.97   1239  137 0.5235 0.5048      5.9852      6.0048|
| 13:  2.0537 -  1.9997 0.99   1255  142 0.5189 0.5288      5.8861      5.8688|
| 14:  1.9997 -  1.9511 0.72    926  101 0.5289 0.4702      5.8585      5.7583|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6559  1378   154  0.69  35.51   0.83     0.73      73521.33|
|  2:  4.6559 -  3.7151  1336   145  0.68  36.55   0.91     0.81     114328.68|
|  3:  3.7151 -  3.2512  1300   147  0.57  46.19   0.94     0.78     125032.85|
|  4:  3.2512 -  2.9566  1294   144  0.47  53.95   0.96     0.67     113406.43|
|  5:  2.9566 -  2.7461  1281   141  0.39  60.39   0.89     0.57      88036.68|
|  6:  2.7461 -  2.5851  1282   145  0.36  63.06   0.90     0.51      75672.04|
|  7:  2.5851 -  2.4563  1279   139  0.36  62.99   0.92     0.50      67346.83|
|  8:  2.4563 -  2.3498  1264   145  0.35  63.47   0.93     0.52      60827.92|
|  9:  2.3498 -  2.2597  1273   139  0.36  62.77   0.92     0.53      53573.48|
| 10:  2.2597 -  2.1820  1249   141  0.36  63.34   0.97     0.52      49636.99|
| 11:  2.1820 -  2.1139  1274   139  0.30  67.45   0.96     0.47      48007.06|
| 12:  2.1139 -  2.0537  1239   137  0.31  66.95   0.99     0.50      45114.69|
| 13:  2.0537 -  1.9997  1255   142  0.33  65.23   0.94     0.53      37266.27|
| 14:  1.9997 -  1.9511   926   101  0.42  58.26   0.96     0.60      26339.66|
|alpha:            min =        0.47 max =            0.81 mean =         0.59|
|beta:             min =    26339.66 max =       125032.85 mean =     71161.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.31|
|phase err.(test): min =        0.00 max =           89.71 mean =        57.55|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.563348             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.092   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.705102              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.847   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.076 -  1.459:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.459 -  1.841:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.841 -  2.223:       28 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.223 -  2.606:       81 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.606 -  2.988:     1869 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.988 -  3.371:     2465 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.371 -  3.753:     3992 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.753 -  4.135:     5652 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.135 -  4.518:     6675 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.518 -  4.900:     8371 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.210 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.076 |       0.946 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4720   r_free= 0.4743   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.275136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4625   r_free= 0.4621   ksol= 0.34   Bsol= 10.06   scale= 0.942   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.59,2.22,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.271857                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.337600              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.003   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.373836              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.672   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4625      final r-factor (work) = 0.3483          |
| start r-factor (free) = 0.4621      final r-factor (free) = 0.3773          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3352 = 8.34 * 0.50 * 6.2669 + 1.00 * 0.2099                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7707 = 8.34 * 0.50 * 6.1495 + 1.00 * 0.1345                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3483      final r-factor (work) = 0.3144          |
| start r-factor (free) = 0.3773      final r-factor (free) = 0.3822          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4544 = 1.37 * 1.00 * 6.1495 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2863 = 1.37 * 1.00 * 6.0160 + 1.00 * 0.0214                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.74   19.37    None  None   None       |
|    all(noH): 2823   0      0.00    97.74   19.37    None  None   None       |
|    Sol.    : 438    0      0.00    95.36   40.00    None  None   None       |
|    Mac.    : 2385   0      0.00    97.74   15.58    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 -   9.774:  868   |   5:    48.870 -  58.644:  107        |
|      1:     9.774 -  19.548:  906   |   6:    58.644 -  68.418:   39        |
|      2:    19.548 -  29.322:  442   |   7:    68.418 -  78.192:   23        |
|      3:    29.322 -  39.096:  287   |   8:    78.192 -  87.966:    9        |
|      4:    39.096 -  48.870:  136   |   9:    87.966 -  97.740:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3144 r_free = 0.3822             target_work(ml) = 6.023         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3141 r_free = 0.3828             target_work(ml) = 6.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3141   r_free= 0.3828   ksol= 0.34   Bsol= 10.06   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.59,2.22,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.022884                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3111   r_free= 0.3821   ksol= 0.33   Bsol= 35.17   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-0.43,0.51,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.018328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.142503              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.834   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.305876              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.158  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3111      final r-factor (work) = 0.2520          |
| start r-factor (free) = 0.3821      final r-factor (free) = 0.3158          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5882 = 4.14 * 0.50 * 6.0130 + 1.00 * 0.1339                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3624 = 4.14 * 0.50 * 5.9343 + 1.00 * 0.0709                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2520      final r-factor (work) = 0.2425          |
| start r-factor (free) = 0.3158      final r-factor (free) = 0.3027          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8365 = 0.31 * 1.00 * 5.9343 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8068 = 0.31 * 1.00 * 5.8292 + 1.00 * 0.0238                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.21   19.01    None  None   None       |
|    all(noH): 2823   0      0.00    96.21   19.01    None  None   None       |
|    Sol.    : 438    0      2.66    93.25   39.65    None  None   None       |
|    Mac.    : 2385   0      0.00    96.21   15.22    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 -   9.621:  762   |   5:    48.104 -  57.724:  101        |
|      1:     9.621 -  19.241: 1089   |   6:    57.724 -  67.345:   37        |
|      2:    19.241 -  28.862:  433   |   7:    67.345 -  76.966:   17        |
|      3:    28.862 -  38.483:  242   |   8:    76.966 -  86.586:   10        |
