# Date 2008-01-16 Time 04:13:11 PST -0800 (1200485591.99 s)
#phil __OFF__

Command line arguments: "../222.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26274
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 222

-------------------------------------------------------------------------------
  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: (68.845, 47.8686, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9401 1.96064
Completeness in resolution range: 0.944503
Completeness with d_max=infinity: 0.941643

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9401
                             d_min =   1.9606

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9401 1.96064
Completeness in resolution range: 0.944503
Completeness with d_max=infinity: 0.941643

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9406 -  4.1958 [2180/2209]  1960   220  10.1%
  bin  2:  4.1958 -  3.3426 [2090/2113]  1882   208  10.0%
  bin  3:  3.3426 -  2.9237 [2065/2090]  1857   208  10.1%
  bin  4:  2.9237 -  2.6580 [2027/2045]  1831   196   9.7%
  bin  5:  2.6580 -  2.4684 [2034/2076]  1822   212  10.4%
  bin  6:  2.4684 -  2.3234 [2027/2055]  1834   193   9.5%
  bin  7:  2.3234 -  2.2075 [2005/2041]  1800   205  10.2%
  bin  8:  2.2075 -  2.1116 [1994/2036]  1803   191   9.6%
  bin  9:  2.1116 -  2.0306 [1987/2045]  1783   204  10.3%
  bin 10:  2.0306 -  1.9606 [1180/2030]  1058   122  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_222/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: 0.11 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:
        1.21 -     1.95: 15
        1.95 -     2.69: 165
        2.69 -     3.43: 4525
        3.43 -     4.16: 9447
        4.16 -     4.90: 14475
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.215 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.436 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.609 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.617 3.040 -x+1/2,-y+1,z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.666 3.270 -x+1,y-1/2,-z+1/2
  ... (remaining 28622 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_222/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_222/model_refine_001.geo

CPU time processing inputs: 7.77


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.8686 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4671   r_free= 0.4614   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.273721                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.6800 0.99   1414  159 0.3740 0.3931      6.5578      6.6143|
|  2:  4.6800 -  3.7338 0.99   1360  151 0.4034 0.3950      6.7984      6.7801|
|  3:  3.7338 -  3.2674 0.99   1335  147 0.4279 0.4165      6.6527      6.7146|
|  4:  3.2674 -  2.9712 0.99   1323  139 0.4457 0.4194      6.5007      6.4413|
|  5:  2.9712 -  2.7597 0.99   1316  151 0.4871 0.4541      6.3567      6.3398|
|  6:  2.7597 -  2.5979 0.99   1307  148 0.4978 0.4870      6.2665      6.1512|
|  7:  2.5979 -  2.4684 0.98   1297  149 0.5058 0.4737      6.2538      6.1821|
|  8:  2.4684 -  2.3614 0.98   1321  136 0.5183 0.5320      6.1741      6.2158|
|  9:  2.3614 -  2.2708 0.99   1289  144 0.5430 0.5230      6.1281      6.1468|
| 10:  2.2708 -  2.1927 0.98   1297  145 0.5137 0.5508      6.1088      6.1369|
| 11:  2.1927 -  2.1243 0.97   1268  145 0.5245 0.5357      6.0239      6.0352|
| 12:  2.1243 -  2.0638 0.98   1285  148 0.5186 0.4895      5.9565      5.9941|
| 13:  2.0638 -  2.0096 0.92   1220  128 0.5164 0.5306      5.8843      5.8701|
| 14:  2.0096 -  1.9606 0.46    598   69 0.5280 0.5006      5.8345      5.6943|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9406 -  4.6800  1414   159  0.66  37.59   0.83     0.69      80450.47|
|  2:  4.6800 -  3.7338  1360   151  0.70  35.56   0.91     0.79     105843.50|
|  3:  3.7338 -  3.2674  1335   147  0.62  42.41   0.93     0.81     107519.10|
|  4:  3.2674 -  2.9712  1323   139  0.56  47.26   0.93     0.77      90083.71|
|  5:  2.9712 -  2.7597  1316   151  0.49  52.79   0.88     0.70      73279.88|
|  6:  2.7597 -  2.5979  1307   148  0.45  55.99   0.90     0.63      63693.42|
|  7:  2.5979 -  2.4684  1297   149  0.41  58.92   0.90     0.56      61811.41|
|  8:  2.4684 -  2.3614  1321   136  0.34  64.35   0.90     0.50      59813.83|
|  9:  2.3614 -  2.2708  1289   144  0.30  67.48   0.90     0.47      58014.40|
| 10:  2.2708 -  2.1927  1297   145  0.30  67.81   0.95     0.43      52846.15|
| 11:  2.1927 -  2.1243  1268   145  0.30  67.79   0.93     0.47      49123.05|
| 12:  2.1243 -  2.0638  1285   148  0.29  68.52   0.95     0.47      45107.98|
| 13:  2.0638 -  2.0096  1220   128  0.28  69.31   0.96     0.44      39218.10|
| 14:  2.0096 -  1.9606   598    69  0.24  72.35   0.92     0.33      32580.25|
|alpha:            min =        0.33 max =            0.81 mean =         0.59|
|beta:             min =    32580.25 max =       107519.10 mean =     67509.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.98 mean =        56.81|
|phase err.(test): min =        0.00 max =           89.92 mean =        56.70|
|-----------------------------------------------------------------------------|

============================== 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 = 9.458976              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.965   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.356427              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.197   (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 |  1.215 -  1.583:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.583 -  1.952:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.952 -  2.320:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.320 -  2.689:      139 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.689 -  3.057:     2209 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.057 -  3.426:     2316 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.426 -  3.794:     4109 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.794 -  4.163:     5338 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.163 -  4.531:     6467 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.531 -  4.900:     8008 |
