# Date 2008-01-16 Time 04:32:27 PST -0800 (1200486747.31 s)
#phil __OFF__

Command line arguments: "../358.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4561
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 358

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 48.1033, 86.822, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0412 1.97078
Completeness in resolution range: 0.930019
Completeness with d_max=infinity: 0.927246

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0412
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0412 1.97078
Completeness in resolution range: 0.930019
Completeness with d_max=infinity: 0.927246

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0416 -  4.2177 [2212/2241]  1986   226  10.2%
  bin  2:  4.2177 -  3.3599 [2121/2144]  1911   210   9.9%
  bin  3:  3.3599 -  2.9388 [2088/2113]  1880   208  10.0%
  bin  4:  2.9388 -  2.6718 [2067/2084]  1859   208  10.1%
  bin  5:  2.6718 -  2.4812 [2052/2095]  1848   204   9.9%
  bin  6:  2.4812 -  2.3355 [2059/2087]  1857   202   9.8%
  bin  7:  2.3355 -  2.2189 [2037/2073]  1836   201   9.9%
  bin  8:  2.2189 -  2.1226 [2024/2066]  1824   200   9.9%
  bin  9:  2.1226 -  2.0411 [2033/2092]  1830   203  10.0%
  bin 10:  2.0411 -  1.9708 [ 896/2068]   799    97  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_358/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:
        1.49 -     2.18: 11
        2.18 -     2.86: 1134
        2.86 -     3.54: 4411
        3.54 -     4.22: 9162
        4.22 -     4.90: 13416
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.494 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.564 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.590 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.741 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28129 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_358/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_358/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 = 69.19625 48.10325 86.82195 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: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4470   r_free= 0.4330   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.265322                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.7045 0.99   1434  159 0.3647 0.4019      6.5519      6.5963|
|  2:  4.7045 -  3.7532 0.99   1389  154 0.3949 0.3851      6.8184      6.7981|
|  3:  3.7532 -  3.2844 0.99   1350  149 0.4227 0.3791      6.6516      6.6213|
|  4:  3.2844 -  2.9866 0.99   1338  144 0.4371 0.3845      6.4905      6.3909|
|  5:  2.9866 -  2.7740 0.99   1335  152 0.4860 0.4369      6.3527      6.3592|
|  6:  2.7740 -  2.6113 0.99   1342  152 0.4708 0.4735      6.2544      6.1266|
|  7:  2.6113 -  2.4812 0.98   1296  146 0.4737 0.4120      6.2064      6.1098|
|  8:  2.4812 -  2.3736 0.98   1336  140 0.4833 0.4690      6.1542      6.1877|
|  9:  2.3736 -  2.2825 0.99   1313  150 0.4925 0.4643      6.1037      6.1033|
| 10:  2.2825 -  2.2040 0.98   1320  142 0.4815 0.4835       6.077      6.0599|
| 11:  2.2040 -  2.1353 0.97   1303  147 0.5039 0.5076      6.0166      6.0056|
| 12:  2.1353 -  2.0744 0.98   1288  148 0.4870 0.4764      5.9264      5.9852|
| 13:  2.0744 -  2.0200 0.90   1197  129 0.4832 0.5082      5.8448       5.818|
| 14:  2.0200 -  1.9708 0.29    389   47 0.4644 0.4716      5.8687      5.7078|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0416 -  4.7045  1434   159  0.67  36.65   0.83     0.70      78877.11|
|  2:  4.7045 -  3.7532  1389   154  0.72  33.66   0.91     0.81      97692.00|
|  3:  3.7532 -  3.2844  1350   149  0.65  39.77   0.90     0.83      96476.00|
|  4:  3.2844 -  2.9866  1338   144  0.60  43.72   0.91     0.79      78111.14|
|  5:  2.9866 -  2.7740  1335   152  0.52  50.11   0.88     0.72      64101.63|
|  6:  2.7740 -  2.6113  1342   152  0.51  50.90   0.90     0.68      53976.73|
|  7:  2.6113 -  2.4812  1296   146  0.49  52.63   0.92     0.66      50865.37|
|  8:  2.4812 -  2.3736  1336   140  0.48  53.29   0.91     0.66      47048.92|
|  9:  2.3736 -  2.2825  1313   150  0.47  54.41   0.93     0.68      45349.99|
| 10:  2.2825 -  2.2040  1320   142  0.47  54.67   0.94     0.67      41400.26|
| 11:  2.2040 -  2.1353  1303   147  0.45  56.29   0.94     0.68      39851.27|
| 12:  2.1353 -  2.0744  1288   148  0.40  60.00   0.93     0.63      38942.07|
| 13:  2.0744 -  2.0200  1197   129  0.35  63.68   0.94     0.55      35161.69|
| 14:  2.0200 -  1.9708   389    47  0.34  64.63   1.00     0.43      28585.17|
|alpha:            min =        0.43 max =            0.83 mean =         0.69|
|beta:             min =    28585.17 max =        97692.00 mean =     58981.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.01|
|phase err.(test): min =        0.00 max =           89.99 mean =        50.10|
|-----------------------------------------------------------------------------|

============================== 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 = 7.611053              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.590   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.474766              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.604   (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 |  1.494 -  1.835:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.835 -  2.175:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.175 -  2.516:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.516 -  2.857:     1103 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.857 -  3.197:     1952 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.197 -  3.538:     2459 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.538 -  3.878:     4614 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.878 -  4.219:     4548 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.219 -  4.559:     6078 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7338 |
|-----------------------------------------------------------------------------|
|-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 |        0.175 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.494 |       0.357 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    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: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4470   r_free= 0.4330   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.265322                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4381   r_free= 0.4196   ksol= 0.30   Bsol= 37.71   scale= 0.930   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,5.20,-1.37,0.00,-0.00,-0.00); trace/3= 0.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.255848                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.891018              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.173   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.838844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.340   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4381      final r-factor (work) = 0.3517          |
| start r-factor (free) = 0.4196      final r-factor (free) = 0.3776          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7286 = 6.89 * 0.50 * 6.2554 + 1.00 * 0.1755                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2579 = 6.89 * 0.50 * 6.1375 + 1.00 * 0.1110                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3517      final r-factor (work) = 0.3235          |
| start r-factor (free) = 0.3776      final r-factor (free) = 0.3861          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1543 = 0.84 * 1.00 * 6.1375 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1027 = 0.84 * 1.00 * 6.0635 + 1.00 * 0.0164                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.43   18.51    None  None   None       |
|    all(noH): 2823   0      0.00    84.43   18.51    None  None   None       |
|    Sol.    : 438    0      0.00    84.43   35.83    None  None   None       |
|    Mac.    : 2385   0      0.00    65.72   15.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.443:  705   |   5:    42.217 -  50.660:  112        |
|      1:     8.443 -  16.887:  897   |   6:    50.660 -  59.103:   71        |
|      2:    16.887 -  25.330:  525   |   7:    59.103 -  67.546:   27        |
|      3:    25.330 -  33.773:  292   |   8:    67.546 -  75.990:    9        |