|      4:    38.483 -  48.104:  127   |   9:    86.586 -  96.207:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2425 r_free = 0.3027             target_work(ml) = 5.810         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2420 r_free = 0.3021             target_work(ml) = 5.809         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2420   r_free= 0.3021   ksol= 0.33   Bsol= 35.17   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-0.43,0.51,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.808771                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2416   r_free= 0.2999   ksol= 0.32   Bsol= 26.75   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.47,-0.61,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.807099                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.173693              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.424   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.364499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.576   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2416      final r-factor (work) = 0.1833          |
| start r-factor (free) = 0.2999      final r-factor (free) = 0.2407          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2312 = 4.17 * 0.50 * 5.8270 + 1.00 * 0.0711                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9328 = 4.17 * 0.50 * 5.6872 + 1.00 * 0.0646                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1833      final r-factor (work) = 0.1627          |
| start r-factor (free) = 0.2407      final r-factor (free) = 0.2195          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1133 = 0.36 * 1.00 * 5.6872 + 1.00 * 0.0404                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0196 = 0.36 * 1.00 * 5.5162 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.47    95.49   18.16    None  None   None       |
|    all(noH): 2823   0      0.47    95.49   18.16    None  None   None       |
|    Sol.    : 438    0      6.30    88.50   42.04    None  None   None       |
|    Mac.    : 2385   0      0.47    95.49   13.78    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:     0.473 -   9.975:  918   |   5:    47.980 -  57.482:  113        |
|      1:     9.975 -  19.476: 1152   |   6:    57.482 -  66.983:   58        |
|      2:    19.476 -  28.977:  275   |   7:    66.983 -  76.485:   20        |
|      3:    28.977 -  38.479:  155   |   8:    76.485 -  85.986:    8        |
|      4:    38.479 -  47.980:  121   |   9:    85.986 -  95.488:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1627 r_free = 0.2195             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1624 r_free = 0.2190             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1624   r_free= 0.2190   ksol= 0.32   Bsol= 26.75   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.47,-0.61,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.462248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1623   r_free= 0.2179   ksol= 0.32   Bsol= 33.74   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.60,-1.80,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.459528                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.793073              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.113  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.748  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1623      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.2179      final r-factor (free) = 0.1769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7777 = 2.79 * 0.50 * 5.5230 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5662 = 2.79 * 0.50 * 5.3762 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1321      final r-factor (work) = 0.1240          |
| start r-factor (free) = 0.1769      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0254 = 0.56 * 1.00 * 5.3762 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9480 = 0.56 * 1.00 * 5.2378 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.95    98.09   18.15    None  None   None       |
|    all(noH): 2823   0      0.95    98.09   18.15    None  None   None       |
|    Sol.    : 438    0      7.47    92.44   43.63    None  None   None       |
|    Mac.    : 2385   0      0.95    98.09   13.47    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:     0.948 -  10.663: 1093   |   5:    49.521 -  59.235:   97        |
|      1:    10.663 -  20.377: 1082   |   6:    59.235 -  68.950:   75        |
|      2:    20.377 -  30.092:  208   |   7:    68.950 -  78.664:   24        |
|      3:    30.092 -  39.806:  121   |   8:    78.664 -  88.379:    9        |
|      4:    39.806 -  49.521:  109   |   9:    88.379 -  98.093:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1240 r_free = 0.1691             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1239 r_free = 0.1690             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1690   ksol= 0.32   Bsol= 33.74   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.60,-1.80,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.213130                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1696   ksol= 0.31   Bsol= 35.16   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.72,-2.04,-0.00,-0.00,-0.00); trace/3= -2.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.213918                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.575157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.163  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.198048              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.118  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8023 = 2.58 * 0.50 * 5.2379 + 1.00 * 0.0581                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7276 = 2.58 * 0.50 * 5.1765 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0344 = 0.20 * 1.00 * 5.1765 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0279 = 0.20 * 1.00 * 5.1495 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.24    97.47   17.74    None  None   None       |
|    all(noH): 2823   0      2.24    97.47   17.74    None  None   None       |
|    Sol.    : 438    0      6.49    92.18   42.01    None  None   None       |
|    Mac.    : 2385   0      2.24    97.47   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.238 -  11.761: 1361   |   5:    49.854 -  59.377:   81        |
|      1:    11.761 -  21.285:  873   |   6:    59.377 -  68.900:   68        |
|      2:    21.285 -  30.808:  179   |   7:    68.900 -  78.423:   18        |
|      3:    30.808 -  40.331:  120   |   8:    78.423 -  87.946:    9        |
|      4:    40.331 -  49.854:  109   |   9:    87.946 -  97.469:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1608             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1606             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1606   ksol= 0.31   Bsol= 35.16   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.72,-2.04,-0.00,-0.00,-0.00); trace/3= -2.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137266                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6559 0.99   1378  154 0.1010 0.1277      5.3829      5.5274|
|  2:  4.6559 -  3.7151 0.99   1336  145 0.0867 0.1254      5.4583      5.7061|
|  3:  3.7151 -  3.2512 0.99   1300  147 0.1076 0.1554      5.5119      5.8851|
|  4:  3.2512 -  2.9566 0.99   1294  144 0.1245 0.1668      5.4781      5.6413|
|  5:  2.9566 -  2.7461 0.99   1281  141 0.1258 0.1605      5.2791      5.4392|
|  6:  2.7461 -  2.5851 0.99   1282  145 0.1139 0.1646      5.1538      5.3619|
|  7:  2.5851 -  2.4563 0.99   1279  139 0.1205 0.1640      5.1221      5.3549|
|  8:  2.4563 -  2.3498 0.98   1264  145 0.1176 0.1792      5.0656      5.3638|
|  9:  2.3498 -  2.2597 0.98   1273  139 0.1166 0.1797      5.0299      5.3195|
| 10:  2.2597 -  2.1820 0.99   1249  141 0.1122 0.1717      4.9554      5.1462|
| 11:  2.1820 -  2.1139 0.99   1274  139 0.1149 0.1851      4.9354      5.3066|
| 12:  2.1139 -  2.0537 0.97   1239  137 0.1109 0.1610      4.8717      5.1087|
| 13:  2.0537 -  1.9997 0.99   1255  142 0.1143 0.1904      4.7963      5.1059|
| 14:  1.9997 -  1.9511 0.72    926  101 0.1082 0.1679      4.6941      4.8862|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6559  1378   154  0.94   8.80   0.99     0.96       6792.49|