|-----------------------------------------------------------------------------|
|-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 |        0.205 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.215 |       0.823 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4671   r_free= 0.4614   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.273721                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4595   r_free= 0.4520   ksol= 0.30   Bsol= 20.00   scale= 0.939   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,3.43,-0.01,0.00,-0.00,-0.00); trace/3= 0.76                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.266494                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.207821              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.618   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.251514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.925   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4595      final r-factor (work) = 0.3573          |
| start r-factor (free) = 0.4520      final r-factor (free) = 0.3800          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9256 = 8.21 * 0.50 * 6.2674 + 1.00 * 0.2046                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.3916 = 8.21 * 0.50 * 6.1585 + 1.00 * 0.1178                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3573      final r-factor (work) = 0.3208          |
| start r-factor (free) = 0.3800      final r-factor (free) = 0.3849          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7134 = 1.25 * 1.00 * 6.1585 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5851 = 1.25 * 1.00 * 6.0440 + 1.00 * 0.0210                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.75  19.96    None  None   None       |
|    all(noH): 2823   0      0.00    102.75  19.96    None  None   None       |
|    Sol.    : 438    0      0.00    102.75  39.09    None  None   None       |
|    Mac.    : 2385   0      0.00    92.00   16.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.275:  948   |   5:    51.376 -  61.651:   87        |
|      1:    10.275 -  20.550:  837   |   6:    61.651 -  71.926:   47        |
|      2:    20.550 -  30.826:  463   |   7:    71.926 -  82.202:   29        |
|      3:    30.826 -  41.101:  260   |   8:    82.202 -  92.477:    5        |
|      4:    41.101 -  51.376:  143   |   9:    92.477 - 102.752:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3208 r_free = 0.3849             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3205 r_free = 0.3851             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3205   r_free= 0.3851   ksol= 0.30   Bsol= 20.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,3.43,-0.01,0.00,-0.00,-0.00); trace/3= 0.76                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.049963                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3196   r_free= 0.3822   ksol= 0.31   Bsol= 35.91   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,2.08,-0.18,0.00,-0.00,-0.00); trace/3= 0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.048221                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.886187              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.149   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.964  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3196      final r-factor (work) = 0.2460          |
| start r-factor (free) = 0.3822      final r-factor (free) = 0.3015          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9462 = 7.89 * 0.50 * 6.0431 + 1.00 * 0.1178                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5398 = 7.89 * 0.50 * 5.9465 + 1.00 * 0.0920                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2460      final r-factor (work) = 0.2241          |
| start r-factor (free) = 0.3015      final r-factor (free) = 0.2814          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2675 = 0.55 * 1.00 * 5.9465 + 1.00 * 0.0209                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1682 = 0.55 * 1.00 * 5.7806 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.27   18.53    None  None   None       |
|    all(noH): 2823   0      0.00    96.27   18.53    None  None   None       |
|    Sol.    : 438    0      3.03    96.27   39.67    None  None   None       |
|    Mac.    : 2385   0      0.00    95.44   14.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.627:  944   |   5:    48.137 -  57.764:   93        |
|      1:     9.627 -  19.255:  990   |   6:    57.764 -  67.392:   56        |
|      2:    19.255 -  28.882:  365   |   7:    67.392 -  77.019:   22        |
|      3:    28.882 -  38.510:  195   |   8:    77.019 -  86.646:   13        |
|      4:    38.510 -  48.137:  138   |   9:    86.646 -  96.274:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2241 r_free = 0.2814             target_work(ml) = 5.751         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2238 r_free = 0.2815             target_work(ml) = 5.751         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2238   r_free= 0.2815   ksol= 0.31   Bsol= 35.91   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,2.08,-0.18,0.00,-0.00,-0.00); trace/3= 0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.750839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2235   r_free= 0.2810   ksol= 0.32   Bsol= 42.32   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,0.47,-0.72,0.00,-0.00,-0.00); trace/3= -0.74                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.749459                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.920735              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.596   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.950572              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.104  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2235      final r-factor (work) = 0.1636          |
| start r-factor (free) = 0.2810      final r-factor (free) = 0.2123          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2085 = 5.92 * 0.50 * 5.7819 + 1.00 * 0.0920                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7446 = 5.92 * 0.50 * 5.6314 + 1.00 * 0.0736                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1636      final r-factor (work) = 0.1454          |