|      4:    33.773 -  42.217:  183   |   9:    75.990 -  84.433:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3235 r_free = 0.3861             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3231 r_free = 0.3857             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3231   r_free= 0.3857   ksol= 0.30   Bsol= 37.71   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,5.20,-1.37,0.00,-0.00,-0.00); trace/3= 0.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.065013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3226   r_free= 0.3836   ksol= 0.30   Bsol= 45.80   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,2.96,-0.56,0.00,-0.00,-0.00); trace/3= 0.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.065350                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.107616              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.325   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.623692              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.225  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3226      final r-factor (work) = 0.2596          |
| start r-factor (free) = 0.3836      final r-factor (free) = 0.3145          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.6955 = 8.11 * 0.50 * 6.0645 + 1.00 * 0.1110                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.3129 = 8.11 * 0.50 * 5.9740 + 1.00 * 0.0954                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2596      final r-factor (work) = 0.2423          |
| start r-factor (free) = 0.3145      final r-factor (free) = 0.3052          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7429 = 0.62 * 1.00 * 5.9740 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6614 = 0.62 * 1.00 * 5.8493 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.17   18.25    None  None   None       |
|    all(noH): 2823   0      0.00    87.17   18.25    None  None   None       |
|    Sol.    : 438    0      2.02    87.17   37.33    None  None   None       |
|    Mac.    : 2385   0      0.00    81.39   14.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.717:  796   |   5:    43.585 -  52.301:   91        |
|      1:     8.717 -  17.434:  982   |   6:    52.301 -  61.018:   79        |
|      2:    17.434 -  26.151:  424   |   7:    61.018 -  69.735:   34        |
|      3:    26.151 -  34.868:  263   |   8:    69.735 -  78.452:   16        |
|      4:    34.868 -  43.585:  133   |   9:    78.452 -  87.169:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2423 r_free = 0.3052             target_work(ml) = 5.840         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2421 r_free = 0.3047             target_work(ml) = 5.840         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2421   r_free= 0.3047   ksol= 0.30   Bsol= 45.80   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,2.96,-0.56,0.00,-0.00,-0.00); trace/3= 0.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.839842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2420   r_free= 0.3047   ksol= 0.32   Bsol= 55.46   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,1.48,-0.30,0.00,-0.00,-0.00); trace/3= -0.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.841124                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.864570              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.165  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.444  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2420      final r-factor (work) = 0.2044          |
| start r-factor (free) = 0.3047      final r-factor (free) = 0.2599          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3990 = 3.86 * 0.50 * 5.8499 + 1.00 * 0.0954                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2044 = 3.86 * 0.50 * 5.7672 + 1.00 * 0.0606                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2044      final r-factor (work) = 0.1985          |
| start r-factor (free) = 0.2599      final r-factor (free) = 0.2504          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6850 = 0.29 * 1.00 * 5.7672 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6756 = 0.29 * 1.00 * 5.6631 + 1.00 * 0.0340                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.30   18.29    None  None   None       |
|    all(noH): 2823   0      0.00    87.30   18.29    None  None   None       |
|    Sol.    : 438    0      5.31    87.30   37.80    None  None   None       |
|    Mac.    : 2385   0      0.00    81.42   14.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.730:  711   |   5:    43.648 -  52.378:   99        |
|      1:     8.730 -  17.459: 1120   |   6:    52.378 -  61.108:   72        |
|      2:    17.459 -  26.189:  404   |   7:    61.108 -  69.837:   32        |
|      3:    26.189 -  34.919:  237   |   8:    69.837 -  78.567:   18        |
|      4:    34.919 -  43.648:  126   |   9:    78.567 -  87.296:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1985 r_free = 0.2504             target_work(ml) = 5.644         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1984 r_free = 0.2502             target_work(ml) = 5.644         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1984   r_free= 0.2502   ksol= 0.32   Bsol= 55.46   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,1.48,-0.30,0.00,-0.00,-0.00); trace/3= -0.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.643683                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1978   r_free= 0.2496   ksol= 0.32   Bsol= 58.07   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-0.40,-1.19,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.644055                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.089155              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.018  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514195              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.608   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1978      final r-factor (work) = 0.1618          |
| start r-factor (free) = 0.2496      final r-factor (free) = 0.2070          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8067 = 3.09 * 0.50 * 5.6625 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6502 = 3.09 * 0.50 * 5.5539 + 1.00 * 0.0718                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1618      final r-factor (work) = 0.1464          |
| start r-factor (free) = 0.2070      final r-factor (free) = 0.1923          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8779 = 0.51 * 1.00 * 5.5539 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7919 = 0.51 * 1.00 * 5.4096 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    87.54   17.96    None  None   None       |
|    all(noH): 2823   0      1.48    87.54   17.96    None  None   None       |
|    Sol.    : 438    0      5.03    87.54   40.83    None  None   None       |
|    Mac.    : 2385   0      1.48    87.10   13.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.475 -  10.082: 1001   |   5:    44.507 -  53.113:  116        |
|      1:    10.082 -  18.688: 1034   |   6:    53.113 -  61.719:   79        |
|      2:    18.688 -  27.294:  267   |   7:    61.719 -  70.326:   28        |
|      3:    27.294 -  35.900:  156   |   8:    70.326 -  78.932:   20        |
|      4:    35.900 -  44.507:  116   |   9:    78.932 -  87.538:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1464 r_free = 0.1923             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1463 r_free = 0.1922             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1463   r_free= 0.1922   ksol= 0.32   Bsol= 58.07   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-0.40,-1.19,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.371647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1466   r_free= 0.1924   ksol= 0.33   Bsol= 60.26   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-1.14,-1.20,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.372755                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.655485              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.461  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 12.493386             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.719  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1466      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1924      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9624 = 3.66 * 0.50 * 5.4114 + 1.00 * 0.0718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7798 = 3.66 * 0.50 * 5.3100 + 1.00 * 0.0746                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1268      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 66.3496 = 12.49 * 1.00 * 5.3100 + 1.00 * 0.0103                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 65.5062 = 12.49 * 1.00 * 5.2423 + 1.00 * 0.0127                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.51    109.90  18.33    None  None   None       |
