# Date 2008-01-16 Time 04:36:27 PST -0800 (1200486987.30 s)
#phil __OFF__

Command line arguments: "../383.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27140
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 383

-------------------------------------------------------------------------------
  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: (69.5475, 45.9914, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.96268
Completeness in resolution range: 0.941598
Completeness with d_max=infinity: 0.938755

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9620
                             d_min =   1.9627

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: (69.5475, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.96268
Completeness in resolution range: 0.941598
Completeness with d_max=infinity: 0.938755

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9625 -  4.2002 [2183/2207]  1962   221  10.1%
  bin  2:  4.2002 -  3.3461 [2107/2127]  1900   207   9.8%
  bin  3:  3.3461 -  2.9267 [2075/2094]  1866   209  10.1%
  bin  4:  2.9267 -  2.6608 [2034/2064]  1825   209  10.3%
  bin  5:  2.6608 -  2.4710 [2057/2076]  1856   201   9.8%
  bin  6:  2.4710 -  2.3259 [2025/2050]  1820   205  10.1%
  bin  7:  2.3259 -  2.2098 [2024/2052]  1824   200   9.9%
  bin  8:  2.2098 -  2.1138 [1996/2032]  1796   200  10.0%
  bin  9:  2.1138 -  2.0327 [2000/2049]  1807   193   9.7%
  bin 10:  2.0327 -  1.9627 [1088/2053]   974   114  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_383/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:
        1.23 -     1.97: 12
        1.97 -     2.70: 163
        2.70 -     3.43: 4582
        3.43 -     4.17: 9440
        4.17 -     4.90: 14312
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.233 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.712 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.763 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.767 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.781 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28504 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_383/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_383/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 69.5475 45.9914 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4624   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.271489                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.6850 0.99   1418  156 0.3637 0.3470      6.5581      6.5034|
|  2:  4.6850 -  3.7377 0.99   1369  153 0.3890 0.4112      6.7738      6.7625|
|  3:  3.7377 -  3.2708 0.99   1338  149 0.4270 0.4003      6.6616      6.6601|
|  4:  3.2708 -  2.9743 0.99   1325  149 0.4573 0.4809      6.5229       6.544|
|  5:  2.9743 -  2.7626 0.99   1313  146 0.4915 0.4498      6.3476      6.3593|
|  6:  2.7626 -  2.6006 0.99   1325  146 0.4928 0.5112       6.264      6.1775|
|  7:  2.6006 -  2.4710 0.99   1321  148 0.4957 0.5019      6.2158      6.1616|
|  8:  2.4710 -  2.3638 0.98   1303  142 0.5195 0.5243      6.1835      6.1759|
|  9:  2.3638 -  2.2732 0.98   1289  144 0.4994 0.5336      6.1031      6.1666|
| 10:  2.2732 -  2.1950 1.00   1296  146 0.5168 0.5212      6.0921       6.091|
| 11:  2.1950 -  2.1265 0.98   1301  142 0.5106 0.5029      6.0157      6.0354|
| 12:  2.1265 -  2.0659 0.98   1292  142 0.5149 0.4767       5.966      5.9498|
| 13:  2.0659 -  2.0117 0.93   1223  138 0.5023 0.5100      5.8788      5.8281|
| 14:  2.0117 -  1.9627 0.40    517   58 0.5296 0.4958       5.897      5.8036|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.6850  1418   156  0.73  31.38   0.82     0.79      63657.87|
|  2:  4.6850 -  3.7377  1369   153  0.71  34.11   0.91     0.83     102168.11|
|  3:  3.7377 -  3.2708  1338   149  0.60  43.70   0.93     0.79     111350.23|
|  4:  3.2708 -  2.9743  1325   149  0.51  51.28   0.91     0.69     104004.90|
|  5:  2.9743 -  2.7626  1313   146  0.44  56.40   0.89     0.63      76839.73|
|  6:  2.7626 -  2.6006  1325   146  0.42  57.95   0.90     0.59      66901.88|
|  7:  2.6006 -  2.4710  1321   148  0.40  59.53   0.91     0.56      60646.03|
|  8:  2.4710 -  2.3638  1303   142  0.37  61.90   0.90     0.54      57149.79|
|  9:  2.3638 -  2.2732  1289   144  0.37  62.26   0.93     0.53      52799.12|
| 10:  2.2732 -  2.1950  1296   146  0.38  61.91   0.93     0.54      46877.01|
| 11:  2.1950 -  2.1265  1301   142  0.36  63.34   0.94     0.56      47224.38|
| 12:  2.1265 -  2.0659  1292   142  0.35  63.77   0.95     0.56      42638.85|
| 13:  2.0659 -  2.0117  1223   138  0.34  64.79   0.94     0.55      37120.36|
| 14:  2.0117 -  1.9627   517    58  0.40  60.35   1.01     0.55      27621.34|
|alpha:            min =        0.53 max =            0.83 mean =         0.63|
|beta:             min =    27621.34 max =       111350.23 mean =     66140.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.65|
|phase err.(test): min =        0.00 max =           89.88 mean =        55.11|
|-----------------------------------------------------------------------------|

============================== 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 = 11.072246             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.802   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.457977              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.619   (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 |  1.233 -  1.599:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.599 -  1.966:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.966 -  2.333:       24 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.333 -  2.700:      139 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.700 -  3.066:     2251 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.066 -  3.433:     2331 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.433 -  3.800:     4111 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.800 -  4.167:     5329 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.167 -  4.533:     6409 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.533 -  4.900:     7903 |
|-----------------------------------------------------------------------------|
|-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 |        0.186 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.233 |       0.539 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.668)------------------------------------------|
|    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: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4624   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.271489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4497   r_free= 0.4521   ksol= 0.33   Bsol= 26.68   scale= 0.943   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,1.88,2.95,0.00,0.00,0.00); trace/3= 0.71                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.263859                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.636148              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.718   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.162332              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.363   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4497      final r-factor (work) = 0.3489          |
| start r-factor (free) = 0.4521      final r-factor (free) = 0.3862          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2099 = 8.64 * 0.50 * 6.2583 + 1.00 * 0.1860                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6511 = 8.64 * 0.50 * 6.1427 + 1.00 * 0.1265                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3489      final r-factor (work) = 0.3162          |
| start r-factor (free) = 0.3862      final r-factor (free) = 0.4014          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1460 = 1.16 * 1.00 * 6.1427 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0375 = 1.16 * 1.00 * 6.0383 + 1.00 * 0.0189                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.668)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.06  18.65    None  None   None       |
|    all(noH): 2823   0      0.00    107.06  18.65    None  None   None       |
|    Sol.    : 438    0      0.00    107.06  37.00    None  None   None       |
|    Mac.    : 2385   0      0.00    80.86   15.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.706:  958   |   5:    53.528 -  64.233:   61        |