| start r-factor (free) = 0.2123      final r-factor (free) = 0.1949          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3654 = 0.95 * 1.00 * 5.6314 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1582 = 0.95 * 1.00 * 5.4140 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.71   18.22    None  None   None       |
|    all(noH): 2823   0      0.00    96.71   18.22    None  None   None       |
|    Sol.    : 438    0      4.83    96.71   43.60    None  None   None       |
|    Mac.    : 2385   0      0.00    96.07   13.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.671:  957   |   5:    48.357 -  58.028:  109        |
|      1:     9.671 -  19.343: 1123   |   6:    58.028 -  67.699:   63        |
|      2:    19.343 -  29.014:  263   |   7:    67.699 -  77.370:   32        |
|      3:    29.014 -  38.685:  125   |   8:    77.370 -  87.042:   17        |
|      4:    38.685 -  48.357:  124   |   9:    87.042 -  96.713:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1454 r_free = 0.1949             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1453 r_free = 0.1949             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1453   r_free= 0.1949   ksol= 0.32   Bsol= 42.32   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,0.47,-0.72,0.00,-0.00,-0.00); trace/3= -0.74                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.366155                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1453   r_free= 0.1937   ksol= 0.31   Bsol= 48.48   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-0.84,-1.43,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.366255                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.490526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.166  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.993655              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.458  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1453      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1937      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8266 = 2.49 * 0.50 * 5.4230 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6742 = 2.49 * 0.50 * 5.3120 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2899 = 0.99 * 1.00 * 5.3120 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2239 = 0.99 * 1.00 * 5.2458 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    103.71  17.94    None  None   None       |
|    all(noH): 2823   0      1.06    103.71  17.94    None  None   None       |
|    Sol.    : 438    0      1.06    96.12   43.91    None  None   None       |
|    Mac.    : 2385   0      1.10    103.71  13.17    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:     1.063 -  11.327: 1333   |   5:    52.385 -  62.650:   88        |
|      1:    11.327 -  21.592:  899   |   6:    62.650 -  72.914:   52        |
|      2:    21.592 -  31.856:  171   |   7:    72.914 -  83.179:   20        |
|      3:    31.856 -  42.121:  119   |   8:    83.179 -  93.443:   16        |
|      4:    42.121 -  52.385:  120   |   9:    93.443 - 103.708:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1229 r_free = 0.1728             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1229 r_free = 0.1726             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1726   ksol= 0.31   Bsol= 48.48   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-0.84,-1.43,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.229511                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1727   ksol= 0.32   Bsol= 50.64   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-0.84,-1.43,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.229783                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.761215              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.398  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.608989              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.744  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6788 = 1.76 * 0.50 * 5.2457 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6476 = 1.76 * 0.50 * 5.2172 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1886 = 0.61 * 1.00 * 5.2172 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1749 = 0.61 * 1.00 * 5.1963 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    109.14  17.45    None  None   None       |
|    all(noH): 2823   0      0.96    109.14  17.45    None  None   None       |
|    Sol.    : 438    0      1.60    98.06   42.30    None  None   None       |
|    Mac.    : 2385   0      0.96    109.14  12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.960 -  11.778: 1456   |   5:    55.049 -  65.866:   76        |
|      1:    11.778 -  22.596:  814   |   6:    65.866 -  76.684:   32        |
|      2:    22.596 -  33.413:  173   |   7:    76.684 -  87.502:   13        |
|      3:    33.413 -  44.231:  130   |   8:    87.502 -  98.319:   10        |
|      4:    44.231 -  55.049:  117   |   9:    98.319 - 109.137:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1178 r_free = 0.1660             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1660             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1660   ksol= 0.32   Bsol= 50.64   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-0.84,-1.43,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.190841                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.6800 0.99   1414  159 0.1001 0.1324      5.3912      5.5576|
|  2:  4.6800 -  3.7338 0.99   1360  151 0.0850 0.1068      5.4391      5.6403|
|  3:  3.7338 -  3.2674 0.99   1335  147 0.1075 0.1591      5.4859      5.8587|
|  4:  3.2674 -  2.9712 0.99   1323  139 0.1313 0.1687      5.5056      5.6913|
|  5:  2.9712 -  2.7597 0.99   1316  151 0.1408 0.1797      5.3804        5.55|
|  6:  2.7597 -  2.5979 0.99   1307  148 0.1401 0.2173      5.2962       5.529|
|  7:  2.5979 -  2.4684 0.98   1297  149 0.1250 0.1646      5.1894      5.3804|
|  8:  2.4684 -  2.3614 0.98   1321  136 0.1277 0.1796      5.1411      5.3827|