|    all(noH): 2823   0      0.51    109.90  18.33    None  None   None       |
|    Sol.    : 438    0      5.43    102.04  44.88    None  None   None       |
|    Mac.    : 2385   0      0.51    109.90  13.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.512 -  11.451: 1301   |   5:    55.207 -  66.146:   91        |
|      1:    11.451 -  22.390:  938   |   6:    66.146 -  77.085:   52        |
|      2:    22.390 -  33.329:  182   |   7:    77.085 -  88.024:   26        |
|      3:    33.329 -  44.268:  122   |   8:    88.024 -  98.963:    4        |
|      4:    44.268 -  55.207:  102   |   9:    98.963 - 109.901:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1211 r_free = 0.1724             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1211 r_free = 0.1723             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1723   ksol= 0.33   Bsol= 60.26   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-1.14,-1.20,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228416                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.7045 0.99   1434  159 0.0954 0.1338      5.3731      5.5852|
|  2:  4.7045 -  3.7532 0.99   1389  154 0.0844 0.1056      5.4423      5.6322|
|  3:  3.7532 -  3.2844 0.99   1350  149 0.1144 0.1703       5.529      5.9101|
|  4:  3.2844 -  2.9866 0.99   1338  144 0.1346 0.1805       5.531      5.7131|
|  5:  2.9866 -  2.7740 0.99   1335  152 0.1457 0.1830      5.4132      5.5861|
|  6:  2.7740 -  2.6113 0.99   1342  152 0.1408 0.2241      5.3148      5.5597|
|  7:  2.6113 -  2.4812 0.98   1296  146 0.1364 0.1776      5.2484      5.4415|
|  8:  2.4812 -  2.3736 0.98   1336  140 0.1312 0.1891       5.186      5.4122|
|  9:  2.3736 -  2.2825 0.99   1313  150 0.1289 0.2072      5.1123      5.4396|
| 10:  2.2825 -  2.2040 0.98   1320  142 0.1245 0.1781      5.0622      5.2562|
| 11:  2.2040 -  2.1353 0.97   1303  147 0.1248 0.2076      5.0004      5.3314|
| 12:  2.1353 -  2.0744 0.98   1288  148 0.1287 0.1733      4.9494       5.196|
| 13:  2.0744 -  2.0200 0.90   1197  129 0.1263 0.1945      4.8624      5.1287|
| 14:  2.0200 -  1.9708 0.29    389   47 0.1110 0.1851      4.7644      4.9698|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0416 -  4.7045  1434   159  0.94   9.61   0.97     0.94       7508.48|
|  2:  4.7045 -  3.7532  1389   154  0.95   8.55   1.01     1.00       9646.96|
|  3:  3.7532 -  3.2844  1350   149  0.93  12.34   1.03     1.03      11626.65|
|  4:  3.2844 -  2.9866  1338   144  0.90  15.67   1.02     1.01      12295.52|
|  5:  2.9866 -  2.7740  1335   152  0.88  18.09   1.01     0.99      10273.17|
|  6:  2.7740 -  2.6113  1342   152  0.88  18.67   0.98     0.94       8677.03|
|  7:  2.6113 -  2.4812  1296   146  0.89  17.63   0.99     0.96       7571.05|
|  8:  2.4812 -  2.3736  1336   140  0.89  17.94   1.00     0.96       7024.10|
|  9:  2.3736 -  2.2825  1313   150  0.88  18.01   0.99     0.94       6007.03|
| 10:  2.2825 -  2.2040  1320   142  0.88  18.45   0.99     0.95       5708.60|
| 11:  2.2040 -  2.1353  1303   147  0.88  18.13   0.99     0.95       5140.51|
| 12:  2.1353 -  2.0744  1288   148  0.89  17.68   0.99     0.97       4580.74|
| 13:  2.0744 -  2.0200  1197   129  0.88  18.44   0.98     0.97       3947.45|
| 14:  2.0200 -  1.9708   389    47  0.89  16.72   0.96     0.91       3199.14|
|alpha:            min =        0.91 max =            1.03 mean =         0.97|
|beta:             min =     3199.14 max =        12295.52 mean =      7649.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.01|
|phase err.(test): min =        0.00 max =           89.86 mean =        15.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1724   ksol= 0.33   Bsol= 66.01   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-1.25,-1.05,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.229178                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1724   ksol= 0.33   Bsol= 66.01   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-1.25,-1.05,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.229178                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.7045 0.99   1434  159 0.0968 0.1334      5.3792      5.5851|
|  2:  4.7045 -  3.7532 0.99   1389  154 0.0859 0.1056      5.4501      5.6383|
|  3:  3.7532 -  3.2844 0.99   1350  149 0.1147 0.1704      5.5329      5.9079|
|  4:  3.2844 -  2.9866 0.99   1338  144 0.1350 0.1796      5.5307       5.708|
|  5:  2.9866 -  2.7740 0.99   1335  152 0.1458 0.1826      5.4105      5.5851|
|  6:  2.7740 -  2.6113 0.99   1342  152 0.1404 0.2233      5.3128      5.5556|
|  7:  2.6113 -  2.4812 0.98   1296  146 0.1362 0.1781      5.2465      5.4423|
|  8:  2.4812 -  2.3736 0.98   1336  140 0.1309 0.1887      5.1854      5.4124|
|  9:  2.3736 -  2.2825 0.99   1313  150 0.1286 0.2072       5.112      5.4393|
| 10:  2.2825 -  2.2040 0.98   1320  142 0.1241 0.1786      5.0614      5.2577|
| 11:  2.2040 -  2.1353 0.97   1303  147 0.1247 0.2075      5.0001      5.3304|
| 12:  2.1353 -  2.0744 0.98   1288  148 0.1286 0.1738      4.9496      5.1968|
| 13:  2.0744 -  2.0200 0.90   1197  129 0.1265 0.1943      4.8627       5.127|
| 14:  2.0200 -  1.9708 0.29    389   47 0.1109 0.1849      4.7635      4.9689|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0416 -  4.7045  1434   159  0.94   9.51   0.97     0.94       7373.47|
|  2:  4.7045 -  3.7532  1389   154  0.95   8.60   1.01     1.00       9672.29|
|  3:  3.7532 -  3.2844  1350   149  0.93  12.38   1.03     1.03      11719.75|
|  4:  3.2844 -  2.9866  1338   144  0.90  15.66   1.02     1.01      12253.27|
|  5:  2.9866 -  2.7740  1335   152  0.88  18.02   1.01     0.99      10193.84|
|  6:  2.7740 -  2.6113  1342   152  0.88  18.63   0.98     0.94       8646.85|
|  7:  2.6113 -  2.4812  1296   146  0.89  17.60   0.99     0.96       7550.69|
|  8:  2.4812 -  2.3736  1336   140  0.89  17.95   1.00     0.96       7028.61|
|  9:  2.3736 -  2.2825  1313   150  0.88  18.02   1.00     0.94       6011.42|
| 10:  2.2825 -  2.2040  1320   142  0.88  18.45   0.99     0.96       5705.46|
| 11:  2.2040 -  2.1353  1303   147  0.88  18.13   0.99     0.95       5139.92|
| 12:  2.1353 -  2.0744  1288   148  0.89  17.68   1.00     0.97       4585.60|
| 13:  2.0744 -  2.0200  1197   129  0.88  18.44   0.99     0.97       3943.45|
| 14:  2.0200 -  1.9708   389    47  0.89  16.70   0.96     0.91       3183.25|
|alpha:            min =        0.91 max =            1.03 mean =         0.97|
|beta:             min =     3183.25 max =        12253.27 mean =      7634.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.86 mean =        16.00|
|phase err.(test): min =        0.00 max =           89.61 mean =        15.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    109.89  18.32    None  None   None       |
|    all(noH): 2823   0      0.50    109.89  18.32    None  None   None       |
|    Sol.    : 438    0      5.42    102.02  44.86    None  None   None       |
|    Mac.    : 2385   0      0.50    109.89  13.44    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:     0.496 -  11.435: 1301   |   5:    55.191 -  66.130:   91        |
|      1:    11.435 -  22.374:  938   |   6:    66.130 -  77.068:   52        |
|      2:    22.374 -  33.313:  182   |   7:    77.068 -  88.007:   26        |
|      3:    33.313 -  44.252:  122   |   8:    88.007 -  98.946:    4        |
|      4:    44.252 -  55.191:  102   |   9:    98.946 - 109.885:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.660 - 4.923
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 320
   mapped sites are within: 0.738 - 4.923

peak=   11.699 closest distance to " O  BHOH Z  74 " =    1.276
peak=    6.047 closest distance to " O   HOH Z 210 " =    1.392
peak=    5.232 closest distance to " O   HOH Z 403 " =    2.106
peak=    5.224 closest distance to " CA  TYR A  30 " =    0.933
peak=    4.995 closest distance to " O   HOH Z  49 " =    1.328
peak=    4.899 closest distance to " O   HOH Z 113 " =    2.258
peak=    4.805 closest distance to " O   HOH Z 102 " =    1.501
peak=    4.707 closest distance to " O   HOH Z  63 " =    2.149
peak=    4.682 closest distance to " O   HOH Z 124 " =    1.160
peak=    4.679 closest distance to " O   HOH Z  43 " =    2.087
peak=    4.584 closest distance to " O   PRO A 198 " =    1.493
peak=    4.547 closest distance to " CG  PRO A  54 " =    1.207
peak=    4.541 closest distance to " CB  SER A  63 " =    1.154
peak=    4.509 closest distance to " O   HOH Z 130 " =    2.458
peak=    4.505 closest distance to " O   HOH Z 134 " =    1.886