|      1:    10.706 -  21.411:  970   |   6:    64.233 -  74.939:   20        |
|      2:    21.411 -  32.117:  464   |   7:    74.939 -  85.644:   10        |
|      3:    32.117 -  42.822:  217   |   8:    85.644 -  96.350:    2        |
|      4:    42.822 -  53.528:  120   |   9:    96.350 - 107.055:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3162 r_free = 0.4014             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3160 r_free = 0.4023             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3160   r_free= 0.4023   ksol= 0.33   Bsol= 26.68   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,1.88,2.95,0.00,0.00,0.00); trace/3= 0.71                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.050015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3152   r_free= 0.4002   ksol= 0.34   Bsol= 60.56   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,0.18,1.38,0.00,0.00,0.00); trace/3= -0.11                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.050453                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.841496              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.174   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.466007              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.974  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3152      final r-factor (work) = 0.2413          |
| start r-factor (free) = 0.4002      final r-factor (free) = 0.3114          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8226 = 8.84 * 0.50 * 6.0389 + 1.00 * 0.1261                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.4380 = 8.84 * 0.50 * 5.9593 + 1.00 * 0.0936                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2413      final r-factor (work) = 0.2205          |
| start r-factor (free) = 0.3114      final r-factor (free) = 0.2846          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7957 = 0.47 * 1.00 * 5.9593 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7072 = 0.47 * 1.00 * 5.7838 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.668)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.08  18.07    None  None   None       |
|    all(noH): 2823   0      0.00    105.08  18.07    None  None   None       |
|    Sol.    : 438    0      2.81    105.08  39.81    None  None   None       |
|    Mac.    : 2385   0      0.00    76.40   14.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.508: 1037   |   5:    52.541 -  63.049:   62        |
|      1:    10.508 -  21.016: 1003   |   6:    63.049 -  73.557:   25        |
|      2:    21.016 -  31.525:  343   |   7:    73.557 -  84.065:    9        |
|      3:    31.525 -  42.033:  191   |   8:    84.065 -  94.573:    1        |
|      4:    42.033 -  52.541:  151   |   9:    94.573 - 105.082:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2205 r_free = 0.2846             target_work(ml) = 5.744         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2204 r_free = 0.2839             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2204   r_free= 0.2839   ksol= 0.34   Bsol= 60.56   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,0.18,1.38,0.00,0.00,0.00); trace/3= -0.11                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.742736                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2202   r_free= 0.2831   ksol= 0.33   Bsol= 60.56   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-1.06,0.48,-0.00,0.00,0.00); trace/3= -0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.740548                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.932237              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.439  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.132121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.448  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2202      final r-factor (work) = 0.1632          |
| start r-factor (free) = 0.2831      final r-factor (free) = 0.2168          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2515 = 5.93 * 0.50 * 5.7846 + 1.00 * 0.0936                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7473 = 5.93 * 0.50 * 5.6217 + 1.00 * 0.0727                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1632      final r-factor (work) = 0.1458          |
| start r-factor (free) = 0.2168      final r-factor (free) = 0.1996          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3757 = 1.13 * 1.00 * 5.6217 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1445 = 1.13 * 1.00 * 5.4169 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.668)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.40  17.98    None  None   None       |
|    all(noH): 2823   0      0.00    104.40  17.98    None  None   None       |
|    Sol.    : 438    0      5.83    104.40  44.60    None  None   None       |
|    Mac.    : 2385   0      0.00    83.61   13.09    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 -  10.440: 1157   |   5:    52.199 -  62.639:  107        |
|      1:    10.440 -  20.880:  996   |   6:    62.639 -  73.079:   63        |
|      2:    20.880 -  31.320:  240   |   7:    73.079 -  83.519:   16        |
|      3:    31.320 -  41.759:  117   |   8:    83.519 -  93.958:    4        |
|      4:    41.759 -  52.199:  122   |   9:    93.958 - 104.398:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1458 r_free = 0.1996             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1457 r_free = 0.1995             target_work(ml) = 5.376         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1457   r_free= 0.1995   ksol= 0.33   Bsol= 60.56   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-1.06,0.48,-0.00,0.00,0.00); trace/3= -0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.376122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1455   r_free= 0.1989   ksol= 0.32   Bsol= 60.56   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.95,-0.08,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.371968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.526132              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.255  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483194              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.762  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1455      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1989      final r-factor (free) = 0.1782          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9180 = 2.53 * 0.50 * 5.4195 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7865 = 2.53 * 0.50 * 5.3276 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1782      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5861 = 0.48 * 1.00 * 5.3276 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5481 = 0.48 * 1.00 * 5.2516 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.668)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.24    101.83  17.56    None  None   None       |
|    all(noH): 2823   0      0.24    101.83  17.56    None  None   None       |
|    Sol.    : 438    0      4.36    101.83  43.61    None  None   None       |
|    Mac.    : 2385   0      0.24    90.75   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.238 -  10.398: 1207   |   5:    51.034 -  61.193:   93        |
|      1:    10.398 -  20.557:  980   |   6:    61.193 -  71.353:   64        |
|      2:    20.557 -  30.716:  220   |   7:    71.353 -  81.512:   23        |
|      3:    30.716 -  40.875:  113   |   8:    81.512 -  91.671:    9        |
|      4:    40.875 -  51.034:  113   |   9:    91.671 - 101.830:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1245 r_free = 0.1729             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1728             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1728   ksol= 0.32   Bsol= 60.56   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.95,-0.08,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1728   ksol= 0.32   Bsol= 57.44   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.95,-0.08,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233973                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.295981              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.199  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.399967              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.238  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7113 = 3.30 * 0.50 * 5.2512 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6419 = 3.30 * 0.50 * 5.2030 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0916 = 0.40 * 1.00 * 5.2030 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0783 = 0.40 * 1.00 * 5.1719 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.668)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.38    98.55   17.11    None  None   None       |