|  2:  4.6559 -  3.7151  1336   145  0.95   8.26   1.04     1.03       9617.81|
|  3:  3.7151 -  3.2512  1300   147  0.93  12.21   1.05     1.04      11507.81|
|  4:  3.2512 -  2.9566  1294   144  0.92  13.48   1.03     1.02      10543.13|
|  5:  2.9566 -  2.7461  1281   141  0.91  14.90   1.01     0.97       7322.70|
|  6:  2.7461 -  2.5851  1282   145  0.91  14.45   1.00     0.97       6126.19|
|  7:  2.5851 -  2.4563  1279   139  0.91  15.06   1.00     0.98       5700.34|
|  8:  2.4563 -  2.3498  1264   145  0.91  14.79   1.01     0.99       5162.19|
|  9:  2.3498 -  2.2597  1273   139  0.91  15.11   1.02     1.01       4982.99|
| 10:  2.2597 -  2.1820  1249   141  0.91  15.20   1.02     0.99       4315.60|
| 11:  2.1820 -  2.1139  1274   139  0.90  16.55   1.02     0.98       4341.87|
| 12:  2.1139 -  2.0537  1239   137  0.91  14.84   1.02     1.00       3836.07|
| 13:  2.0537 -  1.9997  1255   142  0.90  15.99   1.02     1.02       3359.70|
| 14:  1.9997 -  1.9511   926   101  0.91  14.80   1.01     0.98       2669.58|
|alpha:            min =        0.96 max =            1.04 mean =         1.00|
|beta:             min =     2669.58 max =        11507.81 mean =      6271.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1606   ksol= 0.31   Bsol= 35.08   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.64,-1.96,-0.00,-0.00,-0.00); trace/3= -2.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137266                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1606   ksol= 0.31   Bsol= 35.08   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.64,-1.96,-0.00,-0.00,-0.00); trace/3= -2.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137266                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6559 0.99   1378  154 0.1010 0.1277      5.3829      5.5274|
|  2:  4.6559 -  3.7151 0.99   1336  145 0.0867 0.1254      5.4583      5.7061|
|  3:  3.7151 -  3.2512 0.99   1300  147 0.1076 0.1554      5.5119      5.8851|
|  4:  3.2512 -  2.9566 0.99   1294  144 0.1245 0.1668      5.4781      5.6413|
|  5:  2.9566 -  2.7461 0.99   1281  141 0.1258 0.1605      5.2791      5.4392|
|  6:  2.7461 -  2.5851 0.99   1282  145 0.1139 0.1646      5.1538      5.3619|
|  7:  2.5851 -  2.4563 0.99   1279  139 0.1205 0.1640      5.1221      5.3549|
|  8:  2.4563 -  2.3498 0.98   1264  145 0.1176 0.1792      5.0656      5.3638|
|  9:  2.3498 -  2.2597 0.98   1273  139 0.1166 0.1797      5.0299      5.3195|
| 10:  2.2597 -  2.1820 0.99   1249  141 0.1122 0.1717      4.9554      5.1462|
| 11:  2.1820 -  2.1139 0.99   1274  139 0.1149 0.1851      4.9354      5.3066|
| 12:  2.1139 -  2.0537 0.97   1239  137 0.1109 0.1610      4.8717      5.1087|
| 13:  2.0537 -  1.9997 0.99   1255  142 0.1143 0.1904      4.7963      5.1059|
| 14:  1.9997 -  1.9511 0.72    926  101 0.1082 0.1679      4.6941      4.8862|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6559  1378   154  0.94   8.80   0.99     0.96       6792.49|
|  2:  4.6559 -  3.7151  1336   145  0.95   8.26   1.04     1.03       9617.81|
|  3:  3.7151 -  3.2512  1300   147  0.93  12.21   1.05     1.04      11507.81|
|  4:  3.2512 -  2.9566  1294   144  0.92  13.48   1.03     1.02      10543.13|
|  5:  2.9566 -  2.7461  1281   141  0.91  14.90   1.01     0.97       7322.70|
|  6:  2.7461 -  2.5851  1282   145  0.91  14.45   1.00     0.97       6126.19|
|  7:  2.5851 -  2.4563  1279   139  0.91  15.06   1.00     0.98       5700.34|
|  8:  2.4563 -  2.3498  1264   145  0.91  14.79   1.01     0.99       5162.19|
|  9:  2.3498 -  2.2597  1273   139  0.91  15.11   1.02     1.01       4982.99|
| 10:  2.2597 -  2.1820  1249   141  0.91  15.20   1.02     0.99       4315.60|
| 11:  2.1820 -  2.1139  1274   139  0.90  16.55   1.02     0.98       4341.87|
| 12:  2.1139 -  2.0537  1239   137  0.91  14.84   1.02     1.00       3836.07|
| 13:  2.0537 -  1.9997  1255   142  0.90  15.99   1.02     1.02       3359.70|
| 14:  1.9997 -  1.9511   926   101  0.91  14.80   1.01     0.98       2669.58|
|alpha:            min =        0.96 max =            1.04 mean =         1.00|
|beta:             min =     2669.58 max =        11507.81 mean =      6271.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.16    97.39   17.66    None  None   None       |
|    all(noH): 2823   0      2.16    97.39   17.66    None  None   None       |
|    Sol.    : 438    0      6.41    92.10   41.93    None  None   None       |
|    Mac.    : 2385   0      2.16    97.39   13.21    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:     2.157 -  11.680: 1361   |   5:    49.773 -  59.296:   81        |
|      1:    11.680 -  21.204:  873   |   6:    59.296 -  68.819:   68        |
|      2:    21.204 -  30.727:  179   |   7:    68.819 -  78.342:   18        |
|      3:    30.727 -  40.250:  120   |   8:    78.342 -  87.865:    9        |
|      4:    40.250 -  49.773:  109   |   9:    87.865 -  97.388:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 298         
Filter by distance & map next to the model:
   mapped sites are within: 0.395 - 5.783
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 298
   mapped sites are within: 0.733 - 5.783

peak=    6.339 closest distance to " O   HOH Z 142 " =    2.042
peak=    6.310 closest distance to " O   HOH Z 126 " =    2.075
peak=    6.190 closest distance to " NE2 GLN A  11 " =    1.197
peak=    6.143 closest distance to " O   HOH Z 236 " =    1.583
peak=    6.093 closest distance to " O   HOH Z 112 " =    1.483
peak=    5.862 closest distance to " O   HOH Z 278 " =    1.553
peak=    5.694 closest distance to " NH2 ARG A  56 " =    1.995
peak=    5.440 closest distance to " O   HOH Z 124 " =    1.664
peak=    5.391 closest distance to " O   HOH Z 427 " =    2.519
peak=    5.188 closest distance to " CB  ARG A 275 " =    0.937
peak=    5.128 closest distance to " O   HOH Z 108 " =    1.633
peak=    5.099 closest distance to " O   HOH Z 202 " =    1.417
peak=    5.079 closest distance to " O   HOH Z 214 " =    1.210
peak=    5.037 closest distance to " O   HOH Z 213 " =    1.950
peak=    4.957 closest distance to " O   HOH Z 260 " =    1.424
peak=    4.945 closest distance to " O   HOH Z 193 " =    1.662
peak=    4.945 closest distance to " CG  PRO A 213 " =    1.235
peak=    4.912 closest distance to " CG  PRO A  54 " =    1.195
peak=    4.845 closest distance to " O   HOH Z  78 " =    1.690
peak=    4.823 closest distance to " O   HOH Z  11 " =    1.397
peak=    4.774 closest distance to " O   HOH Z 207 " =    1.685
peak=    4.717 closest distance to " O   HOH Z 369 " =    2.122
peak=    4.667 closest distance to " CB  ASN A 148 " =    1.499
peak=    4.657 closest distance to " O   HOH Z 373 " =    2.057
peak=    4.604 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.604 closest distance to " O   HOH Z  52 " =    1.441
peak=    4.602 closest distance to " O   HOH Z 234 " =    3.529
peak=    4.578 closest distance to " C   PRO A 198 " =    1.501
peak=    4.534 closest distance to " O   HOH Z 134 " =    1.412
peak=    4.522 closest distance to " CB  SER A   3 " =    1.338
peak=    4.388 closest distance to " O   HOH Z 352 " =    1.768
peak=    4.375 closest distance to " CB  GLN A 223 " =    1.571
peak=    4.337 closest distance to " O   HOH Z 380 " =    1.629
peak=    4.331 closest distance to " CB  SER A  63 " =    1.209
peak=    4.301 closest distance to " O   HOH Z  61 " =    1.621
peak=    4.295 closest distance to " O   HOH Z 423 " =    1.413
peak=    4.292 closest distance to " NZ  LYS A 117 " =    3.165
peak=    4.278 closest distance to " O   HOH Z 232 " =    2.280
peak=    4.266 closest distance to " CB  GLN A 183 " =    1.190
peak=    4.227 closest distance to " O   HOH Z 316 " =    2.894
peak=    4.205 closest distance to " O   HOH Z 371 " =    1.887
peak=    4.202 closest distance to " O   HOH Z 199 " =    0.909