peak=    4.500 closest distance to " O   HOH Z  44 " =    2.068
peak=    4.493 closest distance to " O   HOH Z 433 " =    1.784
peak=    4.445 closest distance to " CG1 ILE A  33 " =    1.147
peak=    4.433 closest distance to " CD2 TRP A 179 " =    1.383
peak=    4.427 closest distance to " O   HOH Z 357 " =    2.137
peak=    4.412 closest distance to " O   HOH Z  80 " =    1.911
peak=    4.400 closest distance to " CB  GLN A 183 " =    1.280
peak=    4.378 closest distance to " O   HOH Z 154 " =    1.761
peak=    4.377 closest distance to " O   HOH Z 209 " =    2.267
peak=    4.331 closest distance to " CB  ARG A 275 " =    0.825
peak=    4.317 closest distance to " CB  GLN A 223 " =    1.460
peak=    4.304 closest distance to " O   GLY A  23 " =    2.505
peak=    4.296 closest distance to " O   HOH Z 428 " =    1.143
peak=    4.276 closest distance to " OE1 GLN A  55 " =    1.561
peak=    4.243 closest distance to " O   HOH Z 422 " =    0.839
peak=    4.231 closest distance to " O   HOH Z 431 " =    1.285
peak=    4.220 closest distance to " CB  ASN A 285 " =    0.965
peak=    4.166 closest distance to " CB  ARG A 190 " =    1.834
peak=    4.159 closest distance to " O   HOH Z 369 " =    1.982
peak=    4.155 closest distance to " O   HOH Z 234 " =    3.656
peak=    4.132 closest distance to " O   HOH Z 128 " =    1.410
peak=    4.121 closest distance to " O   HOH Z 245 " =    1.309
peak=    4.105 closest distance to " O   HOH Z 232 " =    2.444
peak=    4.091 closest distance to " CG  PRO A  90 " =    1.205
peak=    4.071 closest distance to " CD  LYS A 166 " =    1.557
peak=    4.068 closest distance to " O   HOH Z 406 " =    1.603
peak=    4.065 closest distance to " O   HOH Z 247 " =    1.515
peak=    4.065 closest distance to " O   HOH Z 298 " =    1.940
peak=    4.059 closest distance to " CA  ALA A  51 " =    1.027
peak=    4.057 closest distance to " OD1 ASN A 301 " =    1.121
peak=    4.053 closest distance to " O   HOH Z  40 " =    1.999
peak=    4.035 closest distance to " CB  PRO A  54 " =    0.889
peak=    4.028 closest distance to " O   HOH Z 412 " =    3.525
peak=    4.026 closest distance to " NH2BARG A 145 " =    2.061
peak=    4.010 closest distance to " ND2 ASN A 249 " =    2.079
peak=    4.007 closest distance to " NZ  LYS A 117 " =    3.010
peak=    3.989 closest distance to " O   HOH Z 154 " =    2.253
peak=    3.987 closest distance to " O   HOH Z 361 " =    3.249
peak=    3.966 closest distance to " CG  PRO A 213 " =    1.208
peak=    3.965 closest distance to " O   HOH Z  39 " =    1.723
peak=    3.954 closest distance to " O   HOH Z 132 " =    2.803
peak=    3.933 closest distance to " NE2 GLN A  11 " =    0.960
peak=    3.929 closest distance to " CG  ARG A  66 " =    0.978
peak=    3.928 closest distance to " CA  ARG A 195 " =    1.183
peak=    3.922 closest distance to " CG2 VAL A 197 " =    1.201
peak=    3.922 closest distance to " O   HOH Z 214 " =    1.488
peak=    3.918 closest distance to " CZ  PHE A  38 " =    1.211
peak=    3.907 closest distance to " O   HOH Z  68 " =    2.008
peak=    3.905 closest distance to " O   HOH Z 352 " =    1.834
peak=    3.902 closest distance to " O   HOH Z 423 " =    1.821
peak=    3.894 closest distance to " CG  PRO A 198 " =    1.282
peak=    3.892 closest distance to " O   HOH Z 132 " =    2.379
peak=    3.889 closest distance to " O   HOH Z   7 " =    1.211
peak=    3.886 closest distance to " O   HOH Z 346 " =    1.676
peak=    3.885 closest distance to " O   HOH Z 117 " =    1.108
peak=    3.884 closest distance to " O   HOH Z 126 " =    1.530
peak=    3.883 closest distance to " O   SER A  87 " =    2.221
peak=    3.881 closest distance to " O   HOH Z 402 " =    1.642
peak=    3.881 closest distance to " O   HOH Z 142 " =    1.384
peak=    3.876 closest distance to " O   ASP A 124 " =    1.812
peak=    3.875 closest distance to " CG2BVAL A  41 " =    0.900
peak=    3.855 closest distance to " CB  SER A  26 " =    1.736
peak=    3.853 closest distance to " CB  GLU A 277 " =    3.762
peak=    3.852 closest distance to " O   GLN A  11 " =    0.995
peak=    3.842 closest distance to " O   HOH Z 189 " =    2.544
peak=    3.839 closest distance to " CB  SER A 141 " =    1.068
peak=    3.835 closest distance to " NH2 ARG A 156 " =    1.214
peak=    3.835 closest distance to " N   SER A 164 " =    0.988
peak=    3.826 closest distance to " O   HOH Z 146 " =    1.185
peak=    3.822 closest distance to " O   HOH Z 248 " =    1.560
peak=    3.821 closest distance to " O   HOH Z 336 " =    1.856
peak=    3.818 closest distance to " O   ALA A 165 " =    1.368
peak=    3.811 closest distance to " O   HOH Z 176 " =    1.450
peak=    3.793 closest distance to " O   HOH Z 414 " =    1.838
peak=    3.771 closest distance to " O   HOH Z 365 " =    2.611
peak=    3.769 closest distance to " O   HOH Z 265 " =    2.031
peak=    3.768 closest distance to " O   HOH Z 185 " =    1.753
peak=    3.766 closest distance to " O   ASN A  74 " =    1.793
peak=    3.754 closest distance to " O   HOH Z 130 " =    1.119
peak=    3.745 closest distance to " O   HOH Z 146 " =    1.439
peak=    3.740 closest distance to " CB  TRP A 179 " =    1.245
peak=    3.737 closest distance to " O   HOH Z 109 " =    1.790
peak=    3.735 closest distance to " CG1BVAL A  72 " =    1.901
peak=    3.732 closest distance to " O   HOH Z 258 " =    2.290
peak=    3.729 closest distance to " CG2 ILE A  20 " =    1.377
peak=    3.710 closest distance to " CA  ASN A 176 " =    1.502
peak=    3.707 closest distance to " CB  MET A 105 " =    1.152
peak=    3.705 closest distance to " CB  ASN A 148 " =    1.417
peak=    3.705 closest distance to " O   HOH Z  88 " =    3.174
peak=    3.698 closest distance to " O   HOH Z 417 " =    2.925
peak=    3.692 closest distance to " O   HOH Z 186 " =    1.111
peak=    3.692 closest distance to " ND1 HIS A  81 " =    1.202
peak=    3.688 closest distance to " CB  SER A  62 " =    0.815
peak=    3.677 closest distance to " O   HOH Z 196 " =    1.543
peak=    3.677 closest distance to " CA  ALA A 160 " =    0.897
peak=    3.676 closest distance to " CA  ALA A  21 " =    1.442
peak=    3.667 closest distance to " OH  TYR A 116 " =    1.204
peak=    3.661 closest distance to " C   ILE A 106 " =    1.813
peak=    3.659 closest distance to " O   HOH Z  15 " =    2.114
peak=    3.655 closest distance to " CB  THR A  52 " =    0.865
peak=    3.651 closest distance to " CZ  PHE A 218 " =    1.179
peak=    3.643 closest distance to " O   HOH Z 394 " =    1.584
peak=    3.637 closest distance to " O   HOH Z 227 " =    1.812
peak=    3.633 closest distance to " O   HOH Z 425 " =    1.453
peak=    3.612 closest distance to " O   HOH Z 214 " =    2.368
peak=    3.611 closest distance to " CB  ARG A  79 " =    1.667
peak=    3.609 closest distance to " CD  ARG A 159 " =    0.840
peak=    3.604 closest distance to " CB  GLU A 128 " =    1.210
peak=    3.593 closest distance to " O   HOH Z 279 " =    2.100
peak=    3.581 closest distance to " CE  LYS A 119 " =    1.199
peak=    3.581 closest distance to " CA  LEU A  83 " =    1.274
peak=    3.580 closest distance to " N   CYS A 260 " =    0.800
peak=    3.578 closest distance to " O   HOH Z 345 " =    2.626
peak=    3.577 closest distance to " CD  ARG A 195 " =    1.046
peak=    3.571 closest distance to " O   HOH Z  35 " =    1.903
peak=    3.566 closest distance to " O  BHOH Z 338 " =    1.025
peak=    3.563 closest distance to " CG AARG A 275 " =    1.296
peak=    3.562 closest distance to " O   HOH Z 386 " =    2.275
peak=    3.558 closest distance to " O   HOH Z 423 " =    3.228
peak=    3.557 closest distance to " O   HOH Z 130 " =    2.385
peak=    3.555 closest distance to " O   HOH Z  97 " =    1.840
peak=    3.554 closest distance to " O   HOH Z 189 " =    2.546
peak=    3.549 closest distance to " CD  PRO A  54 " =    1.080
peak=    3.546 closest distance to " O   HOH Z  78 " =    1.720
peak=    3.545 closest distance to " CA  SER A  12 " =    1.441
peak=    3.543 closest distance to " O   HOH Z 301 " =    1.473
peak=    3.534 closest distance to " O   HOH Z 358 " =    1.365
peak=    3.514 closest distance to " O   HOH Z 418 " =    1.700
peak=    3.514 closest distance to " CB  ASN A  39 " =    0.867
peak=    3.509 closest distance to " O   HOH Z 291 " =    1.408
peak=    3.507 closest distance to " NH2AARG A 275 " =    2.654
peak=    3.502 closest distance to " O   HOH Z 128 " =    1.903
peak=    3.500 closest distance to " O   HOH Z 368 " =    2.050
peak=    3.500 closest distance to " O   HOH Z 261 " =    2.383
peak=    3.498 closest distance to " CD  LYS A 119 " =    1.968
peak=    3.492 closest distance to " CB  VAL A 202 " =    1.513