|    all(noH): 2823   0      0.38    98.55   17.11    None  None   None       |
|    Sol.    : 438    0      5.58    98.55   41.91    None  None   None       |
|    Mac.    : 2385   0      0.38    93.67   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.376 -  10.193: 1174   |   5:    49.462 -  59.279:   75        |
|      1:    10.193 -  20.010: 1023   |   6:    59.279 -  69.097:   71        |
|      2:    20.010 -  29.828:  203   |   7:    69.097 -  78.914:   24        |
|      3:    29.828 -  39.645:  136   |   8:    78.914 -  88.731:    7        |
|      4:    39.645 -  49.462:  107   |   9:    88.731 -  98.548:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1141 r_free = 0.1627             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1140 r_free = 0.1627             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1627   ksol= 0.32   Bsol= 57.44   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.95,-0.08,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166378                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.6850 0.99   1418  156 0.0972 0.1293      5.3895       5.584|
|  2:  4.6850 -  3.7377 0.99   1369  153 0.0834 0.1158      5.4368      5.6468|
|  3:  3.7377 -  3.2708 0.99   1338  149 0.1097 0.1532      5.4973      5.8505|
|  4:  3.2708 -  2.9743 0.99   1325  149 0.1274 0.1772       5.483      5.6457|
|  5:  2.9743 -  2.7626 0.99   1313  146 0.1373 0.1718      5.3616      5.5717|
|  6:  2.7626 -  2.6006 0.99   1325  146 0.1265 0.2097      5.2367      5.5169|
|  7:  2.6006 -  2.4710 0.99   1321  148 0.1352 0.1656      5.2159       5.351|
|  8:  2.4710 -  2.3638 0.98   1303  142 0.1231 0.1683      5.1091      5.3641|
|  9:  2.3638 -  2.2732 0.98   1289  144 0.1203 0.1820        5.04      5.3296|
| 10:  2.2732 -  2.1950 1.00   1296  146 0.1124 0.1778      4.9494      5.2059|
| 11:  2.1950 -  2.1265 0.98   1301  142 0.1124 0.1831      4.9321      5.2834|
| 12:  2.1265 -  2.0659 0.98   1292  142 0.1206 0.1808      4.9203      5.2166|
| 13:  2.0659 -  2.0117 0.93   1223  138 0.1051 0.1716       4.747      4.9817|
| 14:  2.0117 -  1.9627 0.40    517   58 0.0864 0.1572      4.5677       4.859|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.6850  1418   156  0.93   9.78   0.98     0.95       7877.11|
|  2:  4.6850 -  3.7377  1369   153  0.95   8.21   1.02     1.01       9557.52|
|  3:  3.7377 -  3.2708  1338   149  0.93  11.90   1.04     1.03      10946.60|
|  4:  3.2708 -  2.9743  1325   149  0.91  14.62   1.02     1.00      11080.50|
|  5:  2.9743 -  2.7626  1313   146  0.90  16.49   1.01     0.99       8967.14|
|  6:  2.7626 -  2.6006  1325   146  0.89  16.92   0.98     0.96       7491.16|
|  7:  2.6006 -  2.4710  1321   148  0.90  16.69   1.00     0.96       6794.17|
|  8:  2.4710 -  2.3638  1303   142  0.90  16.30   1.00     0.97       5777.46|
|  9:  2.3638 -  2.2732  1289   144  0.91  15.65   1.00     0.96       5047.03|
| 10:  2.2732 -  2.1950  1296   146  0.90  15.80   1.01     0.98       4377.10|
| 11:  2.1950 -  2.1265  1301   142  0.90  16.49   0.99     0.95       4417.89|
| 12:  2.1265 -  2.0659  1292   142  0.89  17.02   1.02     1.02       4333.15|
| 13:  2.0659 -  2.0117  1223   138  0.90  16.05   1.00     0.99       3201.43|
| 14:  2.0117 -  1.9627   517    58  0.95  10.97   1.00     0.97       2099.20|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2099.20 max =        11080.50 mean =      6824.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.59|
|phase err.(test): min =        0.00 max =           89.17 mean =        14.06|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1621   ksol= 0.32   Bsol= 55.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.12,-0.07,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163657                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1621   ksol= 0.32   Bsol= 55.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.12,-0.07,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163657                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.6850 0.99   1418  156 0.0977 0.1273      5.3688      5.5504|
|  2:  4.6850 -  3.7377 0.99   1369  153 0.0839 0.1141      5.4326      5.6416|
|  3:  3.7377 -  3.2708 0.99   1338  149 0.1105 0.1506      5.4975      5.8389|
|  4:  3.2708 -  2.9743 0.99   1325  149 0.1276 0.1790      5.4832      5.6499|
|  5:  2.9743 -  2.7626 0.99   1313  146 0.1373 0.1712      5.3609      5.5708|
|  6:  2.7626 -  2.6006 0.99   1325  146 0.1264 0.2081       5.235      5.5122|
|  7:  2.6006 -  2.4710 0.99   1321  148 0.1353 0.1665      5.2153      5.3526|
|  8:  2.4710 -  2.3638 0.98   1303  142 0.1229 0.1681      5.1083      5.3614|
|  9:  2.3638 -  2.2732 0.98   1289  144 0.1201 0.1811       5.039      5.3288|
| 10:  2.2732 -  2.1950 1.00   1296  146 0.1122 0.1782      4.9487      5.2084|
| 11:  2.1950 -  2.1265 0.98   1301  142 0.1122 0.1829      4.9314      5.2831|
| 12:  2.1265 -  2.0659 0.98   1292  142 0.1204 0.1805      4.9202      5.2158|
| 13:  2.0659 -  2.0117 0.93   1223  138 0.1048 0.1712      4.7441      4.9788|
| 14:  2.0117 -  1.9627 0.40    517   58 0.0864 0.1558      4.5644      4.8539|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.6850  1418   156  0.94   9.48   0.98     0.95       7400.36|
|  2:  4.6850 -  3.7377  1369   153  0.95   8.03   1.02     1.01       9210.20|
|  3:  3.7377 -  3.2708  1338   149  0.93  11.80   1.04     1.03      10832.94|
|  4:  3.2708 -  2.9743  1325   149  0.91  14.60   1.02     1.00      11045.21|
|  5:  2.9743 -  2.7626  1313   146  0.90  16.43   1.01     0.99       8924.98|
|  6:  2.7626 -  2.6006  1325   146  0.89  16.86   0.98     0.96       7452.16|
|  7:  2.6006 -  2.4710  1321   148  0.90  16.66   1.00     0.96       6767.40|
|  8:  2.4710 -  2.3638  1303   142  0.90  16.30   1.00     0.97       5773.13|
|  9:  2.3638 -  2.2732  1289   144  0.91  15.64   1.00     0.96       5045.85|
| 10:  2.2732 -  2.1950  1296   146  0.90  15.80   1.01     0.97       4381.09|
| 11:  2.1950 -  2.1265  1301   142  0.90  16.49   0.99     0.95       4421.81|
| 12:  2.1265 -  2.0659  1292   142  0.89  17.02   1.01     1.02       4333.56|
| 13:  2.0659 -  2.0117  1223   138  0.90  16.00   1.00     0.98       3180.00|
| 14:  2.0117 -  1.9627   517    58  0.95  10.88   0.99     0.97       2076.62|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2076.62 max =        11045.21 mean =      6737.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.52|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.01|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.668)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    98.54   17.09    None  None   None       |
|    all(noH): 2823   0      0.36    98.54   17.09    None  None   None       |
|    Sol.    : 438    0      5.57    98.54   41.90    None  None   None       |
|    Mac.    : 2385   0      0.36    93.65   12.54    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:     0.365 -  10.182: 1174   |   5:    49.451 -  59.268:   75        |
|      1:    10.182 -  19.999: 1023   |   6:    59.268 -  69.085:   71        |
|      2:    19.999 -  29.817:  203   |   7:    69.085 -  78.903:   24        |
|      3:    29.817 -  39.634:  136   |   8:    78.903 -  88.720:    7        |
|      4:    39.634 -  49.451:  107   |   9:    88.720 -  98.537:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.497 - 4.541
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 299
   mapped sites are within: 0.776 - 4.541

peak=    6.204 closest distance to " NE2 GLN A  11 " =    1.277
peak=    5.687 closest distance to " O   HOH Z 142 " =    1.890
peak=    5.604 closest distance to " O   HOH Z  63 " =    1.791
peak=    5.504 closest distance to " O   HOH Z 287 " =    2.112
peak=    5.434 closest distance to " CG  PRO A  54 " =    1.352