|  9:  2.3614 -  2.2708 0.99   1289  144 0.1237 0.1977      5.0713      5.3607|
| 10:  2.2708 -  2.1927 0.98   1297  145 0.1204 0.1784       5.027      5.2384|
| 11:  2.1927 -  2.1243 0.97   1268  145 0.1203 0.1836      4.9515      5.2401|
| 12:  2.1243 -  2.0638 0.98   1285  148 0.1209 0.1716      4.8984       5.133|
| 13:  2.0638 -  2.0096 0.92   1220  128 0.1180 0.1870      4.8302      5.1219|
| 14:  2.0096 -  1.9606 0.46    598   69 0.1133 0.1991      4.7479      4.9977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9406 -  4.6800  1414   159  0.94   9.31   0.98     0.95       7276.21|
|  2:  4.6800 -  3.7338  1360   151  0.95   8.10   1.02     1.01       9190.11|
|  3:  3.7338 -  3.2674  1335   147  0.93  11.59   1.03     1.02      10699.64|
|  4:  3.2674 -  2.9712  1323   139  0.91  14.73   1.02     1.01      11361.38|
|  5:  2.9712 -  2.7597  1316   151  0.89  17.18   1.01     0.98       9388.18|
|  6:  2.7597 -  2.5979  1307   148  0.89  17.43   0.98     0.94       7936.72|
|  7:  2.5979 -  2.4684  1297   149  0.90  16.19   0.99     0.95       6646.30|
|  8:  2.4684 -  2.3614  1321   136  0.90  16.56   1.01     0.99       6247.40|
|  9:  2.3614 -  2.2708  1289   144  0.89  16.96   1.00     0.96       5495.88|
| 10:  2.2708 -  2.1927  1297   145  0.90  16.63   1.00     0.97       5089.78|
| 11:  2.1927 -  2.1243  1268   145  0.90  16.37   1.00     0.97       4459.97|
| 12:  2.1243 -  2.0638  1285   148  0.91  15.92   1.00     0.98       3987.33|
| 13:  2.0638 -  2.0096  1220   128  0.89  16.97   1.00     0.99       3636.04|
| 14:  2.0096 -  1.9606   598    69  0.90  16.69   0.98     0.93       3094.27|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     3094.27 max =        11361.38 mean =      6945.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.90|
|phase err.(test): min =        0.00 max =           89.04 mean =        14.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1658   ksol= 0.32   Bsol= 50.97   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-0.96,-1.24,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.192009                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1658   ksol= 0.32   Bsol= 50.97   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-0.96,-1.24,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.192009                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.6800 0.99   1414  159 0.1007 0.1312      5.3951      5.5563|
|  2:  4.6800 -  3.7338 0.99   1360  151 0.0867 0.1065      5.4498       5.647|
|  3:  3.7338 -  3.2674 0.99   1335  147 0.1076 0.1600      5.4906      5.8616|
|  4:  3.2674 -  2.9712 0.99   1323  139 0.1316 0.1687      5.5055      5.6879|
|  5:  2.9712 -  2.7597 0.99   1316  151 0.1406 0.1790      5.3786      5.5471|
|  6:  2.7597 -  2.5979 0.99   1307  148 0.1398 0.2166      5.2953      5.5284|
|  7:  2.5979 -  2.4684 0.98   1297  149 0.1249 0.1649      5.1894      5.3819|
|  8:  2.4684 -  2.3614 0.98   1321  136 0.1274 0.1796      5.1411      5.3844|
|  9:  2.3614 -  2.2708 0.99   1289  144 0.1233 0.1978      5.0698      5.3586|
| 10:  2.2708 -  2.1927 0.98   1297  145 0.1203 0.1787      5.0268      5.2405|
| 11:  2.1927 -  2.1243 0.97   1268  145 0.1202 0.1831      4.9508      5.2391|
| 12:  2.1243 -  2.0638 0.98   1285  148 0.1209 0.1719      4.8989      5.1348|
| 13:  2.0638 -  2.0096 0.92   1220  128 0.1180 0.1870      4.8306      5.1218|
| 14:  2.0096 -  1.9606 0.46    598   69 0.1133 0.1990      4.7476      4.9968|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9406 -  4.6800  1414   159  0.94   9.36   0.98     0.95       7272.43|
|  2:  4.6800 -  3.7338  1360   151  0.95   8.18   1.02     1.01       9296.81|
|  3:  3.7338 -  3.2674  1335   147  0.93  11.68   1.04     1.02      10830.56|
|  4:  3.2674 -  2.9712  1323   139  0.91  14.71   1.02     1.01      11309.17|
|  5:  2.9712 -  2.7597  1316   151  0.89  17.08   1.01     0.98       9320.49|
|  6:  2.7597 -  2.5979  1307   148  0.89  17.42   0.99     0.94       7936.41|
|  7:  2.5979 -  2.4684  1297   149  0.90  16.19   0.99     0.95       6650.99|
|  8:  2.4684 -  2.3614  1321   136  0.90  16.58   1.01     0.99       6263.78|
|  9:  2.3614 -  2.2708  1289   144  0.89  16.96   1.00     0.96       5497.49|
| 10:  2.2708 -  2.1927  1297   145  0.90  16.62   1.00     0.97       5083.81|
| 11:  2.1927 -  2.1243  1268   145  0.90  16.38   1.00     0.97       4460.33|
| 12:  2.1243 -  2.0638  1285   148  0.91  15.92   1.00     0.98       3994.14|
| 13:  2.0638 -  2.0096  1220   128  0.89  16.96   1.00     0.99       3636.76|
| 14:  2.0096 -  1.9606   598    69  0.90  16.68   0.99     0.94       3083.44|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     3083.44 max =        11309.17 mean =      6956.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.91|
|phase err.(test): min =        0.00 max =           89.36 mean =        14.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    109.10  17.41    None  None   None       |
|    all(noH): 2823   0      0.93    109.10  17.41    None  None   None       |
|    Sol.    : 438    0      1.57    98.03   42.27    None  None   None       |
|    Mac.    : 2385   0      0.93    109.10  12.85    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:     0.927 -  11.745: 1456   |   5:    55.016 -  65.833:   76        |
|      1:    11.745 -  22.563:  814   |   6:    65.833 -  76.651:   32        |
|      2:    22.563 -  33.380:  173   |   7:    76.651 -  87.469:   13        |
|      3:    33.380 -  44.198:  130   |   8:    87.469 -  98.286:   10        |
|      4:    44.198 -  55.016:  117   |   9:    98.286 - 109.104:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.693 - 5.038
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 308
   mapped sites are within: 0.759 - 5.038

peak=   10.058 closest distance to " CB  SER A 216 " =    1.188
peak=    5.787 closest distance to " O   HOH Z  52 " =    1.183
peak=    5.551 closest distance to " O   HOH Z 124 " =    1.555
peak=    5.439 closest distance to " O   HOH Z 102 " =    1.377
peak=    5.350 closest distance to " CB  SER A  63 " =    1.144
peak=    5.247 closest distance to " CG  PRO A  54 " =    1.236
peak=    5.220 closest distance to " CB  ARG A 275 " =    0.950