peak=    3.484 closest distance to " CA  GLY A 196 " =    1.095
peak=    3.481 closest distance to " CD  GLN A 194 " =    1.621
peak=    3.480 closest distance to " N   ALA A   1 " =    1.112
peak=    3.479 closest distance to " O   HOH Z  20 " =    1.579
peak=    3.477 closest distance to " N   TRP A 150 " =    1.104
peak=    3.473 closest distance to " CB  GLU A 152 " =    1.153
peak=    3.472 closest distance to " O   HOH Z 435 " =    1.801
peak=    3.470 closest distance to " N   ASN A  39 " =    1.276
peak=    3.469 closest distance to " O   HOH Z 404 " =    1.491
peak=    3.467 closest distance to " OE1 GLN A  11 " =    2.124
peak=    3.466 closest distance to " O   HOH Z 193 " =    1.616
peak=    3.465 closest distance to " O   HOH Z 344 " =    3.223
peak=    3.459 closest distance to " O   HOH Z 395 " =    1.436
peak=    3.456 closest distance to " O   HOH Z 367 " =    1.334
peak=    3.446 closest distance to " O   HOH Z 394 " =    3.908
peak=    3.445 closest distance to " OG  SER A  62 " =    2.844
peak=    3.443 closest distance to " O   HOH Z 339 " =    1.277
peak=    3.440 closest distance to " O   HOH Z 313 " =    1.836
peak=    3.439 closest distance to " CD1 LEU A  96 " =    0.742
peak=    3.432 closest distance to " O   HOH Z  48 " =    1.796
peak=    3.430 closest distance to " CA  GLN A  73 " =    1.282
peak=    3.425 closest distance to " O   HOH Z  90 " =    3.655
peak=    3.420 closest distance to " CG2 THR A  29 " =    1.235
peak=    3.418 closest distance to " O   HOH Z 427 " =    3.101
peak=    3.416 closest distance to " O   HOH Z 162 " =    1.520
peak=    3.415 closest distance to " O   HOH Z 271 " =    2.490
peak=    3.415 closest distance to " CE1 TYR A 186 " =    1.188
peak=    3.414 closest distance to " O   HOH Z  61 " =    1.553
peak=    3.411 closest distance to " CB  GLU A 175 " =    1.336
peak=    3.410 closest distance to " O   HOH Z 437 " =    1.718
peak=    3.408 closest distance to " O   HOH Z 240 " =    2.335
peak=    3.398 closest distance to " CZ3 TRP A 266 " =    1.048
peak=    3.398 closest distance to " OG  SER A 245 " =    1.458
peak=    3.398 closest distance to " CZ  ARG A  14 " =    1.277
peak=    3.396 closest distance to " CA  VAL A 125 " =    1.333
peak=    3.396 closest distance to " O   HOH Z 299 " =    4.181
peak=    3.395 closest distance to " CG  ARG A  79 " =    2.472
peak=    3.394 closest distance to " CB  TRP A 266 " =    1.033
peak=    3.392 closest distance to " CG  GLN A  58 " =    0.946
peak=    3.387 closest distance to " CG  PRO A 243 " =    1.162
peak=    3.386 closest distance to " CG  GLN A  11 " =    1.340
peak=    3.386 closest distance to " NH1AARG A 275 " =    1.047
peak=    3.385 closest distance to " O   HOH Z 358 " =    2.095
peak=    3.384 closest distance to " CB  TRP A 179 " =    1.624
peak=    3.381 closest distance to " O   HOH Z 250 " =    1.936
peak=    3.380 closest distance to " O   HOH Z 284 " =    2.888
peak=    3.376 closest distance to " CA  CYS A 260 " =    1.702
peak=    3.376 closest distance to " O   HOH Z 345 " =    1.805
peak=    3.376 closest distance to " CA  VAL A 112 " =    1.214
peak=    3.370 closest distance to " NZ  LYS A 117 " =    2.604
peak=    3.369 closest distance to " O   HOH Z 147 " =    1.759
peak=    3.361 closest distance to " CA  ASN A 217 " =    1.263
peak=    3.360 closest distance to " O   HOH Z 371 " =    3.176
peak=    3.358 closest distance to " CD1 LEU A 167 " =    1.219
peak=    3.358 closest distance to " CA  ALA A 295 " =    1.084
peak=    3.355 closest distance to " O   HOH Z 150 " =    1.676
peak=    3.355 closest distance to " CD  ARG A 269 " =    0.989
peak=    3.354 closest distance to " O   HOH Z 282 " =    2.121
peak=    3.351 closest distance to " CA  ASP A 149 " =    1.268
peak=    3.350 closest distance to " NE2 GLN A  77 " =    3.105
peak=    3.349 closest distance to " CE  LYS A  76 " =    0.838
peak=    3.347 closest distance to " ND2 ASN A 301 " =    1.076
peak=    3.344 closest distance to " O   HOH Z 214 " =    2.302
peak=    3.342 closest distance to " O   HOH Z 250 " =    1.428
peak=    3.341 closest distance to " ND2 ASN A 187 " =    1.602
peak=    3.340 closest distance to " CB  PHE A  16 " =    1.203
peak=    3.339 closest distance to " CA  ASP A 191 " =    1.000
peak=    3.338 closest distance to " CG ALYS A 290 " =    1.085
peak=    3.331 closest distance to " CG  ARG A 219 " =    1.251
peak=    3.331 closest distance to " O   HOH Z 316 " =    2.882
peak=    3.326 closest distance to " O   HOH Z 298 " =    4.376
peak=    3.322 closest distance to " CD  ARG A  36 " =    1.180
peak=    3.322 closest distance to " CA  ALA A 100 " =    1.279
peak=    3.322 closest distance to " OG BSER A 210 " =    1.077
peak=    3.317 closest distance to " CB  SER A   3 " =    1.351
peak=    3.316 closest distance to " CG2 THR A 221 " =    1.255
peak=    3.312 closest distance to " O   HOH Z 412 " =    3.731
peak=    3.310 closest distance to " O   HOH Z 327 " =    1.683
peak=    3.307 closest distance to " O   THR A 251 " =    1.335
peak=    3.306 closest distance to " O   PHE A  61 " =    1.438
peak=    3.301 closest distance to " O   ALA A 158 " =    1.182
peak=    3.297 closest distance to " CB  LEU A  83 " =    0.873
peak=    3.292 closest distance to " CB  PRO A 280 " =    1.188
peak=    3.291 closest distance to " O   ASP A 200 " =    1.565
peak=    3.290 closest distance to " CA  ARG A  36 " =    0.989
peak=    3.287 closest distance to " O   HOH Z 380 " =    1.730
peak=    3.285 closest distance to " CD1 LEU A 228 " =    1.663
peak=    3.284 closest distance to " CA  ALA A 158 " =    1.224
peak=    3.284 closest distance to " O   HOH Z  89 " =    1.830
peak=    3.281 closest distance to " O   HOH Z 393 " =    3.484
peak=    3.278 closest distance to " O   HOH Z 334 " =    1.507
peak=    3.277 closest distance to " N   ALA A  10 " =    1.644
peak=    3.273 closest distance to " CB  ARG A  79 " =    0.868
peak=    3.273 closest distance to " O   HOH Z 272 " =    1.901
peak=    3.267 closest distance to " CA  LYS A 117 " =    1.336
peak=    3.265 closest distance to " O   HOH Z 173 " =    2.222
peak=    3.264 closest distance to " O   HOH Z 421 " =    2.075
peak=    3.262 closest distance to " CB  LEU A   5 " =    1.179
peak=    3.260 closest distance to " O   ASP A 191 " =    1.601
peak=    3.260 closest distance to " CA  THR A 246 " =    1.053
peak=    3.260 closest distance to " N   GLU A  44 " =    1.443
peak=    3.258 closest distance to " CA  ASP A 162 " =    1.147
peak=    3.257 closest distance to " O   HOH Z 109 " =    2.513
peak=    3.257 closest distance to " O   HOH Z  30 " =    1.150
peak=    3.254 closest distance to " O   HOH Z 111 " =    1.401
peak=    3.251 closest distance to " O   HOH Z 126 " =    2.289
peak=    3.245 closest distance to " CG1 VAL A 174 " =    1.683
peak=    3.236 closest distance to " OE1 GLU A   2 " =    1.478
peak=    3.235 closest distance to " OG BSER A 164 " =    2.320
peak=    3.232 closest distance to " CA  VAL A  41 " =    0.900
peak=    3.229 closest distance to " CA  SER A  32 " =    1.649
peak=    3.227 closest distance to " O  BHOH Z 338 " =    2.067
peak=    3.226 closest distance to " O   HOH Z 374 " =    2.645
peak=    3.222 closest distance to " CB  TYR A 169 " =    0.898
peak=    3.220 closest distance to " OE1 GLN A  58 " =    3.155
peak=    3.219 closest distance to " O   HOH Z 415 " =    1.053
peak=    3.219 closest distance to " O   HOH Z 139 " =    4.624
peak=    3.217 closest distance to " CA  GLY A  80 " =    0.967
peak=    3.216 closest distance to " OD2 ASP A 286 " =    3.262
peak=    3.212 closest distance to " CG2 VAL A  78 " =    0.810
peak=    3.209 closest distance to " O   HOH Z   6 " =    1.343
peak=    3.203 closest distance to " CA  THR A 294 " =    1.688
peak=    3.186 closest distance to " O   HOH Z 236 " =    1.555
peak=    3.185 closest distance to " CB  LEU A 228 " =    1.207
peak=    3.182 closest distance to " CA  ALA A 291 " =    0.839
peak=    3.181 closest distance to " O   HOH Z 422 " =    2.810
peak=    3.178 closest distance to " CD1 LEU A 222 " =    0.738
peak=    3.175 closest distance to " CB  GLU A  46 " =    1.118
peak=    3.174 closest distance to " CZ3 TRP A  85 " =    0.904
peak=    3.156 closest distance to " O   GLU A   2 " =    1.633
peak=    3.156 closest distance to " CB  ALA A 248 " =    1.343
peak=    3.152 closest distance to " CA  CYS A 254 " =    1.527
peak=    3.150 closest distance to " O   HOH Z 188 " =    4.828
peak=    3.147 closest distance to " CE1 HIS A 108 " =    1.089
peak=    3.146 closest distance to " CA  ALA A 100 " =    2.017
peak=    3.142 closest distance to " CA  ARG A 139 " =    1.468