peak=    5.417 closest distance to " O   HOH Z 126 " =    2.163
peak=    5.378 closest distance to " O   HOH Z  49 " =    1.211
peak=    5.241 closest distance to " O   HOH Z 371 " =    1.956
peak=    5.138 closest distance to " O   HOH Z  69 " =    1.310
peak=    5.129 closest distance to " O   HOH Z 417 " =    2.541
peak=    5.065 closest distance to " O   HOH Z 423 " =    1.722
peak=    5.064 closest distance to " O   HOH Z 403 " =    1.644
peak=    4.921 closest distance to " O   HOH Z   9 " =    1.991
peak=    4.907 closest distance to " O   HOH Z   7 " =    1.467
peak=    4.858 closest distance to " O   HOH Z 427 " =    2.445
peak=    4.742 closest distance to " NH2 ARG A  56 " =    2.080
peak=    4.731 closest distance to " O   HOH Z 380 " =    1.872
peak=    4.681 closest distance to " O   HOH Z 232 " =    2.185
peak=    4.656 closest distance to " O   HOH Z 419 " =    2.411
peak=    4.656 closest distance to " O   HOH Z 298 " =    1.820
peak=    4.594 closest distance to " CB  PRO A  54 " =    1.034
peak=    4.565 closest distance to " O   HOH Z 425 " =    1.455
peak=    4.536 closest distance to " CB  ARG A 275 " =    0.993
peak=    4.497 closest distance to " O   HOH Z  78 " =    1.520
peak=    4.496 closest distance to " CB  GLN A 223 " =    1.543
peak=    4.434 closest distance to " CB  SER A  63 " =    1.215
peak=    4.408 closest distance to " O   HOH Z  65 " =    1.089
peak=    4.401 closest distance to " CB  GLU A 277 " =    3.541
peak=    4.398 closest distance to " O   HOH Z   1 " =    1.877
peak=    4.367 closest distance to " CB  ASN A 148 " =    1.490
peak=    4.322 closest distance to " ND2 ASN A 187 " =    1.668
peak=    4.252 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.218 closest distance to " O   SER A  87 " =    2.308
peak=    4.215 closest distance to " O   HOH Z 422 " =    0.966
peak=    4.205 closest distance to " CG  TRP A 179 " =    2.122
peak=    4.174 closest distance to " CE  LYS A 119 " =    1.246
peak=    4.174 closest distance to " CB  ARG A 190 " =    1.551
peak=    4.163 closest distance to " CB  ARG A  79 " =    1.367
peak=    4.152 closest distance to " O   HOH Z 327 " =    1.652
peak=    4.113 closest distance to " O   HOH Z 368 " =    3.607
peak=    4.086 closest distance to " O   HOH Z 405 " =    1.422
peak=    4.085 closest distance to " CG2 VAL A 257 " =    0.812
peak=    4.084 closest distance to " O   HOH Z  61 " =    1.606
peak=    4.067 closest distance to " CA  TYR A  30 " =    0.990
peak=    4.057 closest distance to " O   HOH Z 406 " =    1.622
peak=    4.041 closest distance to " O   HOH Z 362 " =    2.081
peak=    4.039 closest distance to " O   HOH Z 272 " =    1.765
peak=    4.036 closest distance to " NH2AARG A 190 " =    1.877
peak=    4.034 closest distance to " O   HOH Z  30 " =    1.812
peak=    4.031 closest distance to " CD2 TRP A 179 " =    1.259
peak=    4.025 closest distance to " O   HOH Z  39 " =    1.004
peak=    4.024 closest distance to " O   HOH Z 236 " =    1.517
peak=    4.005 closest distance to " CB  ASN A  39 " =    0.969
peak=    4.004 closest distance to " NZ  LYS A 119 " =    2.484
peak=    3.991 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.986 closest distance to " CZ3 TRP A 266 " =    1.161
peak=    3.974 closest distance to " CB  GLN A 183 " =    1.171
peak=    3.974 closest distance to " O   HOH Z 215 " =    1.452
peak=    3.970 closest distance to " O   HOH Z  40 " =    2.123
peak=    3.969 closest distance to " CA  ARG A 195 " =    1.220
peak=    3.960 closest distance to " CB  VAL A 265 " =    1.361
peak=    3.956 closest distance to " CB  GLN A  88 " =    1.272
peak=    3.949 closest distance to " O   HOH Z 359 " =    1.472
peak=    3.948 closest distance to " CB  ASN A 142 " =    0.967
peak=    3.946 closest distance to " O   HOH Z 112 " =    1.068
peak=    3.944 closest distance to " CG  GLN A  58 " =    0.959
peak=    3.920 closest distance to " CB  ARG A  79 " =    0.912
peak=    3.915 closest distance to " O   HOH Z 346 " =    1.604
peak=    3.908 closest distance to " O   HOH Z 222 " =    1.150
peak=    3.906 closest distance to " NH1AARG A 145 " =    1.231
peak=    3.896 closest distance to " O   HOH Z 365 " =    2.675
peak=    3.893 closest distance to " O   HOH Z  59 " =    1.741
peak=    3.867 closest distance to " O   HOH Z 286 " =    2.245
peak=    3.862 closest distance to " CG  PRO A  90 " =    1.434
peak=    3.855 closest distance to " OG ASER A 258 " =    3.069
peak=    3.851 closest distance to " O   HOH Z 145 " =    1.131
peak=    3.851 closest distance to " CG1BVAL A  72 " =    1.216
peak=    3.840 closest distance to " O   HOH Z  61 " =    1.681
peak=    3.813 closest distance to " CD  ARG A  66 " =    2.394
peak=    3.809 closest distance to " CA  VAL A 125 " =    1.160
peak=    3.804 closest distance to " O   HOH Z 203 " =    1.715
peak=    3.802 closest distance to " O   HOH Z 357 " =    2.002
peak=    3.792 closest distance to " O   HOH Z 214 " =    2.472
peak=    3.789 closest distance to " CB  LYS A 117 " =    1.197
peak=    3.788 closest distance to " O   HOH Z   1 " =    1.723
peak=    3.777 closest distance to " O   HOH Z 422 " =    2.382
peak=    3.769 closest distance to " N   GLN A 278 " =    1.443
peak=    3.765 closest distance to " CB  ASP A 191 " =    1.188
peak=    3.756 closest distance to " O   PRO A 198 " =    1.595
peak=    3.753 closest distance to " NZ  LYS A 117 " =    2.747
peak=    3.751 closest distance to " O   HOH Z 218 " =    1.722
peak=    3.744 closest distance to " O   HOH Z 258 " =    2.130
peak=    3.742 closest distance to " CB  GLU A 128 " =    0.987
peak=    3.739 closest distance to " CG AARG A 275 " =    1.141
peak=    3.736 closest distance to " O   HOH Z 116 " =    2.889
peak=    3.733 closest distance to " CB  SER A 212 " =    1.201
peak=    3.732 closest distance to " OG  SER A  62 " =    2.925
peak=    3.730 closest distance to " CB  ALA A 160 " =    1.454
peak=    3.728 closest distance to " O   HOH Z 402 " =    1.478
peak=    3.728 closest distance to " O   HOH Z 193 " =    1.607
peak=    3.727 closest distance to " O   HOH Z 437 " =    1.674
peak=    3.723 closest distance to " CB  THR A  31 " =    1.653
peak=    3.721 closest distance to " O   HOH Z   2 " =    1.636
peak=    3.715 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.705 closest distance to " O   HOH Z   3 " =    2.075
peak=    3.698 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.696 closest distance to " CG  LYS A  76 " =    1.578
peak=    3.695 closest distance to " OD1 ASN A  69 " =    2.539
peak=    3.695 closest distance to " CB  TRP A 179 " =    1.402
peak=    3.684 closest distance to " O   HOH Z 188 " =    2.808
peak=    3.676 closest distance to " CB  ALA A 114 " =    1.382
peak=    3.676 closest distance to " O   HOH Z 145 " =    2.162
peak=    3.664 closest distance to " O   HOH Z  44 " =    1.711
peak=    3.658 closest distance to " O   HOH Z 394 " =    1.773
peak=    3.657 closest distance to " CB  GLU A 152 " =    1.253
peak=    3.654 closest distance to " CB  TRP A 266 " =    1.103
peak=    3.645 closest distance to " CB  SER A   3 " =    1.381
peak=    3.643 closest distance to " O   HOH Z 394 " =    3.832
peak=    3.643 closest distance to " CA  ASN A 127 " =    1.095
peak=    3.635 closest distance to " O   HOH Z 180 " =    2.196
peak=    3.626 closest distance to " ND2 ASN A 249 " =    0.857
peak=    3.626 closest distance to " CA  SER A  87 " =    1.002
peak=    3.626 closest distance to " CB  GLU A  46 " =    1.077
peak=    3.621 closest distance to " O   HOH Z  68 " =    2.038
peak=    3.619 closest distance to " OG BSER A 164 " =    2.150
peak=    3.613 closest distance to " CZ  PHE A 218 " =    1.062
peak=    3.594 closest distance to " O   HOH Z  10 " =    1.672
peak=    3.590 closest distance to " O   HOH Z 419 " =    1.569
peak=    3.586 closest distance to " CE3 TRP A 150 " =    1.076
peak=    3.582 closest distance to " CG  PRO A 198 " =    1.255
peak=    3.577 closest distance to " CB  SER A 216 " =    0.924
peak=    3.568 closest distance to " ND1 HIS A  86 " =    1.726
peak=    3.566 closest distance to " O   HOH Z 371 " =    1.806
peak=    3.565 closest distance to " CB  PHE A 130 " =    0.945
peak=    3.557 closest distance to " CB  LEU A 300 " =    0.925
peak=    3.555 closest distance to " O   HOH Z  88 " =    3.716
peak=    3.554 closest distance to " O   HOH Z  71 " =    1.261