peak=    5.213 closest distance to " NH2 ARG A  56 " =    2.331
peak=    5.112 closest distance to " O   HOH Z 402 " =    1.584
peak=    5.009 closest distance to " CG  PRO A 213 " =    1.332
peak=    4.969 closest distance to " O   HOH Z  80 " =    1.930
peak=    4.954 closest distance to " O   HOH Z 401 " =    1.203
peak=    4.898 closest distance to " CB  GLN A 223 " =    1.415
peak=    4.814 closest distance to " CA  TYR A  30 " =    0.959
peak=    4.763 closest distance to " O   HOH Z 193 " =    1.742
peak=    4.688 closest distance to " O   HOH Z 389 " =    1.960
peak=    4.680 closest distance to " CG  PRO A 198 " =    1.234
peak=    4.655 closest distance to " O   HOH Z  97 " =    1.812
peak=    4.642 closest distance to " O   HOH Z 209 " =    2.321
peak=    4.574 closest distance to " O   HOH Z  39 " =    1.571
peak=    4.558 closest distance to " O   HOH Z 134 " =    1.764
peak=    4.454 closest distance to " O   HOH Z 232 " =    2.319
peak=    4.449 closest distance to " CG1 ILE A  33 " =    1.278
peak=    4.428 closest distance to " O   HOH Z 189 " =    1.947
peak=    4.411 closest distance to " CG  PRO A  90 " =    1.234
peak=    4.390 closest distance to " CD  ARG A 269 " =    1.134
peak=    4.369 closest distance to " O   HOH Z 403 " =    1.964
peak=    4.363 closest distance to " CB  PRO A  54 " =    0.895
peak=    4.362 closest distance to " O   HOH Z 272 " =    1.896
peak=    4.361 closest distance to " O   HOH Z 130 " =    2.574
peak=    4.360 closest distance to " O   SER A  87 " =    2.253
peak=    4.353 closest distance to " O   HOH Z 154 " =    1.732
peak=    4.353 closest distance to " O   HOH Z 247 " =    1.395
peak=    4.336 closest distance to " CG  ARG A  66 " =    1.059
peak=    4.325 closest distance to " O   HOH Z 154 " =    2.276
peak=    4.324 closest distance to " O   HOH Z  63 " =    1.991
peak=    4.318 closest distance to " O   HOH Z 236 " =    1.455
peak=    4.318 closest distance to " O   HOH Z 163 " =    1.548
peak=    4.315 closest distance to " O   HOH Z 132 " =    1.305
peak=    4.313 closest distance to " NZ  LYS A 117 " =    3.152
peak=    4.297 closest distance to " O   HOH Z 234 " =    3.643
peak=    4.285 closest distance to " O   HOH Z  15 " =    2.150
peak=    4.282 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.243 closest distance to " O   HOH Z  68 " =    1.894
peak=    4.239 closest distance to " O   HOH Z 298 " =    1.901
peak=    4.239 closest distance to " O   HOH Z 406 " =    1.502
peak=    4.232 closest distance to " O   HOH Z  44 " =    2.040
peak=    4.176 closest distance to " O   HOH Z 214 " =    1.234
peak=    4.167 closest distance to " CB  GLU A 277 " =    3.620
peak=    4.155 closest distance to " O   HOH Z 142 " =    1.490
peak=    4.155 closest distance to " O   HOH Z  43 " =    1.455
peak=    4.147 closest distance to " O   HOH Z 345 " =    1.961
peak=    4.139 closest distance to " O   GLY A  23 " =    2.389
peak=    4.136 closest distance to " CB  GLU A 128 " =    1.189
peak=    4.133 closest distance to " ND2 ASN A 187 " =    1.613
peak=    4.133 closest distance to " NH2BARG A 145 " =    2.234
peak=    4.129 closest distance to " O  BHOH Z  74 " =    1.303
peak=    4.128 closest distance to " O   HOH Z 352 " =    1.894
peak=    4.107 closest distance to " O   HOH Z 128 " =    2.183
peak=    4.091 closest distance to " O   HOH Z 227 " =    1.777
peak=    4.082 closest distance to " O   HOH Z 369 " =    2.486
peak=    4.046 closest distance to " O   HOH Z 414 " =    1.831
peak=    4.036 closest distance to " O   HOH Z 279 " =    2.088
peak=    4.008 closest distance to " C   PRO A 198 " =    1.535
peak=    3.991 closest distance to " O   HOH Z  40 " =    1.707
peak=    3.988 closest distance to " O   HOH Z 411 " =    3.465
peak=    3.966 closest distance to " O   HOH Z 132 " =    2.087
peak=    3.957 closest distance to " CB  SER A   3 " =    1.235
peak=    3.953 closest distance to " O   HOH Z 394 " =    1.542
peak=    3.941 closest distance to " CB  GLU A 152 " =    1.092
peak=    3.932 closest distance to " OE1 GLU A   2 " =    2.154
peak=    3.915 closest distance to " N   ASN A  39 " =    1.219
peak=    3.903 closest distance to " CE  LYS A 119 " =    1.190
peak=    3.892 closest distance to " CB  ARG A  79 " =    1.364
peak=    3.886 closest distance to " O   HOH Z 361 " =    3.022
peak=    3.877 closest distance to " O   HOH Z 423 " =    1.861
peak=    3.872 closest distance to " O   HOH Z 303 " =    2.077
peak=    3.862 closest distance to " O   HOH Z 126 " =    1.726
peak=    3.861 closest distance to " O   HOH Z 426 " =    1.422
peak=    3.858 closest distance to " CD2 TRP A 179 " =    1.405
peak=    3.840 closest distance to " O   HOH Z 316 " =    2.787
peak=    3.835 closest distance to " CA  ALA A  51 " =    0.923
peak=    3.832 closest distance to " CA  ASN A 176 " =    1.160
peak=    3.830 closest distance to " O   HOH Z 365 " =    2.542
peak=    3.825 closest distance to " CB  ARG A 190 " =    1.741
peak=    3.820 closest distance to " O   HOH Z 408 " =    1.775
peak=    3.815 closest distance to " CB  PHE A  16 " =    1.014
peak=    3.805 closest distance to " CB  ASN A 148 " =    1.328
peak=    3.804 closest distance to " CB  SER A 141 " =    1.018
peak=    3.803 closest distance to " CG  PRO A 243 " =    1.228
peak=    3.799 closest distance to " O   HOH Z 433 " =    1.465
peak=    3.797 closest distance to " O   HOH Z  54 " =    2.284
peak=    3.789 closest distance to " O   HOH Z 357 " =    1.728
peak=    3.784 closest distance to " CG2BVAL A  41 " =    0.872
peak=    3.782 closest distance to " O   HOH Z 334 " =    1.504
peak=    3.774 closest distance to " O   HOH Z 132 " =    2.451
peak=    3.774 closest distance to " CD  ARG A 159 " =    0.798
peak=    3.772 closest distance to " O   HOH Z 261 " =    1.782
peak=    3.770 closest distance to " CA  ARG A  36 " =    1.018
peak=    3.767 closest distance to " O   HOH Z  20 " =    1.423
peak=    3.765 closest distance to " CG  PRO A 198 " =    1.721
peak=    3.764 closest distance to " CG AARG A 275 " =    1.148
peak=    3.762 closest distance to " O   HOH Z 116 " =    1.121
peak=    3.748 closest distance to " CA  ARG A  66 " =    1.251
peak=    3.746 closest distance to " O   HOH Z 427 " =    3.076