peak=    3.137 closest distance to " O   HOH Z   6 " =    2.630
peak=    3.136 closest distance to " O   HOH Z  85 " =    1.765
peak=    3.134 closest distance to " CB  PHE A 283 " =    0.806
peak=    3.133 closest distance to " O   HOH Z 353 " =    2.733
peak=    3.133 closest distance to " O   CYS A 168 " =    1.500
peak=    3.129 closest distance to " CA  GLU A 152 " =    0.905
peak=    3.126 closest distance to " CB  ARG A 259 " =    1.904
peak=    3.122 closest distance to " CG2 VAL A 126 " =    0.804
peak=    3.119 closest distance to " O   HOH Z 408 " =    1.883
peak=    3.116 closest distance to " CB  ASP A 140 " =    0.987
peak=    3.113 closest distance to " CA  ILE A 106 " =    0.810
peak=    3.098 closest distance to " O   HOH Z 213 " =    2.235
peak=    3.097 closest distance to " CB  PRO A  54 " =    1.343
peak=    3.095 closest distance to " CB  ARG A  79 " =    0.931
peak=    3.092 closest distance to " O   HOH Z 420 " =    4.923
peak=    3.091 closest distance to " CB  SER A 210 " =    1.077
peak=    3.084 closest distance to " N   ARG A 156 " =    1.418
peak=    3.076 closest distance to " CA  VAL A 197 " =    1.007
peak=    3.068 closest distance to " NH2 ARG A  36 " =    1.790
peak=    3.063 closest distance to " O   HOH Z 298 " =    2.186
peak=    3.060 closest distance to " ND2 ASN A 249 " =    0.867
peak=    3.060 closest distance to " CB  LYS A 289 " =    1.068
peak=    3.057 closest distance to " O   HOH Z 163 " =    1.407
peak=    3.055 closest distance to " O   HOH Z  78 " =    1.933
peak=    3.055 closest distance to " O   HOH Z 141 " =    1.665
peak=    3.052 closest distance to " O   HOH Z 426 " =    1.346
peak=    3.047 closest distance to " CB  SER A  97 " =    0.800
peak=    3.034 closest distance to " O   HOH Z   7 " =    1.014
peak=    3.020 closest distance to " CA  ASP A 140 " =    1.531
peak=    3.016 closest distance to " O   HOH Z 423 " =    2.660

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.880 - 5.960
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 211
   mapped sites are within: 0.880 - 5.960

peak=   -4.760 closest distance to " O   HOH Z 266 " =    5.053
peak=   -4.539 closest distance to " CD  GLN A  58 " =    0.994
peak=   -4.437 closest distance to " CG2 ILE A  20 " =    3.026
peak=   -4.429 closest distance to " CD  GLN A 223 " =    1.545
peak=   -4.358 closest distance to " O   HOH Z 377 " =    2.162
peak=   -4.348 closest distance to " O   HOH Z 166 " =    1.721
peak=   -4.345 closest distance to " NE2 GLN A 223 " =    1.216
peak=   -4.277 closest distance to " O   HOH Z 422 " =    1.216
peak=   -4.188 closest distance to " CG2 ILE A  49 " =    2.666
peak=   -4.119 closest distance to " O   VAL A  67 " =    2.900
peak=   -4.116 closest distance to " CD  ARG A  14 " =    3.399
peak=   -4.114 closest distance to " CD  ARG A 156 " =    1.992
peak=   -4.099 closest distance to " OXT GLY A 302 " =    3.074
peak=   -4.071 closest distance to " CD  GLN A  58 " =    0.933
peak=   -4.067 closest distance to " O   HOH Z   7 " =    1.045
peak=   -4.042 closest distance to " CD1 PHE A  59 " =    2.030
peak=   -4.035 closest distance to " O   HOH Z 155 " =    1.709
peak=   -4.019 closest distance to " CD2 TYR A  30 " =    2.779
peak=   -4.016 closest distance to " CD2 LEU A 237 " =    2.340
peak=   -4.008 closest distance to " OG  SER A  97 " =    2.235
peak=   -4.004 closest distance to " O   PHE A 218 " =    1.411
peak=   -3.964 closest distance to " O   ALA A  34 " =    2.399
peak=   -3.952 closest distance to " CG  PRO A 243 " =    1.581
peak=   -3.936 closest distance to " O   PRO A 163 " =    2.154
peak=   -3.924 closest distance to " C   HIS A 108 " =    1.059
peak=   -3.882 closest distance to " O   HOH Z   6 " =    1.689
peak=   -3.869 closest distance to " O   HOH Z 423 " =    2.267
peak=   -3.855 closest distance to " CB  LEU A 167 " =    2.174
peak=   -3.842 closest distance to " O   GLN A  11 " =    1.145
peak=   -3.818 closest distance to " CA  GLU A 277 " =    1.300
peak=   -3.805 closest distance to " O   HOH Z 418 " =    1.273
peak=   -3.770 closest distance to " CG  GLU A  53 " =    1.296
peak=   -3.760 closest distance to " CD2 PHE A  61 " =    2.106
peak=   -3.729 closest distance to " O   ILE A 109 " =    2.564
peak=   -3.726 closest distance to " CA  VAL A 197 " =    0.954
peak=   -3.723 closest distance to " C   THR A 279 " =    1.159
peak=   -3.717 closest distance to " O   TRP A  92 " =    1.982
peak=   -3.705 closest distance to " O   HOH Z  56 " =    1.298
peak=   -3.692 closest distance to " CG  GLN A  11 " =    1.397
peak=   -3.691 closest distance to " CG2 VAL A 189 " =    2.125
peak=   -3.689 closest distance to " O   HOH Z 196 " =    1.838
peak=   -3.688 closest distance to " CA  GLY A 133 " =    2.093
peak=   -3.687 closest distance to " CB  ALA A  43 " =    2.593
peak=   -3.678 closest distance to " N   ALA A  43 " =    2.761
peak=   -3.674 closest distance to " CG  ARG A 219 " =    2.424
peak=   -3.654 closest distance to " O   PRO A 198 " =    1.425
peak=   -3.653 closest distance to " O   HOH Z  71 " =    2.133
peak=   -3.648 closest distance to " O   VAL A 174 " =    2.116
peak=   -3.633 closest distance to " CD1 ILE A 106 " =    2.090
peak=   -3.623 closest distance to " CG  GLN A  88 " =    0.933
peak=   -3.623 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.620 closest distance to " O   HOH Z 407 " =    1.319
peak=   -3.614 closest distance to " O   HOH Z 234 " =    3.991
peak=   -3.607 closest distance to " ND2 ASN A  69 " =    1.613
peak=   -3.603 closest distance to " CD2 LEU A 237 " =    2.457
peak=   -3.603 closest distance to " O   HOH Z 139 " =    3.523
peak=   -3.602 closest distance to " O   HOH Z 174 " =    2.185
peak=   -3.592 closest distance to " O   HOH Z 115 " =    1.503
peak=   -3.584 closest distance to " CA  SER A 276 " =    1.463
peak=   -3.583 closest distance to " CD2 PHE A  59 " =    2.386
peak=   -3.579 closest distance to " O   HOH Z 165 " =    1.925
peak=   -3.562 closest distance to " O   HOH Z 250 " =    1.713
peak=   -3.554 closest distance to " CD2 PHE A 225 " =    1.363
peak=   -3.552 closest distance to " OG BSER A 134 " =    1.423
peak=   -3.545 closest distance to " OD1 ASN A 187 " =    1.717
peak=   -3.544 closest distance to " O   HOH Z  15 " =    1.544
peak=   -3.516 closest distance to " C   GLY A 133 " =    1.148
peak=   -3.514 closest distance to " ND2 ASN A  60 " =    1.478
peak=   -3.513 closest distance to " O   SER A 276 " =    1.626
peak=   -3.511 closest distance to " O   HOH Z 150 " =    1.027
peak=   -3.506 closest distance to " ND2 ASN A  45 " =    1.262
peak=   -3.497 closest distance to " CB  ALA A 131 " =    2.412
peak=   -3.492 closest distance to " OD1 ASN A 301 " =    0.880
peak=   -3.481 closest distance to " O   HOH Z 215 " =    3.854
peak=   -3.479 closest distance to " O   HOH Z 109 " =    2.833
peak=   -3.473 closest distance to " ND2BASN A 224 " =    2.006
peak=   -3.467 closest distance to " O   SER A  95 " =    1.849
peak=   -3.460 closest distance to " C   ASN A 285 " =    2.347
peak=   -3.459 closest distance to " CG  ASN A 301 " =    1.904
peak=   -3.455 closest distance to " O   SER A 273 " =    1.173
peak=   -3.454 closest distance to " CB  PRO A 213 " =    1.601
peak=   -3.450 closest distance to " O   HOH Z 326 " =    5.034
peak=   -3.448 closest distance to " OD1 ASP A 171 " =    1.535
peak=   -3.437 closest distance to " O   HOH Z 388 " =    2.087
peak=   -3.431 closest distance to " CB  ALA A 248 " =    2.209
peak=   -3.429 closest distance to " O   HOH Z 275 " =    1.530
peak=   -3.427 closest distance to " CA  GLY A 203 " =    2.183
peak=   -3.425 closest distance to " NE2 GLN A  88 " =    1.808
peak=   -3.421 closest distance to " O   ASN A 110 " =    2.287
peak=   -3.421 closest distance to " OD1 ASP A 191 " =    1.806
peak=   -3.416 closest distance to " CD1 LEU A 101 " =    2.411
peak=   -3.413 closest distance to " CG  ASP A 162 " =    1.540
peak=   -3.408 closest distance to " CD1 TRP A 179 " =    1.177
peak=   -3.408 closest distance to " CH2 TRP A 150 " =    1.000
peak=   -3.401 closest distance to " CG1 VAL A 112 " =    2.527
peak=   -3.396 closest distance to " ND2 ASN A  45 " =    1.900
peak=   -3.393 closest distance to " CB  SER A 210 " =    1.173
peak=   -3.391 closest distance to " O   HOH Z 197 " =    1.849
peak=   -3.388 closest distance to " OG BSER A 210 " =    2.523
peak=   -3.386 closest distance to " NH2 ARG A  66 " =    1.712
peak=   -3.386 closest distance to " CG  ASP A 132 " =    2.366
peak=   -3.382 closest distance to " O   HOH Z 392 " =    1.240
peak=   -3.379 closest distance to " O   HOH Z 102 " =    1.729