peak=    3.550 closest distance to " CG1 ILE A 120 " =    1.410
peak=    3.547 closest distance to " O   HOH Z 158 " =    3.134
peak=    3.545 closest distance to " OE2 GLU A  53 " =    1.956
peak=    3.541 closest distance to " O   HOH Z 378 " =    0.932
peak=    3.536 closest distance to " CG  LEU A 167 " =    1.273
peak=    3.535 closest distance to " O   HOH Z 225 " =    1.491
peak=    3.535 closest distance to " O   HOH Z 132 " =    2.340
peak=    3.528 closest distance to " O   HOH Z  28 " =    1.809
peak=    3.524 closest distance to " O   HOH Z 250 " =    1.292
peak=    3.523 closest distance to " O   HOH Z 368 " =    1.776
peak=    3.522 closest distance to " O   HOH Z 234 " =    3.649
peak=    3.517 closest distance to " CA  TYR A 116 " =    1.343
peak=    3.516 closest distance to " O   HOH Z  97 " =    2.055
peak=    3.510 closest distance to " O   HOH Z 305 " =    3.549
peak=    3.508 closest distance to " O   HOH Z 345 " =    1.973
peak=    3.508 closest distance to " O   HOH Z  26 " =    1.290
peak=    3.507 closest distance to " O   HOH Z 193 " =    1.664
peak=    3.495 closest distance to " NZ  LYS A 119 " =    1.355
peak=    3.492 closest distance to " O   HOH Z 126 " =    1.461
peak=    3.481 closest distance to " CG2 ILE A  20 " =    1.508
peak=    3.477 closest distance to " N   TYR A 116 " =    1.387
peak=    3.475 closest distance to " CG2 THR A 221 " =    1.139
peak=    3.466 closest distance to " O   PRO A 198 " =    1.315
peak=    3.463 closest distance to " NZ  LYS A  48 " =    1.156
peak=    3.453 closest distance to " CD  ARG A 259 " =    1.783
peak=    3.451 closest distance to " O   HOH Z 411 " =    3.751
peak=    3.444 closest distance to " NH1BARG A 145 " =    1.380
peak=    3.443 closest distance to " O   HOH Z 272 " =    2.112
peak=    3.441 closest distance to " CG2 VAL A 197 " =    1.041
peak=    3.440 closest distance to " O   HOH Z 128 " =    2.113
peak=    3.438 closest distance to " CD  PRO A 243 " =    1.699
peak=    3.433 closest distance to " O   HOH Z 425 " =    1.919
peak=    3.429 closest distance to " O   ASN A  74 " =    1.413
peak=    3.426 closest distance to " O   HOH Z 344 " =    3.131
peak=    3.425 closest distance to " CB  SER A  62 " =    1.010
peak=    3.416 closest distance to " CB  ASN A 110 " =    0.995
peak=    3.411 closest distance to " CB  ASN A 215 " =    1.059
peak=    3.410 closest distance to " O   HOH Z 368 " =    4.195
peak=    3.408 closest distance to " O   HOH Z 188 " =    1.478
peak=    3.406 closest distance to " CB  ALA A   1 " =    4.541
peak=    3.403 closest distance to " O   HOH Z 188 " =    2.006
peak=    3.402 closest distance to " CA  ALA A 233 " =    0.981
peak=    3.401 closest distance to " O   HOH Z 283 " =    2.186
peak=    3.400 closest distance to " CD  ARG A  79 " =    2.178
peak=    3.389 closest distance to " O   HOH Z 119 " =    4.223
peak=    3.388 closest distance to " CG  PRO A 243 " =    1.076
peak=    3.385 closest distance to " CB  ASP A 124 " =    0.816
peak=    3.385 closest distance to " O   HOH Z 194 " =    2.297
peak=    3.383 closest distance to " O   HOH Z 153 " =    3.609
peak=    3.378 closest distance to " OG BSER A  99 " =    2.433
peak=    3.376 closest distance to " CA  PHE A 283 " =    1.280
peak=    3.371 closest distance to " O   HOH Z 216 " =    3.889
peak=    3.371 closest distance to " O   HOH Z 130 " =    2.465
peak=    3.371 closest distance to " CB  SER A 276 " =    1.206
peak=    3.368 closest distance to " O   HOH Z 117 " =    1.285
peak=    3.364 closest distance to " O   THR A 220 " =    1.307
peak=    3.362 closest distance to " O   HOH Z 421 " =    2.100
peak=    3.357 closest distance to " O   HOH Z  48 " =    1.606
peak=    3.351 closest distance to " CA  ALA A 158 " =    1.198
peak=    3.349 closest distance to " CG2 ILE A 120 " =    1.380
peak=    3.346 closest distance to " O   HOH Z 172 " =    2.312
peak=    3.343 closest distance to " CB  SER A  26 " =    1.721
peak=    3.341 closest distance to " NE2 HIS A 207 " =    1.140
peak=    3.338 closest distance to " O   HOH Z 323 " =    1.657
peak=    3.336 closest distance to " O   HOH Z 175 " =    2.153
peak=    3.335 closest distance to " O   HOH Z 128 " =    1.970
peak=    3.335 closest distance to " CA  ALA A 291 " =    0.843
peak=    3.325 closest distance to " CB  THR A 157 " =    1.094
peak=    3.324 closest distance to " O   HOH Z 393 " =    1.326
peak=    3.324 closest distance to " NZ  LYS A 166 " =    1.035
peak=    3.314 closest distance to " O   HOH Z 352 " =    1.363
peak=    3.313 closest distance to " N   CYS A 260 " =    0.887
peak=    3.311 closest distance to " O   HOH Z 245 " =    1.306
peak=    3.309 closest distance to " O   HOH Z 392 " =    1.157
peak=    3.308 closest distance to " O   HOH Z 261 " =    1.670
peak=    3.307 closest distance to " N   SER A  97 " =    0.824
peak=    3.307 closest distance to " O   HOH Z 434 " =    1.342
peak=    3.306 closest distance to " CB  ASN A 187 " =    1.019
peak=    3.305 closest distance to " CD  LYS A 193 " =    1.999
peak=    3.304 closest distance to " CB  ARG A 139 " =    1.357
peak=    3.304 closest distance to " CB  PRO A  90 " =    1.096
peak=    3.303 closest distance to " O  BHOH Z 338 " =    2.388
peak=    3.298 closest distance to " ND2BASN A 224 " =    0.813
peak=    3.294 closest distance to " OG BSER A 134 " =    3.048
peak=    3.293 closest distance to " O   HOH Z  40 " =    2.080
peak=    3.288 closest distance to " CB  ARG A 219 " =    0.936
peak=    3.280 closest distance to " O   HOH Z 128 " =    1.859
peak=    3.278 closest distance to " CA  ILE A 234 " =    1.029
peak=    3.278 closest distance to " O   HOH Z 181 " =    2.154
peak=    3.277 closest distance to " NZ  LYS A 117 " =    1.469
peak=    3.274 closest distance to " O   HOH Z 285 " =    2.501
peak=    3.273 closest distance to " CA  ALA A  51 " =    0.970
peak=    3.267 closest distance to " O   ALA A 165 " =    1.401
peak=    3.267 closest distance to " O   HOH Z 435 " =    1.935
peak=    3.265 closest distance to " O   HOH Z 414 " =    1.273
peak=    3.264 closest distance to " O   HOH Z 119 " =    1.668
peak=    3.263 closest distance to " CA  ASP A 162 " =    1.033
peak=    3.262 closest distance to " CA  ASP A 140 " =    1.666
peak=    3.262 closest distance to " O   HOH Z 244 " =    1.752
peak=    3.261 closest distance to " O   HOH Z 148 " =    3.379
peak=    3.260 closest distance to " O   HOH Z 193 " =    1.926
peak=    3.255 closest distance to " CA  ALA A 129 " =    1.235
peak=    3.251 closest distance to " CB  TYR A  30 " =    1.414
peak=    3.243 closest distance to " N   ASN A  39 " =    1.244
peak=    3.241 closest distance to " O   HOH Z  44 " =    2.866
peak=    3.241 closest distance to " O   HOH Z 148 " =    2.114
peak=    3.239 closest distance to " CA  ASN A 217 " =    1.247
peak=    3.238 closest distance to " O   HOH Z 386 " =    2.914
peak=    3.236 closest distance to " CD2 LEU A 297 " =    1.049
peak=    3.231 closest distance to " CB  ASP A 140 " =    0.967
peak=    3.230 closest distance to " CB  TRP A 150 " =    1.140
peak=    3.228 closest distance to " CD1 ILE A 199 " =    1.225
peak=    3.226 closest distance to " OE1 GLN A  77 " =    1.244
peak=    3.225 closest distance to " NH2BARG A 145 " =    1.870
peak=    3.217 closest distance to " O   HOH Z 156 " =    2.615
peak=    3.216 closest distance to " O   HOH Z 213 " =    2.286
peak=    3.216 closest distance to " O   GLY A 302 " =    2.192
peak=    3.200 closest distance to " O   HOH Z 124 " =    1.282
peak=    3.196 closest distance to " CD2 LEU A   5 " =    1.363
peak=    3.196 closest distance to " O   HOH Z 365 " =    1.439
peak=    3.194 closest distance to " CB  TYR A 169 " =    0.909
peak=    3.193 closest distance to " O   HOH Z 285 " =    2.092
peak=    3.191 closest distance to " O   HOH Z  21 " =    1.725
peak=    3.189 closest distance to " CB  LEU A  83 " =    0.836
peak=    3.187 closest distance to " O   HOH Z 213 " =    2.152
peak=    3.181 closest distance to " O   TYR A 116 " =    1.306
peak=    3.180 closest distance to " N   TYR A  15 " =    1.112
peak=    3.177 closest distance to " CB  LEU A 228 " =    1.081
peak=    3.177 closest distance to " CA  ARG A 102 " =    1.181
peak=    3.172 closest distance to " CA  THR A 264 " =    0.874
peak=    3.171 closest distance to " CB  ALA A 114 " =    0.833
peak=    3.168 closest distance to " O   HOH Z 248 " =    1.542