peak=    4.189 closest distance to " CB  GLU A 152 " =    1.240
peak=    4.180 closest distance to " CG  PRO A 198 " =    1.314
peak=    4.171 closest distance to " O   HOH Z  93 " =    1.790
peak=    4.164 closest distance to " O   HOH Z 132 " =    1.127
peak=    4.138 closest distance to " CB  ARG A 102 " =    0.782
peak=    4.137 closest distance to " O   HOH Z 192 " =    1.512
peak=    4.111 closest distance to " O   HOH Z 276 " =    1.366
peak=    4.108 closest distance to " O   HOH Z 287 " =    1.657
peak=    4.076 closest distance to " O   HOH Z 128 " =    1.958
peak=    4.065 closest distance to " O   HOH Z   9 " =    2.291
peak=    4.057 closest distance to " OD1 ASN A  69 " =    2.689
peak=    4.056 closest distance to " O   HOH Z 419 " =    1.974
peak=    4.043 closest distance to " O   HOH Z  59 " =    1.671
peak=    4.021 closest distance to " O   SER A  87 " =    2.213
peak=    4.009 closest distance to " O   HOH Z 173 " =    2.038
peak=    3.969 closest distance to " CA  TYR A  30 " =    1.004
peak=    3.964 closest distance to " O   HOH Z 313 " =    1.743
peak=    3.958 closest distance to " O   HOH Z 106 " =    2.166
peak=    3.953 closest distance to " ND2 ASN A 187 " =    1.616
peak=    3.948 closest distance to " CB  TYR A 169 " =    0.903
peak=    3.947 closest distance to " O   HOH Z  78 " =    2.149
peak=    3.941 closest distance to " O   HOH Z 411 " =    3.758
peak=    3.937 closest distance to " O   HOH Z  44 " =    1.849
peak=    3.933 closest distance to " O   HOH Z 394 " =    1.480
peak=    3.912 closest distance to " CG1 ILE A  33 " =    1.159
peak=    3.897 closest distance to " CB  ARG A 139 " =    1.036
peak=    3.894 closest distance to " O   HOH Z 271 " =    1.449
peak=    3.888 closest distance to " CB  SER A  26 " =    1.586
peak=    3.882 closest distance to " O   HOH Z 357 " =    1.793
peak=    3.879 closest distance to " CA  ALA A 299 " =    0.968
peak=    3.864 closest distance to " OG BSER A 164 " =    2.507
peak=    3.864 closest distance to " CB  PRO A  54 " =    0.952
peak=    3.854 closest distance to " O   HOH Z 343 " =    1.512
peak=    3.843 closest distance to " O   HOH Z  10 " =    1.749
peak=    3.842 closest distance to " O   HOH Z 183 " =    1.841
peak=    3.839 closest distance to " O   HOH Z 368 " =    1.992
peak=    3.834 closest distance to " CG  GLN A  77 " =    0.881
peak=    3.823 closest distance to " CB  TRP A 179 " =    1.273
peak=    3.822 closest distance to " O   HOH Z  92 " =    1.220
peak=    3.814 closest distance to " O   HOH Z 366 " =    2.529
peak=    3.813 closest distance to " CG  ARG A  66 " =    2.798
peak=    3.790 closest distance to " CG2 VAL A 257 " =    0.887
peak=    3.784 closest distance to " CG  GLU A 277 " =    2.045
peak=    3.783 closest distance to " O   HOH Z 269 " =    3.318
peak=    3.779 closest distance to " O   HOH Z 303 " =    2.344
peak=    3.775 closest distance to " O   HOH Z 425 " =    1.365
peak=    3.771 closest distance to " O   HOH Z 286 " =    2.390
peak=    3.767 closest distance to " O   HOH Z 209 " =    2.157
peak=    3.765 closest distance to " O   HOH Z  97 " =    1.949
peak=    3.740 closest distance to " O   HOH Z 345 " =    3.171
peak=    3.724 closest distance to " CG2 THR A 221 " =    1.248
peak=    3.718 closest distance to " CG  PRO A  90 " =    1.245
peak=    3.705 closest distance to " O   HOH Z   6 " =    2.052
peak=    3.695 closest distance to " NH2BARG A 145 " =    2.125
peak=    3.680 closest distance to " CA  LEU A 282 " =    1.312
peak=    3.680 closest distance to " O   HOH Z 298 " =    1.816
peak=    3.680 closest distance to " NH1BARG A 145 " =    1.476
peak=    3.678 closest distance to " O   HOH Z 140 " =    1.455
peak=    3.673 closest distance to " O   HOH Z 368 " =    3.622
peak=    3.661 closest distance to " O   HOH Z 261 " =    1.709
peak=    3.658 closest distance to " OD2 ASP A 286 " =    2.506
peak=    3.657 closest distance to " O   HOH Z 132 " =    2.095
peak=    3.654 closest distance to " O   HOH Z 425 " =    1.952
peak=    3.653 closest distance to " O   HOH Z  43 " =    2.629
peak=    3.650 closest distance to " O   HOH Z 328 " =    1.963
peak=    3.639 closest distance to " CB  LEU A 228 " =    1.126
peak=    3.632 closest distance to " CG AARG A 275 " =    1.037
peak=    3.632 closest distance to " O   HOH Z 284 " =    1.462
peak=    3.626 closest distance to " O   HOH Z 250 " =    1.431
peak=    3.626 closest distance to " O   HOH Z  73 " =    1.875
peak=    3.613 closest distance to " O   HOH Z 282 " =    1.455
peak=    3.609 closest distance to " O   HOH Z 244 " =    1.638
peak=    3.606 closest distance to " O   HOH Z 289 " =    1.567
peak=    3.603 closest distance to " O   HOH Z 227 " =    1.929
peak=    3.601 closest distance to " CG  GLN A  77 " =    2.196
peak=    3.601 closest distance to " O   HOH Z  28 " =    2.134
peak=    3.598 closest distance to " O   HOH Z   1 " =    1.594
peak=    3.596 closest distance to " O   HOH Z 166 " =    1.383
peak=    3.581 closest distance to " CA  ASN A 215 " =    1.194
peak=    3.579 closest distance to " O   HOH Z 353 " =    2.272
peak=    3.568 closest distance to " O   HOH Z 189 " =    1.727
peak=    3.567 closest distance to " CA  PHE A 283 " =    1.189
peak=    3.566 closest distance to " O   HOH Z 426 " =    1.473
peak=    3.563 closest distance to " O   HOH Z  21 " =    1.760
peak=    3.562 closest distance to " O   HOH Z   1 " =    1.619
peak=    3.559 closest distance to " O   HOH Z 112 " =    1.711
peak=    3.555 closest distance to " O   HOH Z 153 " =    1.725
peak=    3.554 closest distance to " O   HOH Z 100 " =    0.953
peak=    3.541 closest distance to " CB  GLU A 128 " =    1.066
peak=    3.538 closest distance to " O   HOH Z 234 " =    1.906
peak=    3.537 closest distance to " OD1BASN A 224 " =    2.122
peak=    3.532 closest distance to " O   HOH Z 403 " =    1.190
peak=    3.515 closest distance to " OE2 GLU A  53 " =    2.022
peak=    3.503 closest distance to " CG2BVAL A  41 " =    0.733
peak=    3.503 closest distance to " N   TYR A  15 " =    1.024
peak=    3.502 closest distance to " O   HOH Z 227 " =    2.121
peak=    3.501 closest distance to " O   HOH Z 162 " =    2.019
peak=    3.491 closest distance to " O   HOH Z 155 " =    1.672
peak=    3.488 closest distance to " O   HOH Z 327 " =    1.837
peak=    3.485 closest distance to " O   HOH Z 128 " =    2.024
peak=    3.482 closest distance to " CB  ALA A  21 " =    1.806
peak=    3.481 closest distance to " CD2 TRP A 179 " =    1.352
peak=    3.479 closest distance to " O   HOH Z 423 " =    2.208
peak=    3.477 closest distance to " NE AARG A 275 " =    1.302
peak=    3.476 closest distance to " OG  SER A  22 " =    2.619
peak=    3.476 closest distance to " O   HOH Z 344 " =    1.152
peak=    3.476 closest distance to " CB  THR A 157 " =    1.012
peak=    3.474 closest distance to " N   PHE A 130 " =    1.368
peak=    3.471 closest distance to " CA  ALA A 233 " =    1.013
peak=    3.469 closest distance to " O   HOH Z  63 " =    2.345
peak=    3.465 closest distance to " O   HOH Z 389 " =    1.384
peak=    3.460 closest distance to " CB  ARG A  79 " =    1.288
peak=    3.455 closest distance to " O   HOH Z 158 " =    3.071
peak=    3.453 closest distance to " O   HOH Z 383 " =    1.810
peak=    3.453 closest distance to " CB  VAL A 202 " =    1.442
peak=    3.452 closest distance to " NH1 ARG A  14 " =    1.135
peak=    3.447 closest distance to " O   SER A  26 " =    1.562
peak=    3.439 closest distance to " CA  ALA A  21 " =    1.097
peak=    3.438 closest distance to " O   HOH Z  24 " =    1.401
peak=    3.436 closest distance to " O   HOH Z 156 " =    2.953
peak=    3.432 closest distance to " CB  VAL A 265 " =    1.389
peak=    3.429 closest distance to " O   HOH Z 108 " =    1.622
peak=    3.426 closest distance to " O   HOH Z 409 " =    2.331