peak=   -3.369 closest distance to " O   TYR A  15 " =    1.713
peak=   -3.366 closest distance to " CZ  TYR A 169 " =    1.970
peak=   -3.365 closest distance to " O   HOH Z 374 " =    1.889
peak=   -3.363 closest distance to " CB  ASP A 162 " =    2.559
peak=   -3.362 closest distance to " CG  LEU A  83 " =    1.982
peak=   -3.357 closest distance to " C   ASN A 148 " =    1.819
peak=   -3.351 closest distance to " CD2 HIS A 115 " =    1.018
peak=   -3.351 closest distance to " O   HOH Z 150 " =    1.806
peak=   -3.345 closest distance to " ND2 ASN A  39 " =    1.200
peak=   -3.344 closest distance to " CG1 VAL A 112 " =    2.610
peak=   -3.343 closest distance to " O   HOH Z 109 " =    3.241
peak=   -3.343 closest distance to " OG  SER A  87 " =    1.699
peak=   -3.340 closest distance to " N   ALA A 248 " =    1.794
peak=   -3.332 closest distance to " O   HOH Z 251 " =    1.658
peak=   -3.322 closest distance to " NE  ARG A 156 " =    1.690
peak=   -3.315 closest distance to " NE2 GLN A 278 " =    1.782
peak=   -3.315 closest distance to " CD1 ILE A 109 " =    2.708
peak=   -3.310 closest distance to " C   ALA A 158 " =    1.304
peak=   -3.307 closest distance to " O  BHOH Z 338 " =    1.330
peak=   -3.306 closest distance to " CD2 TYR A 293 " =    1.775
peak=   -3.306 closest distance to " OD1 ASP A 298 " =    1.857
peak=   -3.304 closest distance to " O   HOH Z 426 " =    1.646
peak=   -3.303 closest distance to " CA  ASN A 110 " =    1.083
peak=   -3.302 closest distance to " O   HOH Z 242 " =    1.638
peak=   -3.301 closest distance to " OG1 THR A  82 " =    1.557
peak=   -3.294 closest distance to " O   HOH Z  37 " =    1.478
peak=   -3.294 closest distance to " O   HOH Z 251 " =    5.036
peak=   -3.292 closest distance to " O   GLY A  80 " =    2.392
peak=   -3.292 closest distance to " O   HOH Z 157 " =    3.645
peak=   -3.292 closest distance to " CG2 THR A 182 " =    2.308
peak=   -3.284 closest distance to " O   HOH Z 171 " =    2.338
peak=   -3.282 closest distance to " NE2 GLN A  94 " =    1.841
peak=   -3.271 closest distance to " O   HOH Z 397 " =    1.112
peak=   -3.267 closest distance to " OD2 ASP A 191 " =    1.623
peak=   -3.266 closest distance to " OG BSER A 210 " =    1.211
peak=   -3.264 closest distance to " O   HOH Z   2 " =    2.393
peak=   -3.262 closest distance to " CE2 PHE A  61 " =    2.686
peak=   -3.259 closest distance to " O   HOH Z  52 " =    1.958
peak=   -3.258 closest distance to " O   HOH Z 424 " =    3.124
peak=   -3.257 closest distance to " O   HOH Z 196 " =    2.031
peak=   -3.253 closest distance to " O   HOH Z 166 " =    1.571
peak=   -3.250 closest distance to " O   HOH Z 137 " =    1.236
peak=   -3.246 closest distance to " O   HOH Z 200 " =    1.190
peak=   -3.241 closest distance to " CB  PRO A 213 " =    1.674
peak=   -3.238 closest distance to " ND2 ASN A 187 " =    1.614
peak=   -3.237 closest distance to " CG1 VAL A  78 " =    2.672
peak=   -3.236 closest distance to " O   SER A 146 " =    1.141
peak=   -3.236 closest distance to " O   HOH Z 118 " =    1.464
peak=   -3.235 closest distance to " CD  ARG A 139 " =    1.595
peak=   -3.231 closest distance to " CG2AVAL A  41 " =    2.917
peak=   -3.224 closest distance to " OXT GLY A 302 " =    3.130
peak=   -3.220 closest distance to " O   HOH Z  88 " =    4.544
peak=   -3.213 closest distance to " O   HOH Z 298 " =    3.627
peak=   -3.212 closest distance to " CB  SER A 146 " =    2.162
peak=   -3.207 closest distance to " O   HOH Z 103 " =    1.724
peak=   -3.207 closest distance to " O   HOH Z 106 " =    2.293
peak=   -3.206 closest distance to " OD1 ASN A 148 " =    1.446
peak=   -3.203 closest distance to " C   SER A 206 " =    1.485
peak=   -3.199 closest distance to " N   GLY A 302 " =    1.943
peak=   -3.199 closest distance to " OD2 ASP A 298 " =    1.037
peak=   -3.196 closest distance to " O  BHOH Z  74 " =    0.881
peak=   -3.192 closest distance to " O   HOH Z 149 " =    1.816
peak=   -3.191 closest distance to " O   HOH Z 364 " =    5.627
peak=   -3.189 closest distance to " NH2 ARG A 159 " =    2.569
peak=   -3.184 closest distance to " O   HOH Z 283 " =    2.029
peak=   -3.181 closest distance to " CE3 TRP A 274 " =    2.302
peak=   -3.178 closest distance to " O   HOH Z  10 " =    1.719
peak=   -3.177 closest distance to " O   HOH Z  40 " =    2.714
peak=   -3.172 closest distance to " O   HOH Z  19 " =    2.403
peak=   -3.170 closest distance to " O   HOH Z 336 " =    5.563
peak=   -3.169 closest distance to " CZ  PHE A  38 " =    2.324
peak=   -3.168 closest distance to " O   HOH Z 301 " =    2.263
peak=   -3.160 closest distance to " O   HOH Z 252 " =    4.124
peak=   -3.159 closest distance to " O   HOH Z 210 " =    1.507
peak=   -3.156 closest distance to " CA  ASN A 127 " =    1.073
peak=   -3.147 closest distance to " CG  PRO A 280 " =    2.330
peak=   -3.146 closest distance to " O   ARG A  79 " =    0.960
peak=   -3.140 closest distance to " O   ASN A 187 " =    1.597
peak=   -3.140 closest distance to " O   HOH Z 126 " =    1.859
peak=   -3.140 closest distance to " O   ALA A  10 " =    1.918
peak=   -3.138 closest distance to " CG  ARG A 269 " =    2.264
peak=   -3.136 closest distance to " O   HOH Z 145 " =    2.595
peak=   -3.135 closest distance to " CD2 TYR A 247 " =    2.316
peak=   -3.134 closest distance to " O   HOH Z 345 " =    2.852
peak=   -3.132 closest distance to " O   HOH Z 340 " =    1.693
peak=   -3.132 closest distance to " O   ALA A 256 " =    1.628
peak=   -3.131 closest distance to " OD2 ASP A 171 " =    1.876
peak=   -3.129 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.128 closest distance to " CD1 PHE A 130 " =    2.369
peak=   -3.128 closest distance to " CB  PRO A 163 " =    2.482
peak=   -3.127 closest distance to " O   HOH Z  41 " =    1.928
peak=   -3.125 closest distance to " O   HOH Z 252 " =    3.504
peak=   -3.120 closest distance to " O   HOH Z 348 " =    2.212
peak=   -3.120 closest distance to " O   HOH Z   1 " =    2.194
peak=   -3.114 closest distance to " CH2 TRP A 177 " =    2.012
peak=   -3.110 closest distance to " O   HOH Z 287 " =    2.415
peak=   -3.110 closest distance to " O   HOH Z 231 " =    2.370
peak=   -3.106 closest distance to " O   HOH Z  97 " =    1.237
peak=   -3.098 closest distance to " CD  GLN A  88 " =    0.964
peak=   -3.093 closest distance to " O   HOH Z 109 " =    5.960
peak=   -3.082 closest distance to " O   HOH Z 146 " =    1.338
peak=   -3.078 closest distance to " O   SER A 210 " =    1.967
peak=   -3.077 closest distance to " CG1 VAL A 197 " =    1.946
peak=   -3.060 closest distance to " O   GLY A  75 " =    1.887
peak=   -3.060 closest distance to " O   GLY A 241 " =    2.317
peak=   -3.043 closest distance to " O   HOH Z  44 " =    2.284

================= 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    :  0.4470 0.4330   6.265322e+00   6.238969e+00
   1_bss:  0.4381 0.4196   6.255848e+00   6.227101e+00
   1_xyz:  0.3517 0.3776   6.115323e+00   6.154780e+00
   1_adp:  0.3235 0.3861   6.065938e+00   6.165563e+00
   1_occ:  0.3231 0.3857   6.065013e+00   6.165438e+00
   2_bss:  0.3226 0.3836   6.065350e+00   6.165632e+00
   2_xyz:  0.2596 0.3145   5.878641e+00   6.019731e+00
   2_adp:  0.2423 0.3052   5.840456e+00   6.000319e+00
   2_occ:  0.2421 0.3047   5.839842e+00   5.999990e+00
   3_bss:  0.2420 0.3047   5.841124e+00   6.000443e+00
   3_xyz:  0.2044 0.2599   5.672225e+00   5.855271e+00
   3_adp:  0.1985 0.2504   5.644306e+00   5.821065e+00
   3_occ:  0.1984 0.2502   5.643683e+00   5.820591e+00
   4_bss:  0.1978 0.2496   5.644055e+00   5.819388e+00
   4_xyz:  0.1618 0.2070   5.457713e+00   5.653218e+00
   4_adp:  0.1464 0.1923   5.372067e+00   5.580705e+00
   4_occ:  0.1463 0.1922   5.371647e+00   5.580321e+00
   5_bss:  0.1466 0.1924   5.372755e+00   5.580058e+00
   5_xyz:  0.1268 0.1762   5.263225e+00   5.495892e+00
   5_adp:  0.1211 0.1724   5.228694e+00   5.470081e+00
   5_occ:  0.1211 0.1723   5.228416e+00   5.469765e+00
   5_bss:  0.1215 0.1724   5.229178e+00   5.469312e+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:  0.302  37.714  -2.115   5.202  -1.374   0.000  -0.000  -0.000
   1_xyz:  0.302  37.714  -2.115   5.202  -1.374   0.000  -0.000  -0.000
   1_adp:  0.302  37.714  -2.115   5.202  -1.374   0.000  -0.000  -0.000
   1_occ:  0.302  37.714  -2.115   5.202  -1.374   0.000  -0.000  -0.000
   2_bss:  0.304  45.797  -1.974   2.961  -0.560   0.000  -0.000  -0.000
   2_xyz:  0.304  45.797  -1.974   2.961  -0.560   0.000  -0.000  -0.000
   2_adp:  0.304  45.797  -1.974   2.961  -0.560   0.000  -0.000  -0.000
   2_occ:  0.304  45.797  -1.974   2.961  -0.560   0.000  -0.000  -0.000