peak=    3.168 closest distance to " CA  ARG A 156 " =    1.044
peak=    3.156 closest distance to " CG  LYS A 119 " =    1.075
peak=    3.148 closest distance to " O   HOH Z 143 " =    1.335
peak=    3.143 closest distance to " O   HOH Z 222 " =    2.324
peak=    3.139 closest distance to " N   GLU A   2 " =    1.489
peak=    3.134 closest distance to " O   HOH Z 357 " =    2.376
peak=    3.128 closest distance to " O   HOH Z 294 " =    1.428
peak=    3.127 closest distance to " O   HOH Z 375 " =    1.024
peak=    3.123 closest distance to " CB  ARG A 138 " =    0.906
peak=    3.119 closest distance to " O   HOH Z 153 " =    4.188
peak=    3.117 closest distance to " O  BHOH Z  74 " =    1.289
peak=    3.115 closest distance to " O   HOH Z 388 " =    2.177
peak=    3.114 closest distance to " O   HOH Z 171 " =    2.911
peak=    3.114 closest distance to " O   HOH Z 128 " =    2.925
peak=    3.097 closest distance to " O   HOH Z 198 " =    1.546
peak=    3.088 closest distance to " CB  PHE A 204 " =    0.776
peak=    3.074 closest distance to " CB  ALA A 248 " =    0.978
peak=    3.069 closest distance to " O   HOH Z 109 " =    2.309
peak=    3.066 closest distance to " O   HOH Z  51 " =    1.463
peak=    3.062 closest distance to " NH1 ARG A 138 " =    1.124
peak=    3.061 closest distance to " CA  ALA A 299 " =    0.858
peak=    3.060 closest distance to " O   HOH Z 153 " =    1.537
peak=    3.057 closest distance to " O   HOH Z 158 " =    3.279
peak=    3.055 closest distance to " O   HOH Z  42 " =    1.471
peak=    3.047 closest distance to " O   HOH Z 371 " =    3.111
peak=    3.003 closest distance to " O   HOH Z 375 " =    2.488
peak=    2.977 closest distance to " O   HOH Z 188 " =    2.443

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.693 - 5.614
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 200
   mapped sites are within: 0.792 - 5.614

peak=   -4.572 closest distance to " CD  ARG A  14 " =    3.216
peak=   -4.374 closest distance to " O   HOH Z 377 " =    2.065
peak=   -4.317 closest distance to " O   HOH Z  69 " =    1.627
peak=   -4.294 closest distance to " CB  ALA A  43 " =    2.420
peak=   -4.290 closest distance to " OG BSER A 134 " =    1.374
peak=   -4.267 closest distance to " O   PRO A 198 " =    1.230
peak=   -4.260 closest distance to " CB  PRO A 243 " =    2.640
peak=   -4.240 closest distance to " O   HOH Z 131 " =    3.953
peak=   -4.153 closest distance to " C   HIS A 108 " =    1.235
peak=   -4.115 closest distance to " CD  ARG A 156 " =    2.045
peak=   -4.079 closest distance to " O   VAL A  67 " =    2.609
peak=   -3.994 closest distance to " O   SER A  22 " =    2.630
peak=   -3.980 closest distance to " O   HOH Z 290 " =    1.017
peak=   -3.978 closest distance to " O   HOH Z 211 " =    1.211
peak=   -3.973 closest distance to " O   HOH Z 351 " =    1.595
peak=   -3.933 closest distance to " CB  ALA A 291 " =    2.237
peak=   -3.911 closest distance to " O   HOH Z  60 " =    1.753
peak=   -3.910 closest distance to " O   PRO A 198 " =    1.401
peak=   -3.907 closest distance to " CG2 ILE A  49 " =    2.837
peak=   -3.905 closest distance to " CE BMET A  47 " =    1.193
peak=   -3.897 closest distance to " CD1 LEU A 101 " =    2.200
peak=   -3.895 closest distance to " CA  GLY A  98 " =    1.769
peak=   -3.889 closest distance to " O   GLU A 152 " =    1.376
peak=   -3.859 closest distance to " O   ALA A  10 " =    1.617
peak=   -3.848 closest distance to " O   HOH Z 185 " =    2.165
peak=   -3.808 closest distance to " CD2 TYR A 293 " =    1.853
peak=   -3.807 closest distance to " O   HOH Z 298 " =    2.587
peak=   -3.781 closest distance to " CE2 PHE A 218 " =    2.455
peak=   -3.778 closest distance to " OD1 ASP A 191 " =    1.874
peak=   -3.773 closest distance to " O   PRO A 243 " =    2.474
peak=   -3.768 closest distance to " ND2 ASN A 249 " =    2.142
peak=   -3.765 closest distance to " N   THR A 157 " =    1.542
peak=   -3.759 closest distance to " CG  GLN A  58 " =    1.041
peak=   -3.746 closest distance to " O   HOH Z 266 " =    5.082
peak=   -3.745 closest distance to " CA  GLY A 241 " =    2.253
peak=   -3.735 closest distance to " O   HOH Z 385 " =    1.893
peak=   -3.718 closest distance to " CD1 LEU A 255 " =    2.809
peak=   -3.697 closest distance to " O   HOH Z 231 " =    2.145
peak=   -3.687 closest distance to " O   HOH Z 286 " =    1.553
peak=   -3.677 closest distance to " CG  GLN A 223 " =    2.208
peak=   -3.658 closest distance to " O   HOH Z 429 " =    1.907
peak=   -3.613 closest distance to " NH2 ARG A  79 " =    2.240
peak=   -3.604 closest distance to " O   SER A 135 " =    1.454
peak=   -3.601 closest distance to " CB  ALA A 158 " =    1.688
peak=   -3.596 closest distance to " NE2 GLN A 278 " =    1.481
peak=   -3.595 closest distance to " O   HOH Z  15 " =    1.537
peak=   -3.592 closest distance to " O   HOH Z 372 " =    2.416
peak=   -3.590 closest distance to " CG2 ILE A  20 " =    2.868
peak=   -3.589 closest distance to " CB  ASP A  27 " =    2.350
peak=   -3.586 closest distance to " CZ2 TRP A 274 " =    0.970
peak=   -3.578 closest distance to " O   HOH Z  24 " =    1.081
peak=   -3.575 closest distance to " OD1 ASP A 171 " =    1.643
peak=   -3.564 closest distance to " O   PHE A 218 " =    1.441
peak=   -3.561 closest distance to " O   HOH Z 359 " =    3.182
peak=   -3.557 closest distance to " CB  ASP A 132 " =    2.375
peak=   -3.554 closest distance to " CG2 THR A  18 " =    2.799
peak=   -3.550 closest distance to " CG1 VAL A 112 " =    2.613
peak=   -3.550 closest distance to " CB  ALA A 114 " =    2.513
peak=   -3.545 closest distance to " O   HOH Z 140 " =    1.207
peak=   -3.544 closest distance to " N   GLN A  58 " =    1.741
peak=   -3.523 closest distance to " OXT GLY A 302 " =    3.161
peak=   -3.523 closest distance to " O   HOH Z 105 " =    1.008
peak=   -3.521 closest distance to " O   HOH Z 313 " =    1.711
peak=   -3.516 closest distance to " OD2 ASP A 191 " =    1.325
peak=   -3.514 closest distance to " CB  ASN A  39 " =    2.381
peak=   -3.514 closest distance to " O   HOH Z 198 " =    1.335
peak=   -3.510 closest distance to " O   HOH Z 412 " =    3.866
peak=   -3.509 closest distance to " O   GLN A 240 " =    2.064
peak=   -3.506 closest distance to " O   HOH Z 348 " =    2.075
peak=   -3.505 closest distance to " CG2 THR A 178 " =    2.118
peak=   -3.504 closest distance to " O   HOH Z 389 " =    1.387
peak=   -3.500 closest distance to " CB  ALA A 291 " =    2.032
peak=   -3.496 closest distance to " C   ALA A 114 " =    2.221
peak=   -3.493 closest distance to " ND2 ASN A 285 " =    2.113
peak=   -3.489 closest distance to " CE  MET A 105 " =    2.492
peak=   -3.481 closest distance to " O   HOH Z  65 " =    1.263
peak=   -3.479 closest distance to " CA  GLY A 133 " =    1.977
peak=   -3.476 closest distance to " O   PRO A 163 " =    1.956
peak=   -3.475 closest distance to " CZ3 TRP A 179 " =    1.258
peak=   -3.475 closest distance to " CB  PHE A 192 " =    1.935
peak=   -3.474 closest distance to " O   HOH Z 100 " =    1.085
peak=   -3.469 closest distance to " CD  GLU A 277 " =    1.240
peak=   -3.468 closest distance to " O   HOH Z  49 " =    1.156
peak=   -3.467 closest distance to " CD2 LEU A 237 " =    2.781
peak=   -3.465 closest distance to " OE1 GLN A 183 " =    1.567
peak=   -3.463 closest distance to " O   HOH Z 111 " =    2.044
peak=   -3.461 closest distance to " O   HOH Z  39 " =    1.122
peak=   -3.454 closest distance to " CA  ASP A 298 " =    1.131
peak=   -3.452 closest distance to " O   HOH Z 231 " =    1.113
peak=   -3.447 closest distance to " O   HOH Z 407 " =    2.965
peak=   -3.432 closest distance to " OG  SER A  97 " =    2.143
peak=   -3.431 closest distance to " O   ALA A 161 " =    1.658
peak=   -3.411 closest distance to " CB  GLN A  11 " =    1.781
peak=   -3.406 closest distance to " O   HOH Z 219 " =    4.640
peak=   -3.404 closest distance to " O   ALA A 180 " =    1.105
peak=   -3.403 closest distance to " CB  ASN A  45 " =    2.028
peak=   -3.403 closest distance to " CB  TRP A  85 " =    2.418
peak=   -3.392 closest distance to " CG2 ILE A 263 " =    2.244
peak=   -3.392 closest distance to " O   HOH Z 276 " =    1.448
peak=   -3.391 closest distance to " N   PRO A 163 " =    1.538
peak=   -3.388 closest distance to " O   HOH Z 174 " =    2.604
peak=   -3.386 closest distance to " O   SER A 210 " =    1.893