peak=    3.745 closest distance to " CB  SER A  62 " =    0.820
peak=    3.732 closest distance to " O   HOH Z 346 " =    1.538
peak=    3.732 closest distance to " O   HOH Z  78 " =    1.732
peak=    3.725 closest distance to " O   HOH Z 345 " =    2.388
peak=    3.714 closest distance to " CB  TRP A 179 " =    1.097
peak=    3.713 closest distance to " O   HOH Z 120 " =    0.851
peak=    3.711 closest distance to " CB  ASP A 191 " =    1.275
peak=    3.706 closest distance to " CB  TYR A 169 " =    0.759
peak=    3.695 closest distance to " O   HOH Z 368 " =    1.940
peak=    3.695 closest distance to " O   HOH Z 173 " =    2.146
peak=    3.690 closest distance to " O   HOH Z 431 " =    1.129
peak=    3.685 closest distance to " CD  ARG A 195 " =    0.980
peak=    3.677 closest distance to " CB  VAL A 202 " =    1.549
peak=    3.670 closest distance to " OE1 GLN A  11 " =    1.886
peak=    3.643 closest distance to " O   HOH Z  54 " =    1.680
peak=    3.640 closest distance to " O   HOH Z  66 " =    2.176
peak=    3.639 closest distance to " O   HOH Z 126 " =    1.565
peak=    3.638 closest distance to " CG2 ILE A 120 " =    1.226
peak=    3.636 closest distance to " OG BSER A 210 " =    1.187
peak=    3.633 closest distance to " CB  PRO A  54 " =    1.358
peak=    3.629 closest distance to " O   HOH Z 133 " =    1.140
peak=    3.627 closest distance to " CA  ASP A 162 " =    1.144
peak=    3.621 closest distance to " O   HOH Z 245 " =    1.401
peak=    3.614 closest distance to " NE2 GLN A  11 " =    0.968
peak=    3.613 closest distance to " O   HOH Z  49 " =    1.334
peak=    3.598 closest distance to " CG2 VAL A 197 " =    1.164
peak=    3.592 closest distance to " O   HOH Z  61 " =    1.541
peak=    3.591 closest distance to " OH  TYR A  30 " =    1.193
peak=    3.591 closest distance to " CG2 ILE A  20 " =    1.433
peak=    3.583 closest distance to " CE1 HIS A 108 " =    1.188
peak=    3.582 closest distance to " O   HOH Z 337 " =    3.678
peak=    3.580 closest distance to " C   ILE A 106 " =    1.820
peak=    3.569 closest distance to " OG  SER A  62 " =    2.939
peak=    3.566 closest distance to " O   HOH Z 336 " =    1.647
peak=    3.562 closest distance to " N   TRP A 150 " =    1.224
peak=    3.558 closest distance to " CB  LEU A 228 " =    1.197
peak=    3.556 closest distance to " O   HOH Z 419 " =    2.666
peak=    3.553 closest distance to " CA  GLU A 152 " =    0.872
peak=    3.543 closest distance to " O   HOH Z  88 " =    3.461
peak=    3.538 closest distance to " O   HOH Z 163 " =    2.139
peak=    3.536 closest distance to " CA  ARG A 195 " =    1.319
peak=    3.532 closest distance to " O   HOH Z  63 " =    2.150
peak=    3.531 closest distance to " O   HOH Z 287 " =    1.728
peak=    3.521 closest distance to " NH2 ARG A 156 " =    1.143
peak=    3.516 closest distance to " CA  ALA A  21 " =    1.283
peak=    3.513 closest distance to " O   HOH Z  21 " =    1.828
peak=    3.511 closest distance to " O   HOH Z 427 " =    2.849
peak=    3.510 closest distance to " O   HOH Z 371 " =    3.160
peak=    3.503 closest distance to " CD  LYS A 166 " =    1.400
peak=    3.495 closest distance to " OG BSER A 164 " =    2.430
peak=    3.493 closest distance to " O   HOH Z 437 " =    1.451
peak=    3.490 closest distance to " CD1 LEU A  96 " =    0.819
peak=    3.490 closest distance to " NH1AARG A 275 " =    1.079
peak=    3.489 closest distance to " NH2AARG A 145 " =    2.102
peak=    3.483 closest distance to " O   HOH Z 425 " =    1.389
peak=    3.482 closest distance to " O   HOH Z 130 " =    1.136
peak=    3.478 closest distance to " CB  ALA A  71 " =    1.187
peak=    3.475 closest distance to " O   HOH Z 214 " =    3.101
peak=    3.473 closest distance to " O   HOH Z 250 " =    1.372
peak=    3.473 closest distance to " O   HOH Z 327 " =    1.766
peak=    3.468 closest distance to " O   HOH Z 412 " =    3.362
peak=    3.461 closest distance to " CB  ARG A 139 " =    0.764
peak=    3.459 closest distance to " CZ  PHE A  38 " =    1.420
peak=    3.457 closest distance to " O   HOH Z 271 " =    2.717
peak=    3.455 closest distance to " O   HOH Z 267 " =    1.945
peak=    3.451 closest distance to " O   HOH Z 128 " =    1.553
peak=    3.450 closest distance to " NZ  LYS A 119 " =    1.580
peak=    3.448 closest distance to " CB  GLN A 194 " =    0.963
peak=    3.448 closest distance to " O   HOH Z 423 " =    3.407
peak=    3.448 closest distance to " CB  ASN A 285 " =    0.943
peak=    3.445 closest distance to " CB  GLN A  58 " =    1.025
peak=    3.443 closest distance to " O   HOH Z 144 " =    1.780
peak=    3.440 closest distance to " O   HOH Z 435 " =    1.669
peak=    3.439 closest distance to " O   HOH Z 257 " =    2.203
peak=    3.438 closest distance to " CD2 LEU A 297 " =    0.957
peak=    3.436 closest distance to " CD  PRO A  54 " =    1.167
peak=    3.432 closest distance to " O   HOH Z 130 " =    2.541
peak=    3.428 closest distance to " CB  VAL A 265 " =    1.234
peak=    3.427 closest distance to " CB  SER A  26 " =    1.710
peak=    3.415 closest distance to " O   HOH Z 284 " =    2.881
peak=    3.411 closest distance to " O   HOH Z  47 " =    1.401
peak=    3.402 closest distance to " OD2 ASP A 286 " =    2.686
peak=    3.401 closest distance to " O   HOH Z 273 " =    2.737
peak=    3.397 closest distance to " O   HOH Z 185 " =    1.677
peak=    3.391 closest distance to " NE1 TRP A 274 " =    0.848
peak=    3.389 closest distance to " CD  ARG A 139 " =    1.355
peak=    3.388 closest distance to " O   HOH Z 156 " =    2.620
peak=    3.387 closest distance to " O   HOH Z 250 " =    1.800
peak=    3.387 closest distance to " O   HOH Z 404 " =    1.394
peak=    3.385 closest distance to " O   HOH Z 193 " =    2.278
peak=    3.385 closest distance to " O   HOH Z 374 " =    2.646
peak=    3.379 closest distance to " CB  ALA A 248 " =    1.321
peak=    3.379 closest distance to " CD  LYS A 119 " =    1.810
peak=    3.373 closest distance to " O   HOH Z 274 " =    1.607
peak=    3.371 closest distance to " O   HOH Z 128 " =    1.942
peak=    3.370 closest distance to " C   GLY A  80 " =    1.187
peak=    3.368 closest distance to " CD  GLN A 194 " =    1.679
peak=    3.368 closest distance to " O   HOH Z 155 " =    3.056