   3_bss:  0.320  55.455  -1.827   1.481  -0.296   0.000  -0.000  -0.000
   3_xyz:  0.320  55.455  -1.827   1.481  -0.296   0.000  -0.000  -0.000
   3_adp:  0.320  55.455  -1.827   1.481  -0.296   0.000  -0.000  -0.000
   3_occ:  0.320  55.455  -1.827   1.481  -0.296   0.000  -0.000  -0.000
   4_bss:  0.321  58.066  -2.763  -0.401  -1.186  -0.000  -0.000  -0.000
   4_xyz:  0.321  58.066  -2.763  -0.401  -1.186  -0.000  -0.000  -0.000
   4_adp:  0.321  58.066  -2.763  -0.401  -1.186  -0.000  -0.000  -0.000
   4_occ:  0.321  58.066  -2.763  -0.401  -1.186  -0.000  -0.000  -0.000
   5_bss:  0.326  60.259  -3.050  -1.140  -1.202  -0.000  -0.000  -0.000
   5_xyz:  0.326  60.259  -3.050  -1.140  -1.202  -0.000  -0.000  -0.000
   5_adp:  0.326  60.259  -3.050  -1.140  -1.202  -0.000  -0.000  -0.000
   5_occ:  0.326  60.259  -3.050  -1.140  -1.202  -0.000  -0.000  -0.000
   5_bss:  0.327  66.014  -2.933  -1.255  -1.054  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.021 0.5222  0.6914    58971.236
   1_bss:  48.886 0.5353  0.7239    55637.121
   1_xyz:  43.106 0.6053  0.7985    43128.467
   1_adp:  43.582 0.5993  0.7969    44338.794
   1_occ:  43.535 0.5998  0.7958    44173.376
   2_bss:  43.221 0.6036  0.7922    43680.136
   2_xyz:  34.572 0.7050  0.9056    28194.167
   2_adp:  33.300 0.7200  0.9042    26721.099
   2_occ:  33.279 0.7203  0.9043    26678.965
   3_bss:  33.216 0.7212  0.8957    26690.325
   3_xyz:  26.744 0.7924  0.9577    17808.098
   3_adp:  25.177 0.8100  0.9850    16570.587
   3_occ:  25.156 0.8102  0.9857    16543.300
   4_bss:  25.069 0.8111  0.9456    16474.566
   4_xyz:  20.215 0.8592  0.9758    11052.881
   4_adp:  18.416 0.8765  0.9764     9537.589
   4_occ:  18.404 0.8766  0.9765     9532.412
   5_bss:  18.390 0.8767  0.9649     9512.923
   5_xyz:  16.548 0.8932  0.9745     8016.317
   5_adp:  15.958 0.8986  0.9691     7654.624
   5_occ:  15.950 0.8987  0.9690     7647.985
   5_bss:  15.935 0.8988  0.9702     7633.228
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7546e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7546e-01
   1_xyz:   1.467  0.011  0.089 15.333  0.005  4.108   1.1097e-01
   1_adp:   1.467  0.011  0.089 15.333  0.005  4.108   1.1097e-01
   1_occ:   1.467  0.011  0.089 15.333  0.005  4.108   1.1097e-01
   2_bss:   1.467  0.011  0.089 15.333  0.005  4.108   1.1097e-01
   2_xyz:   1.349  0.010  0.090 15.130  0.005  4.109   9.5370e-02
   2_adp:   1.349  0.010  0.090 15.130  0.005  4.109   9.5370e-02
   2_occ:   1.349  0.010  0.090 15.130  0.005  4.109   9.5370e-02
   3_bss:   1.349  0.010  0.090 15.130  0.005  4.109   9.5370e-02
   3_xyz:   1.006  0.007  0.065 14.496  0.004  4.118   6.0559e-02
   3_adp:   1.006  0.007  0.065 14.496  0.004  4.118   6.0559e-02
   3_occ:   1.006  0.007  0.065 14.496  0.004  4.118   6.0559e-02
   4_bss:   1.006  0.007  0.065 14.496  0.004  4.118   6.0559e-02
   4_xyz:   1.079  0.008  0.078 14.486  0.004  4.113   7.1786e-02
   4_adp:   1.079  0.008  0.078 14.486  0.004  4.113   7.1786e-02
   4_occ:   1.079  0.008  0.078 14.486  0.004  4.113   7.1786e-02
   5_bss:   1.079  0.008  0.078 14.486  0.004  4.113   7.1786e-02
   5_xyz:   1.134  0.009  0.080 14.813  0.004  4.113   7.4611e-02
   5_adp:   1.134  0.009  0.080 14.813  0.004  4.113   7.4611e-02
   5_occ:   1.134  0.009  0.080 14.813  0.004  4.113   7.4611e-02
   5_bss:   1.134  0.009  0.080 14.813  0.004  4.113   7.4611e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.494   2.4264e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.494   2.4264e-01
   1_xyz:   9.279  0.064  0.458 82.803  0.017  1.789   1.0428e-01
   1_adp:   9.279  0.064  0.458 82.803  0.017  1.789   1.0428e-01
   1_occ:   9.279  0.064  0.458 82.803  0.017  1.789   1.0428e-01
   2_bss:   9.279  0.064  0.458 82.803  0.017  1.789   1.0428e-01
   2_xyz:   7.832  0.050  0.318 88.322  0.031  2.180   9.6932e-02
   2_adp:   7.832  0.050  0.318 88.322  0.031  2.180   9.6932e-02
   2_occ:   7.832  0.050  0.318 88.322  0.031  2.180   9.6932e-02
   3_bss:   7.832  0.050  0.318 88.322  0.031  2.180   9.6932e-02
   3_xyz:   6.874  0.040  0.274 81.574  0.048  2.284   4.9427e-02
   3_adp:   6.874  0.040  0.274 81.574  0.048  2.284   4.9427e-02
   3_occ:   6.874  0.040  0.274 81.574  0.048  2.284   4.9427e-02
   4_bss:   6.874  0.040  0.274 81.574  0.048  2.284   4.9427e-02
   4_xyz:   7.328  0.063  0.225 79.536  0.036  2.291   1.4587e-01
   4_adp:   7.328  0.063  0.225 79.536  0.036  2.291   1.4587e-01
   4_occ:   7.328  0.063  0.225 79.536  0.036  2.291   1.4587e-01
   5_bss:   7.328  0.063  0.225 79.536  0.036  2.291   1.4587e-01
   5_xyz:   8.308  0.057  0.278 82.938  0.040  2.295   6.6770e-02
   5_adp:   8.308  0.057  0.278 82.938  0.040  2.295   6.6770e-02
   5_occ:   8.308  0.057  0.278 82.938  0.040  2.295   6.6770e-02
   5_bss:   8.308  0.057  0.278 82.938  0.040  2.295   6.6770e-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:  84.43   0.00  18.51  65.72   0.00  15.33  84.43   0.00  35.83
   1_occ:  84.43   0.00  18.51  65.72   0.00  15.33  84.43   0.00  35.83
   2_bss:  84.43   0.00  18.51  65.72   0.00  15.33  84.43   0.00  35.83
   2_xyz:  84.43   0.00  18.51  65.72   0.00  15.33  84.43   0.00  35.83
   2_adp:  87.17   0.00  18.25  81.39   0.00  14.75  87.17   2.02  37.33
   2_occ:  87.17   0.00  18.25  81.39   0.00  14.75  87.17   2.02  37.33
   3_bss:  87.17   0.00  18.25  81.39   0.00  14.75  87.17   2.02  37.33
   3_xyz:  87.17   0.00  18.25  81.39   0.00  14.75  87.17   2.02  37.33
   3_adp:  87.30   0.00  18.29  81.42   0.00  14.71  87.30   5.31  37.80
   3_occ:  87.30   0.00  18.29  81.42   0.00  14.71  87.30   5.31  37.80
   4_bss:  87.30   0.00  18.29  81.42   0.00  14.71  87.30   5.31  37.80
   4_xyz:  87.30   0.00  18.29  81.42   0.00  14.71  87.30   5.31  37.80
   4_adp:  87.54   1.48  17.96  87.10   1.48  13.76  87.54   5.03  40.83
   4_occ:  87.54   1.48  17.96  87.10   1.48  13.76  87.54   5.03  40.83
   5_bss:  87.54   1.48  17.96  87.10   1.48  13.76  87.54   5.03  40.83
   5_xyz:  87.54   1.48  17.96  87.10   1.48  13.76  87.54   5.03  40.83
   5_adp: 109.90   0.51  18.33 109.90   0.51  13.46 102.04   5.43  44.88
   5_occ: 109.90   0.51  18.33 109.90   0.51  13.46 102.04   5.43  44.88
   5_bss: 109.89   0.50  18.32 109.89   0.50  13.44 102.02   5.42  44.86
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.845    0.013    0.324
   1_adp:    1.845    0.013    0.324
   1_occ:    1.845    0.013    0.324
   2_bss:    1.845    0.013    0.324
   2_xyz:    1.589    0.020    0.522
   2_adp:    1.589    0.020    0.522
   2_occ:    1.589    0.020    0.522
   3_bss:    1.589    0.020    0.522
   3_xyz:    1.576    0.064    0.646
   3_adp:    1.576    0.064    0.646
   3_occ:    1.576    0.064    0.646
   4_bss:    1.576    0.064    0.646
   4_xyz:    1.541    0.044    0.736
   4_adp:    1.541    0.044    0.736
   4_occ:    1.541    0.044    0.736
   5_bss:    1.541    0.044    0.736
   5_xyz:    1.534    0.075    0.791
   5_adp:    1.534    0.075    0.791
   5_occ:    1.534    0.075    0.791
   5_bss:    1.534    0.075    0.791
------------------------------------------------------------------------

CPU time actual refinement: 338.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_358/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_358/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_358/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_358/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_358/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.71 
  Macro-tasks:
    bulk solvent and scale       = 39.38  
    individual site refinement   = 141.86 
    weights calculation          = 29.15  
    collect and process          = 6.47   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 216.96 
  Micro-tasks:
    mask                            = 3.00   
    f_calc                          = 108.84 
    alpha_beta                      = 8.24   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 117.74 
    fmodel                         = 6.02   
    r_factors                      = 0.18   
    phase_errors                   = 10.68  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 256.18 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.787 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    645 calls, 108.49 s
gradients_fft:          590 calls, 104.15 s

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

# Date 2008-01-16 Time 04:38:18 PST -0800 (1200487099.00 s)
Start R-work = 0.4470, R-free = 0.4330 (no bulk solvent and anisotropic scale)
Final R-work = 0.1436, R-free = 0.1901 (no bulk solvent and anisotropic scale)

Start R-work = 0.4381, R-free = 0.4196
Final R-work = 0.1215, R-free = 0.1724