peak=   -3.376 closest distance to " N   ALA A  43 " =    2.595
peak=   -3.370 closest distance to " CG1 VAL A 230 " =    2.042
peak=   -3.358 closest distance to " OG BSER A 134 " =    1.749
peak=   -3.358 closest distance to " O   ALA A   1 " =    1.568
peak=   -3.357 closest distance to " CB  ALA A 291 " =    2.511
peak=   -3.357 closest distance to " ND2 ASN A  45 " =    2.239
peak=   -3.352 closest distance to " CD2 PHE A  61 " =    1.965
peak=   -3.350 closest distance to " O   HOH Z   9 " =    2.612
peak=   -3.349 closest distance to " CG  LEU A  83 " =    2.170
peak=   -3.345 closest distance to " O   HOH Z  11 " =    1.674
peak=   -3.344 closest distance to " SG BCYS A 201 " =    1.909
peak=   -3.340 closest distance to " OE2 GLU A 152 " =    1.211
peak=   -3.337 closest distance to " CG1 VAL A 112 " =    3.074
peak=   -3.335 closest distance to " O   ILE A  49 " =    1.600
peak=   -3.334 closest distance to " ND2 ASN A 187 " =    1.413
peak=   -3.331 closest distance to " CE3 TRP A 274 " =    2.299
peak=   -3.327 closest distance to " CA  GLY A  57 " =    2.134
peak=   -3.325 closest distance to " O   HOH Z 389 " =    2.208
peak=   -3.314 closest distance to " O   HOH Z 357 " =    2.156
peak=   -3.310 closest distance to " CG2 ILE A 151 " =    2.519
peak=   -3.300 closest distance to " NZ  LYS A 166 " =    1.303
peak=   -3.298 closest distance to " CB  ALA A  10 " =    2.319
peak=   -3.294 closest distance to " O   HOH Z 421 " =    2.766
peak=   -3.291 closest distance to " CE2 TYR A  30 " =    2.584
peak=   -3.291 closest distance to " O   HOH Z  90 " =    2.476
peak=   -3.289 closest distance to " CG  PHE A 283 " =    2.594
peak=   -3.288 closest distance to " O   HOH Z  26 " =    0.989
peak=   -3.283 closest distance to " O   HOH Z 216 " =    1.425
peak=   -3.279 closest distance to " N   LYS A 166 " =    1.774
peak=   -3.275 closest distance to " O   HOH Z 292 " =    1.487
peak=   -3.274 closest distance to " CG  ASN A  39 " =    1.643
peak=   -3.274 closest distance to " CG  GLN A  88 " =    0.851
peak=   -3.271 closest distance to " CZ  PHE A  38 " =    2.551
peak=   -3.269 closest distance to " O   HOH Z 275 " =    1.676
peak=   -3.268 closest distance to " O   HOH Z 102 " =    1.566
peak=   -3.267 closest distance to " CB  ASP A 171 " =    2.229
peak=   -3.266 closest distance to " O   HOH Z   5 " =    1.018
peak=   -3.264 closest distance to " O   HOH Z 318 " =    1.770
peak=   -3.264 closest distance to " O   HOH Z 152 " =    4.731
peak=   -3.262 closest distance to " CG2 THR A  42 " =    1.887
peak=   -3.253 closest distance to " O   HOH Z 191 " =    5.614
peak=   -3.251 closest distance to " O   HOH Z 134 " =    3.838
peak=   -3.247 closest distance to " OG1 THR A  82 " =    2.012
peak=   -3.244 closest distance to " O   HOH Z 166 " =    1.804
peak=   -3.243 closest distance to " OE1 GLN A  88 " =    1.112
peak=   -3.242 closest distance to " O   HOH Z 364 " =    1.577
peak=   -3.236 closest distance to " CE1 TYR A 247 " =    2.727
peak=   -3.234 closest distance to " CD2 PHE A 225 " =    1.141
peak=   -3.230 closest distance to " O   HOH Z 265 " =    2.758
peak=   -3.230 closest distance to " O   HOH Z  52 " =    1.310
peak=   -3.228 closest distance to " O   LYS A  76 " =    1.812
peak=   -3.223 closest distance to " CZ  TYR A 169 " =    1.877
peak=   -3.220 closest distance to " O   HOH Z 152 " =    0.839
peak=   -3.215 closest distance to " N   PHE A  59 " =    2.000
peak=   -3.210 closest distance to " O   HOH Z 278 " =    1.183
peak=   -3.208 closest distance to " ND2BASN A 224 " =    1.751
peak=   -3.206 closest distance to " O   HOH Z 193 " =    1.214
peak=   -3.204 closest distance to " O   HOH Z 253 " =    3.823
peak=   -3.204 closest distance to " O   HOH Z  68 " =    1.404
peak=   -3.202 closest distance to " OH  TYR A 172 " =    1.772
peak=   -3.202 closest distance to " O   VAL A 189 " =    2.570
peak=   -3.190 closest distance to " O   HOH Z 383 " =    1.132
peak=   -3.180 closest distance to " CB  SER A 245 " =    2.174
peak=   -3.179 closest distance to " N   VAL A 232 " =    2.024
peak=   -3.178 closest distance to " CD  GLN A  77 " =    1.298
peak=   -3.177 closest distance to " O   HOH Z 414 " =    1.320
peak=   -3.176 closest distance to " O   HOH Z 428 " =    2.544
peak=   -3.175 closest distance to " O   ARG A 145 " =    1.176
peak=   -3.175 closest distance to " O   HOH Z   1 " =    1.338
peak=   -3.162 closest distance to " N   SER A 141 " =    1.805
peak=   -3.161 closest distance to " O   HOH Z 281 " =    2.676
peak=   -3.161 closest distance to " CE  LYS A  76 " =    2.785
peak=   -3.159 closest distance to " OG  SER A 245 " =    1.455
peak=   -3.158 closest distance to " CB  GLN A  55 " =    1.293
peak=   -3.158 closest distance to " OG  SER A  87 " =    1.397
peak=   -3.150 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.146 closest distance to " CD  LYS A 166 " =    2.507
peak=   -3.146 closest distance to " CB  PRO A 213 " =    2.216
peak=   -3.145 closest distance to " O   HOH Z 427 " =    1.543
peak=   -3.140 closest distance to " O   HOH Z 137 " =    1.558
peak=   -3.138 closest distance to " OG BSER A 210 " =    2.362
peak=   -3.134 closest distance to " O   HOH Z 438 " =    1.210
peak=   -3.133 closest distance to " O   HOH Z 384 " =    3.043
peak=   -3.133 closest distance to " O   HOH Z  73 " =    2.402
peak=   -3.129 closest distance to " C   LEU A 222 " =    0.822
peak=   -3.125 closest distance to " NE2 GLN A 194 " =    1.826
peak=   -3.099 closest distance to " CB  SER A 210 " =    1.164
peak=   -3.096 closest distance to " O   HOH Z  28 " =    1.815
peak=   -3.093 closest distance to " OE1 GLU A 277 " =    2.279
peak=   -3.091 closest distance to " O   HOH Z  37 " =    1.659
peak=   -3.083 closest distance to " CB  PHE A  59 " =    1.953
peak=   -3.077 closest distance to " O   HOH Z  51 " =    0.792
peak=   -3.066 closest distance to " NH2 ARG A 219 " =    1.814
peak=   -3.056 closest distance to " O   HOH Z 346 " =    1.722
peak=   -3.046 closest distance to " NE2 GLN A 278 " =    1.490
peak=   -3.010 closest distance to " OD2 ASP A 132 " =    2.227

================= 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    :  0.4602 0.4624   6.271489e+00   6.256223e+00
   1_bss:  0.4497 0.4521   6.263859e+00   6.244977e+00
   1_xyz:  0.3489 0.3862   6.090561e+00   6.149324e+00
   1_adp:  0.3162 0.4014   6.049629e+00   6.170986e+00
   1_occ:  0.3160 0.4023   6.050015e+00   6.171918e+00
   2_bss:  0.3152 0.4002   6.050453e+00   6.172558e+00
   2_xyz:  0.2413 0.3114   5.819225e+00   5.995006e+00
   2_adp:  0.2205 0.2846   5.743793e+00   5.924509e+00
   2_occ:  0.2204 0.2839   5.742736e+00   5.922833e+00
   3_bss:  0.2202 0.2831   5.740548e+00   5.920962e+00
   3_xyz:  0.1632 0.2168   5.469698e+00   5.683658e+00
   3_adp:  0.1458 0.1996   5.376897e+00   5.608774e+00
   3_occ:  0.1457 0.1995   5.376122e+00   5.607803e+00
   4_bss:  0.1455 0.1989   5.371968e+00   5.604392e+00
   4_xyz:  0.1285 0.1782   5.264832e+00   5.500435e+00
   4_adp:  0.1245 0.1729   5.234442e+00   5.469677e+00
   4_occ:  0.1244 0.1728   5.233972e+00   5.469072e+00
   5_bss:  0.1244 0.1728   5.233973e+00   5.469068e+00
   5_xyz:  0.1154 0.1647   5.175539e+00   5.424804e+00
   5_adp:  0.1141 0.1627   5.166863e+00   5.415722e+00
   5_occ:  0.1140 0.1627   5.166378e+00   5.415206e+00
   5_bss:  0.1142 0.1621   5.163657e+00   5.410781e+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:  0.328  26.679  -2.707   1.881   2.949   0.000   0.000   0.000
   1_xyz:  0.328  26.679  -2.707   1.881   2.949   0.000   0.000   0.000
   1_adp:  0.328  26.679  -2.707   1.881   2.949   0.000   0.000   0.000
   1_occ:  0.328  26.679  -2.707   1.881   2.949   0.000   0.000   0.000
   2_bss:  0.344  60.562  -1.886   0.179   1.380   0.000   0.000   0.000
   2_xyz:  0.344  60.562  -1.886   0.179   1.380   0.000   0.000   0.000
   2_adp:  0.344  60.562  -1.886   0.179   1.380   0.000   0.000   0.000
   2_occ:  0.344  60.562  -1.886   0.179   1.380   0.000   0.000   0.000
   3_bss:  0.333  60.562  -2.089  -1.060   0.479  -0.000   0.000   0.000
   3_xyz:  0.333  60.562  -2.089  -1.060   0.479  -0.000   0.000   0.000
   3_adp:  0.333  60.562  -2.089  -1.060   0.479  -0.000   0.000   0.000
   3_occ:  0.333  60.562  -2.089  -1.060   0.479  -0.000   0.000   0.000