peak=    3.424 closest distance to " O  BHOH Z 338 " =    2.280
peak=    3.421 closest distance to " CA  VAL A  41 " =    0.994
peak=    3.417 closest distance to " O   HOH Z 392 " =    1.331
peak=    3.409 closest distance to " CG2 THR A 220 " =    0.925
peak=    3.406 closest distance to " O   HOH Z 116 " =    2.264
peak=    3.405 closest distance to " CG  MET A 185 " =    1.324
peak=    3.404 closest distance to " OG  SER A  62 " =    2.928
peak=    3.397 closest distance to " O   HOH Z 125 " =    2.169
peak=    3.394 closest distance to " O   HOH Z 146 " =    1.735
peak=    3.394 closest distance to " CE1 TYR A 186 " =    1.252
peak=    3.393 closest distance to " CE  LYS A 119 " =    1.154
peak=    3.391 closest distance to " NE2 GLN A  73 " =    3.402
peak=    3.391 closest distance to " NH2 ARG A 219 " =    1.825
peak=    3.387 closest distance to " O   HOH Z 278 " =    1.325
peak=    3.378 closest distance to " O   HOH Z 215 " =    1.191
peak=    3.375 closest distance to " O   HOH Z 389 " =    2.936
peak=    3.369 closest distance to " CB  ILE A 120 " =    1.358
peak=    3.364 closest distance to " CB  ALA A  34 " =    1.003
peak=    3.363 closest distance to " CB  GLU A 277 " =    3.393
peak=    3.363 closest distance to " O   HOH Z  61 " =    1.684
peak=    3.359 closest distance to " N   ARG A 156 " =    1.236
peak=    3.359 closest distance to " O   HOH Z 344 " =    2.938
peak=    3.359 closest distance to " CD  LYS A 166 " =    1.288
peak=    3.358 closest distance to " O   HOH Z  88 " =    2.931
peak=    3.357 closest distance to " O   HOH Z 222 " =    2.336
peak=    3.356 closest distance to " O   HOH Z  54 " =    1.528
peak=    3.356 closest distance to " O   HOH Z 247 " =    1.156
peak=    3.354 closest distance to " O   HOH Z 118 " =    1.256
peak=    3.352 closest distance to " CD1 LEU A 228 " =    1.638
peak=    3.350 closest distance to " O   HOH Z 257 " =    2.245
peak=    3.350 closest distance to " O   HOH Z  43 " =    1.876
peak=    3.349 closest distance to " CD BLYS A 290 " =    1.119
peak=    3.343 closest distance to " O   HOH Z 435 " =    1.733
peak=    3.339 closest distance to " CB  ALA A 291 " =    1.448
peak=    3.338 closest distance to " O   HOH Z 196 " =    1.403
peak=    3.335 closest distance to " O   HOH Z 144 " =    2.145
peak=    3.335 closest distance to " O   HOH Z  59 " =    1.926
peak=    3.318 closest distance to " O   HOH Z 326 " =    1.331
peak=    3.311 closest distance to " O   HOH Z 172 " =    3.092
peak=    3.310 closest distance to " N   ASN A  39 " =    1.061
peak=    3.306 closest distance to " O   HOH Z 216 " =    1.826
peak=    3.305 closest distance to " O   HOH Z 407 " =    1.973
peak=    3.303 closest distance to " O   HOH Z 269 " =    1.072
peak=    3.298 closest distance to " O   HOH Z 260 " =    1.983
peak=    3.291 closest distance to " O   HOH Z  88 " =    2.463
peak=    3.290 closest distance to " CD  LYS A 119 " =    2.276
peak=    3.289 closest distance to " CE AMET A  47 " =    1.246
peak=    3.276 closest distance to " O   HOH Z 193 " =    2.024
peak=    3.276 closest distance to " N   GLY A 196 " =    1.000
peak=    3.274 closest distance to " O   HOH Z 284 " =    2.728
peak=    3.256 closest distance to " O   HOH Z  50 " =    1.515
peak=    3.256 closest distance to " CA  THR A 264 " =    0.786
peak=    3.252 closest distance to " O   HOH Z 130 " =    2.811
peak=    3.248 closest distance to " NZ  LYS A  48 " =    2.167
peak=    3.243 closest distance to " O   GLY A 302 " =    1.740
peak=    3.241 closest distance to " NH1AARG A 145 " =    1.038
peak=    3.236 closest distance to " O   HOH Z  15 " =    1.433
peak=    3.235 closest distance to " CD2 HIS A  81 " =    1.238
peak=    3.231 closest distance to " O   HOH Z  28 " =    1.366
peak=    3.231 closest distance to " OD1 ASP A 238 " =    0.882
peak=    3.230 closest distance to " NE2 GLN A 278 " =    3.365
peak=    3.226 closest distance to " CG  LEU A 167 " =    1.189
peak=    3.226 closest distance to " O   HOH Z 299 " =    2.287
peak=    3.221 closest distance to " CD  PRO A 243 " =    1.602
peak=    3.218 closest distance to " O   HOH Z 303 " =    1.780
peak=    3.217 closest distance to " NH2AARG A 190 " =    1.353
peak=    3.217 closest distance to " O   HOH Z 337 " =    3.565
peak=    3.214 closest distance to " O   HOH Z 152 " =    2.715
peak=    3.213 closest distance to " O   HOH Z 119 " =    1.555
peak=    3.213 closest distance to " O   HOH Z 215 " =    0.996
peak=    3.212 closest distance to " O   HOH Z 181 " =    1.693
peak=    3.210 closest distance to " CB  PRO A 163 " =    3.902
peak=    3.210 closest distance to " O   HOH Z 291 " =    1.832
peak=    3.206 closest distance to " O   HOH Z  40 " =    1.848
peak=    3.205 closest distance to " CB  TYR A  30 " =    1.452
peak=    3.200 closest distance to " O   GLY A  57 " =    2.315
peak=    3.197 closest distance to " CB  ASN A  39 " =    0.762
peak=    3.196 closest distance to " O   HOH Z 334 " =    1.411
peak=    3.192 closest distance to " OG  SER A  26 " =    1.314
peak=    3.190 closest distance to " O   HOH Z 291 " =    1.505
peak=    3.185 closest distance to " N   GLN A 278 " =    0.958
peak=    3.184 closest distance to " CB  THR A  31 " =    1.686
peak=    3.180 closest distance to " O   HOH Z 281 " =    4.545
peak=    3.180 closest distance to " O   HOH Z   3 " =    2.370
peak=    3.180 closest distance to " CD  GLN A  58 " =    5.783
peak=    3.179 closest distance to " OD1 ASN A  60 " =    1.520
peak=    3.178 closest distance to " O   HOH Z   5 " =    1.261
peak=    3.176 closest distance to " CG1BVAL A  72 " =    1.269
peak=    3.175 closest distance to " O   HOH Z 373 " =    1.521
peak=    3.175 closest distance to " O   HOH Z  44 " =    3.019
peak=    3.173 closest distance to " NH2 ARG A 269 " =    0.968
peak=    3.173 closest distance to " CB  ASN A 284 " =    1.788
peak=    3.173 closest distance to " O   HOH Z 145 " =    1.034
peak=    3.172 closest distance to " CA  ALA A 248 " =    1.132
peak=    3.167 closest distance to " O   HOH Z 423 " =    1.753
peak=    3.165 closest distance to " O   HOH Z  80 " =    2.080
peak=    3.155 closest distance to " O   HOH Z  48 " =    1.497
peak=    3.155 closest distance to " O   HOH Z  68 " =    1.600
peak=    3.146 closest distance to " O   HOH Z 356 " =    1.177
peak=    3.142 closest distance to " OG BSER A 258 " =    2.966
peak=    3.141 closest distance to " O   HOH Z 273 " =    3.047
peak=    3.139 closest distance to " O   HOH Z 299 " =    4.148
peak=    3.138 closest distance to " O   HOH Z  97 " =    1.352
peak=    3.137 closest distance to " CG  LYS A 119 " =    1.097
peak=    3.136 closest distance to " O   HOH Z 214 " =    1.994
peak=    3.126 closest distance to " CB  VAL A 265 " =    2.271
peak=    3.125 closest distance to " O   HOH Z 111 " =    2.639
peak=    3.124 closest distance to " O   HOH Z 388 " =    1.789
peak=    3.123 closest distance to " O   ASN A 217 " =    1.114
peak=    3.121 closest distance to " O   HOH Z  85 " =    1.482
peak=    3.120 closest distance to " O   HOH Z 287 " =    2.012
peak=    3.118 closest distance to " CB  LEU A 300 " =    1.070
peak=    3.115 closest distance to " N   SER A 210 " =    1.290
peak=    3.114 closest distance to " O   HOH Z 346 " =    1.441
peak=    3.110 closest distance to " O   HOH Z  32 " =    1.659
peak=    3.107 closest distance to " O   HOH Z 172 " =    5.283
peak=    3.107 closest distance to " O   HOH Z 140 " =    1.851
peak=    3.104 closest distance to " O   HOH Z 381 " =    1.755
peak=    3.102 closest distance to " N   ALA A 256 " =    1.638
peak=    3.100 closest distance to " CB  LYS A 193 " =    0.881
peak=    3.099 closest distance to " CB  ASN A 215 " =    0.964
peak=    3.099 closest distance to " CB  ARG A 190 " =    1.819
peak=    3.096 closest distance to " O   HOH Z 188 " =    1.897