peak=    3.366 closest distance to " O   HOH Z 114 " =    1.239
peak=    3.358 closest distance to " OG1 THR A 294 " =    2.289
peak=    3.350 closest distance to " CG  GLN A  11 " =    1.469
peak=    3.346 closest distance to " CB  ALA A  34 " =    1.028
peak=    3.341 closest distance to " O   HOH Z 419 " =    1.537
peak=    3.340 closest distance to " CB  MET A  40 " =    0.830
peak=    3.338 closest distance to " CA  ASP A 191 " =    0.937
peak=    3.336 closest distance to " O   HOH Z  18 " =    1.288
peak=    3.333 closest distance to " O   HOH Z 282 " =    2.017
peak=    3.331 closest distance to " O   HOH Z 424 " =    3.891
peak=    3.330 closest distance to " CB  ARG A 269 " =    1.008
peak=    3.328 closest distance to " O   ALA A 165 " =    1.263
peak=    3.328 closest distance to " N   CYS A 260 " =    0.806
peak=    3.324 closest distance to " O   HOH Z 145 " =    2.231
peak=    3.319 closest distance to " O   HOH Z 194 " =    1.735
peak=    3.310 closest distance to " O   THR A 251 " =    1.254
peak=    3.298 closest distance to " O   HOH Z  85 " =    1.765
peak=    3.298 closest distance to " O   HOH Z 358 " =    2.042
peak=    3.294 closest distance to " CB  PRO A 198 " =    1.140
peak=    3.288 closest distance to " O   HOH Z 173 " =    1.678
peak=    3.285 closest distance to " CH2 TRP A 274 " =    2.047
peak=    3.285 closest distance to " O   HOH Z 263 " =    2.317
peak=    3.283 closest distance to " CD BLYS A 290 " =    1.076
peak=    3.282 closest distance to " O   HOH Z  97 " =    2.220
peak=    3.281 closest distance to " CG1BVAL A  72 " =    1.658
peak=    3.278 closest distance to " CA  ALA A  84 " =    1.238
peak=    3.277 closest distance to " O   HOH Z 313 " =    1.685
peak=    3.272 closest distance to " CG2 THR A 220 " =    0.851
peak=    3.272 closest distance to " O   HOH Z 298 " =    2.180
peak=    3.272 closest distance to " O   HOH Z 109 " =    1.329
peak=    3.267 closest distance to " CB  TRP A 266 " =    1.133
peak=    3.263 closest distance to " CB  PRO A 163 " =    3.941
peak=    3.262 closest distance to " CD  LYS A  76 " =    1.918
peak=    3.259 closest distance to " O   HOH Z 280 " =    2.498
peak=    3.257 closest distance to " CB  SER A 273 " =    0.877
peak=    3.257 closest distance to " CD  GLN A 240 " =    1.461
peak=    3.255 closest distance to " CB  MET A  47 " =    1.085
peak=    3.245 closest distance to " CA  GLN A 194 " =    0.935
peak=    3.244 closest distance to " O   HOH Z 421 " =    1.952
peak=    3.241 closest distance to " O   HOH Z 150 " =    1.498
peak=    3.240 closest distance to " O   HOH Z  35 " =    2.196
peak=    3.238 closest distance to " O   HOH Z 434 " =    1.354
peak=    3.229 closest distance to " CA  THR A 221 " =    0.998
peak=    3.226 closest distance to " O   HOH Z 171 " =    1.835
peak=    3.224 closest distance to " CA  VAL A 126 " =    1.119
peak=    3.223 closest distance to " OD1 ASN A 173 " =    1.698
peak=    3.220 closest distance to " O   HOH Z  51 " =    1.671
peak=    3.218 closest distance to " O   HOH Z 162 " =    1.629
peak=    3.210 closest distance to " O   HOH Z 402 " =    2.906
peak=    3.210 closest distance to " O   HOH Z 240 " =    2.078
peak=    3.209 closest distance to " CA  ASN A 215 " =    1.104
peak=    3.208 closest distance to " CG2 VAL A 257 " =    0.825
peak=    3.208 closest distance to " O   HOH Z 124 " =    2.921
peak=    3.208 closest distance to " O   HOH Z 162 " =    1.874
peak=    3.197 closest distance to " O   HOH Z 261 " =    1.875
peak=    3.195 closest distance to " O   SER A  26 " =    1.655
peak=    3.192 closest distance to " O   HOH Z  46 " =    1.327
peak=    3.189 closest distance to " ND2 ASN A 209 " =    1.646
peak=    3.188 closest distance to " O   HOH Z 299 " =    4.396
peak=    3.178 closest distance to " CB  VAL A 296 " =    1.462
peak=    3.177 closest distance to " O   HOH Z 147 " =    1.807
peak=    3.171 closest distance to " CB  THR A  52 " =    1.016
peak=    3.167 closest distance to " CA  VAL A  41 " =    0.915
peak=    3.166 closest distance to " CA  LYS A 117 " =    1.347
peak=    3.165 closest distance to " OD2 ASP A 298 " =    4.020
peak=    3.162 closest distance to " CB  GLN A 278 " =    0.815
peak=    3.162 closest distance to " O   HOH Z 353 " =    2.777
peak=    3.162 closest distance to " CD  ARG A  66 " =    1.328
peak=    3.159 closest distance to " CD2 HIS A  81 " =    1.072
peak=    3.159 closest distance to " CG2 VAL A 268 " =    1.030
peak=    3.158 closest distance to " O   HOH Z 291 " =    1.508
peak=    3.151 closest distance to " CB  ASN A  39 " =    0.854
peak=    3.147 closest distance to " CB  ALA A 291 " =    1.245
peak=    3.143 closest distance to " O   CYS A 168 " =    1.489
peak=    3.142 closest distance to " CG2 VAL A  78 " =    0.872
peak=    3.138 closest distance to " CB  ASN A 148 " =    1.943
peak=    3.134 closest distance to " CB  LEU A   5 " =    1.125
peak=    3.133 closest distance to " CA  ALA A 160 " =    0.902
peak=    3.128 closest distance to " NH1BARG A 145 " =    1.037
peak=    3.127 closest distance to " CG2 THR A  82 " =    0.847
peak=    3.126 closest distance to " NH1AARG A 145 " =    1.255
peak=    3.125 closest distance to " O   ASP A 124 " =    1.700
peak=    3.124 closest distance to " CB  PRO A 243 " =    1.223
peak=    3.120 closest distance to " O   HOH Z 264 " =    1.574
peak=    3.115 closest distance to " CA  PRO A  90 " =    0.885
peak=    3.113 closest distance to " N   ARG A 156 " =    1.477
peak=    3.111 closest distance to " OD1 ASN A  60 " =    1.425
peak=    3.108 closest distance to " CA  ASP A 140 " =    1.140
peak=    3.107 closest distance to " O   HOH Z 217 " =    2.110
peak=    3.104 closest distance to " OD1 ASN A  45 " =    1.405
peak=    3.101 closest distance to " CA  SER A  87 " =    1.082
peak=    3.098 closest distance to " CA  ASP A 124 " =    0.773
peak=    3.091 closest distance to " NZ  LYS A  76 " =    1.271
peak=    3.081 closest distance to " OG  SER A 245 " =    1.405
peak=    3.077 closest distance to " N   TYR A  15 " =    0.818
peak=    3.069 closest distance to " O   HOH Z 298 " =    5.038
peak=    3.066 closest distance to " NZ  LYS A 117 " =    1.319
peak=    3.055 closest distance to " OG BSER A 216 " =    3.092