   4_bss:  0.324  60.562  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   4_xyz:  0.324  60.562  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   4_adp:  0.324  60.562  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   4_occ:  0.324  60.562  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   5_bss:  0.320  57.440  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   5_xyz:  0.320  57.440  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   5_adp:  0.320  57.440  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   5_occ:  0.320  57.440  -2.454  -1.947  -0.079  -0.000  -0.000  -0.000
   5_bss:  0.319  55.347  -2.395  -2.115  -0.073  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.696 0.4620  0.6284    66145.308
   1_bss:  53.461 0.4763  0.6662    62984.977
   1_xyz:  42.654 0.6107  0.8300    43213.741
   1_adp:  44.572 0.5863  0.8078    46717.377
   1_occ:  44.706 0.5847  0.8050    46914.706
   2_bss:  44.380 0.5887  0.7898    46484.211
   2_xyz:  32.752 0.7254  0.9436    26064.587
   2_adp:  28.956 0.7691  0.9683    21675.164
   2_occ:  28.905 0.7696  0.9685    21571.059
   3_bss:  28.753 0.7711  0.9433    21369.170
   3_xyz:  21.235 0.8489  0.9956    12125.468
   3_adp:  19.253 0.8685  0.9930    10384.605
   3_occ:  19.227 0.8687  0.9929    10359.117
   4_bss:  19.103 0.8696  0.9722    10229.952
   4_xyz:  16.526 0.8933  0.9850     8099.882
   4_adp:  15.738 0.9006  0.9817     7678.949
   4_occ:  15.730 0.9007  0.9816     7660.781
   5_bss:  15.733 0.9006  0.9815     7661.051
   5_xyz:  14.790 0.9083  0.9858     6939.951
   5_adp:  14.541 0.9107  0.9814     6834.454
   5_occ:  14.533 0.9107  0.9814     6824.448
   5_bss:  14.470 0.9111  0.9803     6737.850
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8599e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8599e-01
   1_xyz:   1.548  0.011  0.102 15.837  0.007  4.102   1.2645e-01
   1_adp:   1.548  0.011  0.102 15.837  0.007  4.102   1.2645e-01
   1_occ:   1.548  0.011  0.102 15.837  0.007  4.102   1.2645e-01
   2_bss:   1.548  0.011  0.102 15.837  0.007  4.102   1.2645e-01
   2_xyz:   1.312  0.010  0.095 15.549  0.004  4.112   9.3615e-02
   2_adp:   1.312  0.010  0.095 15.549  0.004  4.112   9.3615e-02
   2_occ:   1.312  0.010  0.095 15.549  0.004  4.112   9.3615e-02
   3_bss:   1.312  0.010  0.095 15.549  0.004  4.112   9.3615e-02
   3_xyz:   1.117  0.009  0.079 15.133  0.004  4.112   7.2718e-02
   3_adp:   1.117  0.009  0.079 15.133  0.004  4.112   7.2718e-02
   3_occ:   1.117  0.009  0.079 15.133  0.004  4.112   7.2718e-02
   4_bss:   1.117  0.009  0.079 15.133  0.004  4.112   7.2718e-02
   4_xyz:   0.968  0.006  0.072 14.740  0.004  4.119   5.7331e-02
   4_adp:   0.968  0.006  0.072 14.740  0.004  4.119   5.7331e-02
   4_occ:   0.968  0.006  0.072 14.740  0.004  4.119   5.7331e-02
   5_bss:   0.968  0.006  0.072 14.740  0.004  4.119   5.7331e-02
   5_xyz:   1.065  0.008  0.078 14.857  0.004  4.109   6.7404e-02
   5_adp:   1.065  0.008  0.078 14.857  0.004  4.109   6.7404e-02
   5_occ:   1.065  0.008  0.078 14.857  0.004  4.109   6.7404e-02
   5_bss:   1.065  0.008  0.078 14.857  0.004  4.109   6.7404e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.233   2.4075e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.233   2.4075e-01
   1_xyz:   9.663  0.071  0.329 83.543  0.048  1.958   1.0045e-01
   1_adp:   9.663  0.071  0.329 83.543  0.048  1.958   1.0045e-01
   1_occ:   9.663  0.071  0.329 83.543  0.048  1.958   1.0045e-01
   2_bss:   9.663  0.071  0.329 83.543  0.048  1.958   1.0045e-01
   2_xyz:   8.241  0.094  0.342 86.846  0.022  2.115   9.5879e-02
   2_adp:   8.241  0.094  0.342 86.846  0.022  2.115   9.5879e-02
   2_occ:   8.241  0.094  0.342 86.846  0.022  2.115   9.5879e-02
   3_bss:   8.241  0.094  0.342 86.846  0.022  2.115   9.5879e-02
   3_xyz:   6.080  0.062  0.253 83.756  0.033  2.314   6.1821e-02
   3_adp:   6.080  0.062  0.253 83.756  0.033  2.314   6.1821e-02
   3_occ:   6.080  0.062  0.253 83.756  0.033  2.314   6.1821e-02
   4_bss:   6.080  0.062  0.253 83.756  0.033  2.314   6.1821e-02
   4_xyz:   6.729  0.048  0.229 81.921  0.035  2.340   7.5135e-02
   4_adp:   6.729  0.048  0.229 81.921  0.035  2.340   7.5135e-02
   4_occ:   6.729  0.048  0.229 81.921  0.035  2.340   7.5135e-02
   5_bss:   6.729  0.048  0.229 81.921  0.035  2.340   7.5135e-02
   5_xyz:   6.724  0.047  0.275 83.161  0.038  2.266   5.4585e-02
   5_adp:   6.724  0.047  0.275 83.161  0.038  2.266   5.4585e-02
   5_occ:   6.724  0.047  0.275 83.161  0.038  2.266   5.4585e-02
   5_bss:   6.724  0.047  0.275 83.161  0.038  2.266   5.4585e-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: 107.06   0.00  18.65  80.86   0.00  15.28 107.06   0.00  37.00
   1_occ: 107.06   0.00  18.65  80.86   0.00  15.28 107.06   0.00  37.00
   2_bss: 107.06   0.00  18.65  80.86   0.00  15.28 107.06   0.00  37.00
   2_xyz: 107.06   0.00  18.65  80.86   0.00  15.28 107.06   0.00  37.00
   2_adp: 105.08   0.00  18.07  76.40   0.00  14.08 105.08   2.81  39.81
   2_occ: 105.08   0.00  18.07  76.40   0.00  14.08 105.08   2.81  39.81
   3_bss: 105.08   0.00  18.07  76.40   0.00  14.08 105.08   2.81  39.81
   3_xyz: 105.08   0.00  18.07  76.40   0.00  14.08 105.08   2.81  39.81
   3_adp: 104.40   0.00  17.98  83.61   0.00  13.09 104.40   5.83  44.60
   3_occ: 104.40   0.00  17.98  83.61   0.00  13.09 104.40   5.83  44.60
   4_bss: 104.40   0.00  17.98  83.61   0.00  13.09 104.40   5.83  44.60
   4_xyz: 104.40   0.00  17.98  83.61   0.00  13.09 104.40   5.83  44.60
   4_adp: 101.83   0.24  17.56  90.75   0.24  12.77 101.83   4.36  43.61
   4_occ: 101.83   0.24  17.56  90.75   0.24  12.77 101.83   4.36  43.61
   5_bss: 101.83   0.24  17.56  90.75   0.24  12.77 101.83   4.36  43.61
   5_xyz: 101.83   0.24  17.56  90.75   0.24  12.77 101.83   4.36  43.61
   5_adp:  98.55   0.38  17.11  93.67   0.38  12.55  98.55   5.58  41.91
   5_occ:  98.55   0.38  17.11  93.67   0.38  12.55  98.55   5.58  41.91
   5_bss:  98.54   0.36  17.09  93.65   0.36  12.54  98.54   5.57  41.90
------------------------------------------------------------------------
 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:    2.818    0.019    0.352
   1_adp:    2.818    0.019    0.352
   1_occ:    2.818    0.019    0.352
   2_bss:    2.818    0.019    0.352
   2_xyz:    2.297    0.017    0.572
   2_adp:    2.297    0.017    0.572
   2_occ:    2.297    0.017    0.572
   3_bss:    2.297    0.017    0.572
   3_xyz:    1.974    0.033    0.709
   3_adp:    1.974    0.033    0.709
   3_occ:    1.974    0.033    0.709
   4_bss:    1.974    0.033    0.709
   4_xyz:    1.709    0.020    0.744
   4_adp:    1.709    0.020    0.744
   4_occ:    1.709    0.020    0.744
   5_bss:    1.709    0.020    0.744
   5_xyz:    1.839    0.031    0.764
   5_adp:    1.839    0.031    0.764
   5_occ:    1.839    0.031    0.764
   5_bss:    1.839    0.031    0.764
------------------------------------------------------------------------

CPU time actual refinement: 324.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_383/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_383/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_383/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_383/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_383/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.68 
  Macro-tasks:
    bulk solvent and scale       = 37.52  
    individual site refinement   = 134.81 
    weights calculation          = 28.98  
    collect and process          = 6.43   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 207.85 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 102.92 
    alpha_beta                      = 8.25   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 111.81 
    fmodel                         = 6.07   
    r_factors                      = 0.14   
    phase_errors                   = 10.54  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 243.44 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.632 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    638 calls, 102.63 s
gradients_fft:          583 calls,  98.68 s

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

# Date 2008-01-16 Time 04:42:03 PST -0800 (1200487323.99 s)
Start R-work = 0.4602, R-free = 0.4624 (no bulk solvent and anisotropic scale)
Final R-work = 0.1364, R-free = 0.1807 (no bulk solvent and anisotropic scale)

Start R-work = 0.4497, R-free = 0.4521
Final R-work = 0.1142, R-free = 0.1621