peak=    3.095 closest distance to " O   HOH Z 296 " =    1.299
peak=    3.093 closest distance to " CB  ARG A 138 " =    0.858
peak=    3.086 closest distance to " CB  MET A 188 " =    1.630
peak=    3.084 closest distance to " CB  GLN A  88 " =    1.209
peak=    3.080 closest distance to " O   HOH Z 365 " =    3.150
peak=    3.067 closest distance to " O   HOH Z 422 " =    2.644
peak=    3.062 closest distance to " N   ASN A 127 " =    1.234

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.705 - 5.804
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 195
   mapped sites are within: 0.705 - 5.804

peak=   -4.727 closest distance to " O   HOH Z  52 " =    0.766
peak=   -4.682 closest distance to " SG  CYS A 254 " =    3.241
peak=   -4.463 closest distance to " C   HIS A 108 " =    1.177
peak=   -4.424 closest distance to " N   GLN A  58 " =    1.586
peak=   -4.398 closest distance to " O   PRO A 198 " =    1.341
peak=   -4.332 closest distance to " CB  TYR A  15 " =    2.142
peak=   -4.233 closest distance to " CD  ARG A 156 " =    1.927
peak=   -4.222 closest distance to " O   HOH Z 290 " =    1.116
peak=   -4.147 closest distance to " O   VAL A  67 " =    2.634
peak=   -4.073 closest distance to " CB  PRO A 243 " =    2.483
peak=   -4.036 closest distance to " CB  CYS A 201 " =    2.334
peak=   -4.023 closest distance to " CA  VAL A  67 " =    2.875
peak=   -4.018 closest distance to " O   HOH Z 198 " =    1.917
peak=   -4.016 closest distance to " O   HOH Z  13 " =    1.240
peak=   -4.012 closest distance to " NE2 GLN A  94 " =    2.400
peak=   -4.001 closest distance to " N   HIS A 115 " =    2.010
peak=   -3.987 closest distance to " O   HOH Z  43 " =    1.902
peak=   -3.981 closest distance to " O   HOH Z 407 " =    3.016
peak=   -3.961 closest distance to " CA  GLY A  98 " =    1.866
peak=   -3.957 closest distance to " O   HOH Z 377 " =    2.046
peak=   -3.955 closest distance to " N   GLN A 122 " =    1.413
peak=   -3.946 closest distance to " CG  PHE A 283 " =    2.566
peak=   -3.936 closest distance to " CZ  PHE A  59 " =    1.458
peak=   -3.921 closest distance to " OD2 ASP A 191 " =    1.395
peak=   -3.906 closest distance to " CG  MET A 105 " =    0.948
peak=   -3.903 closest distance to " O   ALA A 161 " =    1.658
peak=   -3.890 closest distance to " O   PRO A 198 " =    1.182
peak=   -3.890 closest distance to " CG  ASP A 231 " =    0.762
peak=   -3.845 closest distance to " OXT GLY A 302 " =    2.691
peak=   -3.822 closest distance to " O   HOH Z 263 " =    2.986
peak=   -3.799 closest distance to " O   HOH Z 126 " =    1.848
peak=   -3.790 closest distance to " C   ALA A 158 " =    1.270
peak=   -3.787 closest distance to " O   HOH Z 351 " =    1.440
peak=   -3.787 closest distance to " ND2 ASN A  45 " =    0.960
peak=   -3.753 closest distance to " O   VAL A 153 " =    2.373
peak=   -3.751 closest distance to " O   ALA A  51 " =    1.281
peak=   -3.728 closest distance to " CB  ALA A 248 " =    1.942
peak=   -3.728 closest distance to " OD1 ASP A 191 " =    1.773
peak=   -3.721 closest distance to " O   HOH Z 102 " =    1.686
peak=   -3.721 closest distance to " O   MET A  40 " =    2.672
peak=   -3.713 closest distance to " CD1 LEU A 255 " =    2.835
peak=   -3.699 closest distance to " CB  ALA A 291 " =    2.291
peak=   -3.696 closest distance to " O   ILE A  49 " =    1.392
peak=   -3.684 closest distance to " CD  GLN A  88 " =    0.890
peak=   -3.682 closest distance to " O   HOH Z  93 " =    1.578
peak=   -3.679 closest distance to " CG  LYS A 193 " =    2.347
peak=   -3.670 closest distance to " CD2 TYR A 293 " =    2.002
peak=   -3.669 closest distance to " O   HOH Z 166 " =    1.409
peak=   -3.656 closest distance to " OG  SER A   3 " =    1.243
peak=   -3.651 closest distance to " O   TRP A  70 " =    1.413
peak=   -3.646 closest distance to " O   SER A 146 " =    0.705
peak=   -3.625 closest distance to " O   HOH Z 109 " =    5.804
peak=   -3.623 closest distance to " N   SER A 276 " =    1.189
peak=   -3.615 closest distance to " CG  GLN A 223 " =    1.496
peak=   -3.613 closest distance to " CB  ALA A   7 " =    1.983
peak=   -3.607 closest distance to " C   GLN A 205 " =    1.950
peak=   -3.603 closest distance to " N   THR A 157 " =    1.607
peak=   -3.600 closest distance to " O   HOH Z 266 " =    4.413
peak=   -3.596 closest distance to " O   HOH Z 137 " =    1.394
peak=   -3.586 closest distance to " O   HOH Z  24 " =    1.250
peak=   -3.585 closest distance to " O   HOH Z  47 " =    1.526
peak=   -3.572 closest distance to " CD1 LEU A 101 " =    2.279
peak=   -3.564 closest distance to " O   HOH Z 388 " =    1.894
peak=   -3.560 closest distance to " O   HOH Z 250 " =    1.430
peak=   -3.543 closest distance to " NH2 ARG A  79 " =    1.975
peak=   -3.529 closest distance to " O   HOH Z 231 " =    2.048
peak=   -3.519 closest distance to " CD2 LEU A 237 " =    2.552
peak=   -3.509 closest distance to " NH1 ARG A  56 " =    2.489
peak=   -3.507 closest distance to " OE1 GLN A  88 " =    1.175
peak=   -3.499 closest distance to " OD1 ASP A 200 " =    1.225
peak=   -3.498 closest distance to " O   VAL A 189 " =    2.546
peak=   -3.493 closest distance to " CG2 THR A   4 " =    1.819
peak=   -3.493 closest distance to " CE2 PHE A 218 " =    2.493
peak=   -3.487 closest distance to " CG2AVAL A  41 " =    2.941
peak=   -3.483 closest distance to " NH1AARG A 275 " =    1.762
peak=   -3.479 closest distance to " O   SER A 135 " =    1.504
peak=   -3.472 closest distance to " N   GLN A  88 " =    1.913
peak=   -3.471 closest distance to " O   HOH Z 438 " =    0.961
peak=   -3.466 closest distance to " O   HOH Z 427 " =    1.485
peak=   -3.462 closest distance to " O   HOH Z 174 " =    4.704
peak=   -3.462 closest distance to " OG  SER A  87 " =    1.259
peak=   -3.461 closest distance to " CA  GLY A 133 " =    1.945
peak=   -3.460 closest distance to " O   HOH Z  88 " =    1.900
peak=   -3.460 closest distance to " OG BSER A 134 " =    1.389
peak=   -3.456 closest distance to " CE2 TYR A  30 " =    2.837
peak=   -3.454 closest distance to " CG  GLU A 152 " =    1.203
peak=   -3.453 closest distance to " C   ASN A 285 " =    2.159
peak=   -3.450 closest distance to " CB  ALA A 161 " =    2.446
peak=   -3.449 closest distance to " CE2 TYR A 116 " =    3.002
peak=   -3.426 closest distance to " O   HOH Z   3 " =    1.403
peak=   -3.422 closest distance to " O   HOH Z 421 " =    2.946
peak=   -3.421 closest distance to " CA  TYR A  30 " =    2.941
peak=   -3.418 closest distance to " CE3 TRP A 123 " =    1.244
peak=   -3.415 closest distance to " O   SER A  95 " =    1.348
peak=   -3.407 closest distance to " O   SER A  22 " =    2.441
peak=   -3.404 closest distance to " CB  PHE A 192 " =    1.716
peak=   -3.399 closest distance to " OG  SER A  97 " =    1.985
peak=   -3.396 closest distance to " ND2 ASN A  39 " =    1.338
peak=   -3.389 closest distance to " O   HOH Z 313 " =    1.848
peak=   -3.386 closest distance to " O   HOH Z 143 " =    2.468
peak=   -3.385 closest distance to " OD2 ASP A  50 " =    1.392
peak=   -3.385 closest distance to " O   HOH Z  37 " =    1.602
peak=   -3.382 closest distance to " O   HOH Z 298 " =    1.332
peak=   -3.381 closest distance to " O   PRO A 163 " =    1.216
peak=   -3.380 closest distance to " CD1 LEU A 228 " =    2.075
peak=   -3.370 closest distance to " O   HOH Z 211 " =    1.608
peak=   -3.369 closest distance to " NE2 GLN A 278 " =    1.658
peak=   -3.364 closest distance to " CG  GLU A 152 " =    2.528
peak=   -3.358 closest distance to " O   HOH Z 393 " =    3.233
peak=   -3.345 closest distance to " O   HOH Z 385 " =    1.836
peak=   -3.342 closest distance to " NH2 ARG A  66 " =    4.116
peak=   -3.342 closest distance to " OG  SER A 245 " =    1.214
peak=   -3.337 closest distance to " O   HOH Z 423 " =    2.254
peak=   -3.335 closest distance to " C   LEU A 143 " =    1.151
peak=   -3.333 closest distance to " CB  ALA A  51 " =    1.794
peak=   -3.331 closest distance to " O   HOH Z 395 " =    4.969
peak=   -3.313 closest distance to " CB  ASN A  39 " =    2.277
peak=   -3.311 closest distance to " O   HOH Z 233 " =    2.391
peak=   -3.311 closest distance to " CD  GLU A 236 " =    1.046
peak=   -3.309 closest distance to " O   HOH Z 210 " =    1.062
peak=   -3.306 closest distance to " SG ACYS A 201 " =    1.789
peak=   -3.298 closest distance to " N   ALA A 248 " =    1.657
peak=   -3.290 closest distance to " CZ  TYR A 169 " =    1.738
peak=   -3.290 closest distance to " CD2 LEU A 300 " =    2.845
peak=   -3.286 closest distance to " CE2 PHE A 204 " =    1.817
peak=   -3.283 closest distance to " CB  ALA A 244 " =    2.051
peak=   -3.279 closest distance to " OG  SER A 206 " =    1.651
peak=   -3.279 closest distance to " OE2 GLU A 152 " =    1.200
peak=   -3.277 closest distance to " CB  ASP A 132 " =    2.262
peak=   -3.274 closest distance to " O   TRP A  92 " =    1.739
peak=   -3.274 closest distance to " CB  ASP A  27 " =    2.284
peak=   -3.269 closest distance to " O   ARG A  66 " =    1.145
peak=   -3.269 closest distance to " O   HOH Z 218 " =    3.278
peak=   -3.267 closest distance to " O   HOH Z   3 " =    1.855
peak=   -3.265 closest distance to " O   HOH Z 131 " =    3.950
peak=   -3.264 closest distance to " CB  ALA A 291 " =    2.129
peak=   -3.254 closest distance to " O   HOH Z 337 " =    1.714
peak=   -3.249 closest distance to " O   HOH Z  97 " =    1.677
peak=   -3.244 closest distance to " CB  SER A 210 " =    1.364
peak=   -3.242 closest distance to " O   SER A  26 " =    1.062
peak=   -3.240 closest distance to " O   THR A 220 " =    1.718
peak=   -3.239 closest distance to " CE  MET A 105 " =    2.240
peak=   -3.235 closest distance to " OE2 GLU A   2 " =    1.020
peak=   -3.231 closest distance to " CD1 ILE A 239 " =    2.500
peak=   -3.227 closest distance to " O   HOH Z 185 " =    2.090
peak=   -3.223 closest distance to " CA  ALA A 227 " =    2.265
peak=   -3.221 closest distance to " CG2 VAL A  78 " =    1.410
peak=   -3.219 closest distance to " CZ  TYR A 214 " =    1.335
peak=   -3.218 closest distance to " CG2 THR A 178 " =    2.174
peak=   -3.209 closest distance to " ND2 ASN A 142 " =    1.835
peak=   -3.204 closest distance to " CE3 TRP A 274 " =    2.363
peak=   -3.200 closest distance to " O   LEU A 282 " =    2.304
peak=   -3.199 closest distance to " OD1 ASN A 148 " =    1.695
peak=   -3.186 closest distance to " O   PHE A 218 " =    1.425
peak=   -3.178 closest distance to " O   HOH Z  15 " =    1.677
peak=   -3.176 closest distance to " CG2 VAL A 189 " =    2.038
peak=   -3.175 closest distance to " OG1 THR A 246 " =    1.120
peak=   -3.175 closest distance to " O   ASP A 162 " =    2.164
peak=   -3.174 closest distance to " O   HOH Z 377 " =    0.789
peak=   -3.167 closest distance to " O   HOH Z 210 " =    1.989
peak=   -3.167 closest distance to " O   HOH Z  65 " =    1.172
peak=   -3.162 closest distance to " CA  ARG A 139 " =    1.130
peak=   -3.162 closest distance to " OG BSER A 134 " =    1.429
peak=   -3.160 closest distance to " O   HOH Z  60 " =    1.820
peak=   -3.159 closest distance to " OG  SER A  63 " =    1.424
peak=   -3.159 closest distance to " O   HOH Z 359 " =    3.260
peak=   -3.158 closest distance to " CG  PRO A 163 " =    2.560
peak=   -3.157 closest distance to " OE1 GLN A 183 " =    1.437
peak=   -3.156 closest distance to " ND2 ASN A  60 " =    1.627
peak=   -3.155 closest distance to " NH2 ARG A 139 " =    1.443
peak=   -3.152 closest distance to " O   HOH Z 385 " =    1.997
peak=   -3.148 closest distance to " O   ASN A 127 " =    1.502
peak=   -3.147 closest distance to " ND2 ASN A  69 " =    1.357
peak=   -3.145 closest distance to " O   HOH Z 436 " =    1.105
peak=   -3.139 closest distance to " O   HOH Z 298 " =    2.541
peak=   -3.137 closest distance to " O   HOH Z 198 " =    1.424
peak=   -3.134 closest distance to " OD1 ASN A 301 " =    1.978
peak=   -3.134 closest distance to " O   HOH Z 410 " =    2.347
peak=   -3.131 closest distance to " OG  SER A  97 " =    1.635
peak=   -3.130 closest distance to " O   HOH Z  56 " =    1.365
peak=   -3.124 closest distance to " CG  ASN A 110 " =    1.270
peak=   -3.122 closest distance to " N   GLY A 302 " =    1.343
peak=   -3.111 closest distance to " OG ASER A 134 " =    1.204
peak=   -3.107 closest distance to " NE2 GLN A  58 " =    1.058
peak=   -3.099 closest distance to " O   HOH Z 165 " =    2.333
peak=   -3.095 closest distance to " CE1 HIS A  81 " =    1.437
peak=   -3.081 closest distance to " O   HOH Z 281 " =    3.081
peak=   -3.075 closest distance to " OE1 GLN A  58 " =    2.888
peak=   -3.071 closest distance to " CD  LYS A 166 " =    2.487
peak=   -3.066 closest distance to " CA  SER A 245 " =    2.206
peak=   -3.044 closest distance to " OD1 ASP A 171 " =    1.684
peak=   -3.036 closest distance to " O   HOH Z 305 " =    2.021
peak=   -3.030 closest distance to " O   HOH Z 429 " =    2.038
peak=   -2.981 closest distance to " O   HOH Z 377 " =    0.826

================= 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    :  0.4720 0.4743   6.275136e+00   6.272818e+00
   1_bss:  0.4625 0.4621   6.271857e+00   6.255403e+00
   1_xyz:  0.3483 0.3773   6.078657e+00   6.132580e+00
   1_adp:  0.3144 0.3822   6.022697e+00   6.142128e+00
   1_occ:  0.3141 0.3828   6.022884e+00   6.142845e+00
   2_bss:  0.3111 0.3821   6.018328e+00   6.140935e+00
   2_xyz:  0.2520 0.3158   5.843425e+00   6.004169e+00
   2_adp:  0.2425 0.3027   5.810151e+00   5.972269e+00
   2_occ:  0.2420 0.3021   5.808771e+00   5.971890e+00
   3_bss:  0.2416 0.2999   5.807099e+00   5.969108e+00
   3_xyz:  0.1833 0.2407   5.569439e+00   5.774653e+00
   3_adp:  0.1627 0.2195   5.463849e+00   5.682310e+00
   3_occ:  0.1624 0.2190   5.462248e+00   5.679872e+00
   4_bss:  0.1623 0.2179   5.459528e+00   5.675939e+00
   4_xyz:  0.1321 0.1769   5.266597e+00   5.490281e+00
   4_adp:  0.1240 0.1691   5.213867e+00   5.443881e+00
   4_occ:  0.1239 0.1690   5.213130e+00   5.442789e+00
   5_bss:  0.1242 0.1696   5.213918e+00   5.444026e+00
   5_xyz:  0.1134 0.1637   5.153369e+00   5.402785e+00
   5_adp:  0.1122 0.1608   5.138305e+00   5.383209e+00
   5_occ:  0.1120 0.1606   5.137266e+00   5.382154e+00
   5_bss:  0.1120 0.1606   5.137266e+00   5.382154e+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:  0.345  10.059  -1.991   0.592   2.224   0.000   0.000   0.000
   1_xyz:  0.345  10.059  -1.991   0.592   2.224   0.000   0.000   0.000
   1_adp:  0.345  10.059  -1.991   0.592   2.224   0.000   0.000   0.000
   1_occ:  0.345  10.059  -1.991   0.592   2.224   0.000   0.000   0.000
   2_bss:  0.328  35.171  -1.710  -0.426   0.514  -0.000   0.000   0.000
   2_xyz:  0.328  35.171  -1.710  -0.426   0.514  -0.000   0.000   0.000
   2_adp:  0.328  35.171  -1.710  -0.426   0.514  -0.000   0.000   0.000
   2_occ:  0.328  35.171  -1.710  -0.426   0.514  -0.000   0.000   0.000
   3_bss:  0.319  26.750  -2.135  -1.466  -0.607  -0.000  -0.000  -0.000
   3_xyz:  0.319  26.750  -2.135  -1.466  -0.607  -0.000  -0.000  -0.000
   3_adp:  0.319  26.750  -2.135  -1.466  -0.607  -0.000  -0.000  -0.000
   3_occ:  0.319  26.750  -2.135  -1.466  -0.607  -0.000  -0.000  -0.000
   4_bss:  0.315  33.741  -2.907  -2.602  -1.800  -0.000  -0.000  -0.000
   4_xyz:  0.315  33.741  -2.907  -2.602  -1.800  -0.000  -0.000  -0.000
   4_adp:  0.315  33.741  -2.907  -2.602  -1.800  -0.000  -0.000  -0.000
   4_occ:  0.315  33.741  -2.907  -2.602  -1.800  -0.000  -0.000  -0.000
   5_bss:  0.314  35.164  -3.060  -2.721  -2.040  -0.000  -0.000  -0.000
   5_xyz:  0.314  35.164  -3.060  -2.721  -2.040  -0.000  -0.000  -0.000
   5_adp:  0.314  35.164  -3.060  -2.721  -2.040  -0.000  -0.000  -0.000
   5_occ:  0.314  35.164  -3.060  -2.721  -2.040  -0.000  -0.000  -0.000
   5_bss:  0.314  35.083  -2.979  -2.640  -1.959  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.332 0.4284  0.5920    71162.270
   1_bss:  55.646 0.4480  0.6239    65981.629
   1_xyz:  40.002 0.6434  0.8637    39281.503
   1_adp:  40.931 0.6316  0.8546    40333.642
   1_occ:  41.042 0.6302  0.8520    40454.580
   2_bss:  40.765 0.6333  0.8381    40071.271
   2_xyz:  32.524 0.7290  0.9477    26111.156
   2_adp:  30.515 0.7523  0.9833    23833.947
   2_occ:  30.481 0.7527  0.9826    23759.651
   3_bss:  30.370 0.7536  0.9514    23495.700
   3_xyz:  23.508 0.8269  1.0080    14683.997
   3_adp:  20.657 0.8558  1.0176    12007.271
   3_occ:  20.605 0.8563  1.0179    11934.758
   4_bss:  20.425 0.8577  0.9812    11756.068
   4_xyz:  16.141 0.8967  1.0017     7742.162
   4_adp:  15.057 0.9063  1.0011     7086.034
   4_occ:  15.036 0.9065  1.0012     7066.931
   5_bss:  15.073 0.9061  0.9944     7107.790
   5_xyz:  14.252 0.9128  0.9969     6482.064
   5_adp:  13.808 0.9166  0.9953     6290.374
   5_occ:  13.782 0.9168  0.9952     6271.773
   5_bss:  13.782 0.9168  0.9952     6271.773
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.0993e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.0993e-01
   1_xyz:   1.553  0.012  0.099 15.651  0.007  4.101   1.3448e-01
   1_adp:   1.553  0.012  0.099 15.651  0.007  4.101   1.3448e-01
   1_occ:   1.553  0.012  0.099 15.651  0.007  4.101   1.3448e-01
   2_bss:   1.553  0.012  0.099 15.651  0.007  4.101   1.3448e-01
   2_xyz:   1.138  0.008  0.075 14.129  0.005  4.117   7.0946e-02
   2_adp:   1.138  0.008  0.075 14.129  0.005  4.117   7.0946e-02
   2_occ:   1.138  0.008  0.075 14.129  0.005  4.117   7.0946e-02
   3_bss:   1.138  0.008  0.075 14.129  0.005  4.117   7.0946e-02
   3_xyz:   1.066  0.007  0.070 14.510  0.004  4.104   6.4577e-02
   3_adp:   1.066  0.007  0.070 14.510  0.004  4.104   6.4577e-02
   3_occ:   1.066  0.007  0.070 14.510  0.004  4.104   6.4577e-02
   4_bss:   1.066  0.007  0.070 14.510  0.004  4.104   6.4577e-02
   4_xyz:   1.014  0.006  0.069 14.490  0.004  4.104   5.8083e-02
   4_adp:   1.014  0.006  0.069 14.490  0.004  4.104   5.8083e-02
   4_occ:   1.014  0.006  0.069 14.490  0.004  4.104   5.8083e-02
   5_bss:   1.014  0.006  0.069 14.490  0.004  4.104   5.8083e-02
   5_xyz:   1.025  0.007  0.069 14.713  0.004  4.104   6.2483e-02
   5_adp:   1.025  0.007  0.069 14.713  0.004  4.104   6.2483e-02
   5_occ:   1.025  0.007  0.069 14.713  0.004  4.104   6.2483e-02
   5_bss:   1.025  0.007  0.069 14.713  0.004  4.104   6.2483e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.076   2.3821e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.076   2.3821e-01
   1_xyz:  10.201  0.068  0.433 86.107  0.076  1.979   9.9786e-02
   1_adp:  10.201  0.068  0.433 86.107  0.076  1.979   9.9786e-02
   1_occ:  10.201  0.068  0.433 86.107  0.076  1.979   9.9786e-02
   2_bss:  10.201  0.068  0.433 86.107  0.076  1.979   9.9786e-02
   2_xyz:   7.900  0.063  0.244 86.922  0.038  2.350   1.1881e-01
   2_adp:   7.900  0.063  0.244 86.922  0.038  2.350   1.1881e-01
   2_occ:   7.900  0.063  0.244 86.922  0.038  2.350   1.1881e-01
   3_bss:   7.900  0.063  0.244 86.922  0.038  2.350   1.1881e-01
   3_xyz:   7.777  0.039  0.266 81.031  0.034  2.290   5.1602e-02
   3_adp:   7.777  0.039  0.266 81.031  0.034  2.290   5.1602e-02
   3_occ:   7.777  0.039  0.266 81.031  0.034  2.290   5.1602e-02
   4_bss:   7.777  0.039  0.266 81.031  0.034  2.290   5.1602e-02
   4_xyz:   7.163  0.036  0.220 82.771  0.038  2.329   3.9550e-02
   4_adp:   7.163  0.036  0.220 82.771  0.038  2.329   3.9550e-02
   4_occ:   7.163  0.036  0.220 82.771  0.038  2.329   3.9550e-02
   5_bss:   7.163  0.036  0.220 82.771  0.038  2.329   3.9550e-02
   5_xyz:   6.850  0.040  0.219 84.789  0.041  2.285   7.7256e-02
   5_adp:   6.850  0.040  0.219 84.789  0.041  2.285   7.7256e-02
   5_occ:   6.850  0.040  0.219 84.789  0.041  2.285   7.7256e-02
   5_bss:   6.850  0.040  0.219 84.789  0.041  2.285   7.7256e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  97.74   0.00  19.37  97.74   0.00  15.58  95.36   0.00  40.00
   1_occ:  97.74   0.00  19.37  97.74   0.00  15.58  95.36   0.00  40.00
   2_bss:  97.74   0.00  19.37  97.74   0.00  15.58  95.36   0.00  40.00
   2_xyz:  97.74   0.00  19.37  97.74   0.00  15.58  95.36   0.00  40.00
   2_adp:  96.21   0.00  19.01  96.21   0.00  15.22  93.25   2.66  39.65
   2_occ:  96.21   0.00  19.01  96.21   0.00  15.22  93.25   2.66  39.65
   3_bss:  96.21   0.00  19.01  96.21   0.00  15.22  93.25   2.66  39.65
   3_xyz:  96.21   0.00  19.01  96.21   0.00  15.22  93.25   2.66  39.65
   3_adp:  95.49   0.47  18.16  95.49   0.47  13.78  88.50   6.30  42.04
   3_occ:  95.49   0.47  18.16  95.49   0.47  13.78  88.50   6.30  42.04
   4_bss:  95.49   0.47  18.16  95.49   0.47  13.78  88.50   6.30  42.04
   4_xyz:  95.49   0.47  18.16  95.49   0.47  13.78  88.50   6.30  42.04
   4_adp:  98.09   0.95  18.15  98.09   0.95  13.47  92.44   7.47  43.63
   4_occ:  98.09   0.95  18.15  98.09   0.95  13.47  92.44   7.47  43.63
   5_bss:  98.09   0.95  18.15  98.09   0.95  13.47  92.44   7.47  43.63
   5_xyz:  98.09   0.95  18.15  98.09   0.95  13.47  92.44   7.47  43.63
   5_adp:  97.47   2.24  17.74  97.47   2.24  13.29  92.18   6.49  42.01
   5_occ:  97.47   2.24  17.74  97.47   2.24  13.29  92.18   6.49  42.01
   5_bss:  97.39   2.16  17.66  97.39   2.16  13.21  92.10   6.41  41.93
------------------------------------------------------------------------
 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:    2.859    0.027    0.383
   1_adp:    2.859    0.027    0.383
   1_occ:    2.859    0.027    0.383
   2_bss:    2.859    0.027    0.383
   2_xyz:    2.699    0.023    0.498
   2_adp:    2.699    0.023    0.498
   2_occ:    2.699    0.023    0.498
   3_bss:    2.699    0.023    0.498
   3_xyz:    2.588    0.043    0.651
   3_adp:    2.588    0.043    0.651
   3_occ:    2.588    0.043    0.651
   4_bss:    2.588    0.043    0.651
   4_xyz:    2.364    0.035    0.722
   4_adp:    2.364    0.035    0.722
   4_occ:    2.364    0.035    0.722
   5_bss:    2.364    0.035    0.722
   5_xyz:    2.066    0.054    0.744
   5_adp:    2.066    0.054    0.744
   5_occ:    2.066    0.054    0.744
   5_bss:    2.066    0.054    0.744
------------------------------------------------------------------------

CPU time actual refinement: 333.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_264/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/noshake/run_264/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_264/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_264/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_264/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.67 
  Macro-tasks:
    bulk solvent and scale       = 41.62  
    individual site refinement   = 134.63 
    weights calculation          = 29.82  
    collect and process          = 6.54   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.71 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 105.96 
    alpha_beta                      = 8.36   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 114.02 
    fmodel                         = 7.04   
    r_factors                      = 0.21   
    phase_errors                   = 10.50  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 249.89 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.781 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    636 calls, 105.48 s
gradients_fft:          581 calls, 101.27 s

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

# Date 2008-01-16 Time 04:25:10 PST -0800 (1200486310.52 s)
Start R-work = 0.4720, R-free = 0.4743 (no bulk solvent and anisotropic scale)
Final R-work = 0.1398, R-free = 0.1832 (no bulk solvent and anisotropic scale)

Start R-work = 0.4625, R-free = 0.4621
Final R-work = 0.1120, R-free = 0.1606