peak=    3.028 closest distance to " N   ASP A 162 " =    1.363
peak=    3.023 closest distance to " CA  ARG A 156 " =    1.151
peak=    3.019 closest distance to " CZ3 TRP A 274 " =    2.458
peak=    3.018 closest distance to " O   HOH Z 392 " =    2.162

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.719 - 5.893
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.719 - 5.893

peak=   -4.904 closest distance to " O   HOH Z 266 " =    4.423
peak=   -4.801 closest distance to " C   HIS A 108 " =    1.065
peak=   -4.466 closest distance to " O   HOH Z 422 " =    1.140
peak=   -4.403 closest distance to " CA  VAL A  67 " =    2.886
peak=   -4.402 closest distance to " CD  ARG A 156 " =    2.078
peak=   -4.399 closest distance to " OXT GLY A 302 " =    2.785
peak=   -4.287 closest distance to " CG  MET A  93 " =    2.466
peak=   -4.273 closest distance to " O   HOH Z 210 " =    0.756
peak=   -4.195 closest distance to " O   HOH Z 377 " =    1.973
peak=   -4.191 closest distance to " O   HOH Z 155 " =    1.652
peak=   -4.186 closest distance to " O   HOH Z 165 " =    1.954
peak=   -4.151 closest distance to " O   TRP A  92 " =    1.886
peak=   -4.114 closest distance to " O   PRO A 163 " =    2.021
peak=   -4.022 closest distance to " OG BSER A 134 " =    1.421
peak=   -4.011 closest distance to " O   HOH Z 120 " =    1.077
peak=   -4.011 closest distance to " CD2 LEU A 237 " =    2.445
peak=   -4.003 closest distance to " O   HOH Z  52 " =    1.388
peak=   -3.953 closest distance to " C   THR A 279 " =    1.229
peak=   -3.950 closest distance to " O  BHOH Z 338 " =    1.374
peak=   -3.925 closest distance to " ND2 ASN A  69 " =    1.568
peak=   -3.916 closest distance to " O   PHE A 218 " =    1.470
peak=   -3.848 closest distance to " CB  ALA A 161 " =    2.496
peak=   -3.826 closest distance to " ND2 ASN A  45 " =    1.024
peak=   -3.822 closest distance to " O   ASN A 187 " =    1.446
peak=   -3.811 closest distance to " CD2 TYR A  30 " =    2.706
peak=   -3.810 closest distance to " CD2 LEU A 300 " =    2.771
peak=   -3.810 closest distance to " CD1 PHE A  59 " =    1.911
peak=   -3.809 closest distance to " O   HOH Z 401 " =    0.719
peak=   -3.792 closest distance to " O   PRO A 198 " =    1.336
peak=   -3.791 closest distance to " O   HOH Z  71 " =    1.557
peak=   -3.786 closest distance to " O   HOH Z 234 " =    4.018
peak=   -3.784 closest distance to " O   HOH Z 372 " =    2.390
peak=   -3.763 closest distance to " CA  SER A 276 " =    1.488
peak=   -3.733 closest distance to " O   HOH Z  52 " =    0.943
peak=   -3.724 closest distance to " OG  SER A  97 " =    2.057
peak=   -3.716 closest distance to " CD  ARG A 195 " =    5.043
peak=   -3.706 closest distance to " O   ALA A  34 " =    2.364
peak=   -3.697 closest distance to " CZ  TYR A 169 " =    1.898
peak=   -3.690 closest distance to " CG1AVAL A  41 " =    2.499
peak=   -3.682 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.680 closest distance to " OD2 ASP A 171 " =    2.202
peak=   -3.656 closest distance to " O   HOH Z 407 " =    3.277
peak=   -3.656 closest distance to " O   HOH Z 119 " =    2.077
peak=   -3.607 closest distance to " O   HOH Z 114 " =    3.546
peak=   -3.606 closest distance to " SG  CYS A 254 " =    3.301
peak=   -3.596 closest distance to " O   HOH Z 196 " =    1.893
peak=   -3.596 closest distance to " C   GLY A  91 " =    1.269
peak=   -3.593 closest distance to " O   HOH Z  97 " =    1.203
peak=   -3.589 closest distance to " O   HOH Z 423 " =    2.438
peak=   -3.580 closest distance to " CD1 LEU A 228 " =    2.164
peak=   -3.580 closest distance to " CD  GLN A  58 " =    1.257
peak=   -3.570 closest distance to " OD2 ASP A  50 " =    1.375
peak=   -3.564 closest distance to " N   ALA A 248 " =    1.822
peak=   -3.561 closest distance to " CD1 TYR A 247 " =    2.319
peak=   -3.552 closest distance to " O   HOH Z 348 " =    2.336
peak=   -3.544 closest distance to " NH2 ARG A  66 " =    5.146
peak=   -3.538 closest distance to " NE2 GLN A 223 " =    1.206
peak=   -3.530 closest distance to " ND2 ASN A  45 " =    1.100
peak=   -3.529 closest distance to " O   SER A  26 " =    1.254
peak=   -3.529 closest distance to " O   HOH Z 250 " =    1.421
peak=   -3.515 closest distance to " CG  GLU A  53 " =    1.314
peak=   -3.514 closest distance to " O   HOH Z 290 " =    0.937
peak=   -3.512 closest distance to " O   HOH Z 418 " =    1.361
peak=   -3.508 closest distance to " CG  ARG A 219 " =    2.312
peak=   -3.506 closest distance to " N   ALA A 226 " =    1.902
peak=   -3.502 closest distance to " O   VAL A 174 " =    1.935
peak=   -3.502 closest distance to " O   HOH Z 396 " =    1.893
peak=   -3.496 closest distance to " CB  ALA A 244 " =    2.056
peak=   -3.494 closest distance to " OE2 GLU A   2 " =    1.619
peak=   -3.492 closest distance to " ND2 ASN A  39 " =    1.217
peak=   -3.490 closest distance to " CB  LEU A 167 " =    2.119
peak=   -3.483 closest distance to " O   HOH Z 195 " =    3.450
peak=   -3.480 closest distance to " CE  MET A 105 " =    2.285
peak=   -3.473 closest distance to " OG  SER A   3 " =    1.645
peak=   -3.469 closest distance to " O   HOH Z  41 " =    2.184
peak=   -3.467 closest distance to " CD1 TRP A 179 " =    1.201
peak=   -3.466 closest distance to " OD1 ASP A 191 " =    1.467
peak=   -3.465 closest distance to " O   HOH Z  11 " =    1.773
peak=   -3.460 closest distance to " O   HOH Z  37 " =    1.779
peak=   -3.457 closest distance to " O   HOH Z 351 " =    1.494
peak=   -3.447 closest distance to " O   GLN A  11 " =    1.162
peak=   -3.442 closest distance to " OD1 ASN A  39 " =    2.263
peak=   -3.436 closest distance to " O   SER A 146 " =    0.918
peak=   -3.435 closest distance to " N   ALA A  43 " =    2.483
peak=   -3.432 closest distance to " O   ALA A 161 " =    2.677
peak=   -3.430 closest distance to " NH2 ARG A  79 " =    2.053
peak=   -3.415 closest distance to " CA  GLY A 133 " =    1.856
peak=   -3.402 closest distance to " O   HOH Z 197 " =    1.907
peak=   -3.400 closest distance to " CD2 PHE A 192 " =    2.026
peak=   -3.390 closest distance to " O   ALA A 161 " =    1.468
peak=   -3.384 closest distance to " O   THR A  52 " =    1.697
peak=   -3.383 closest distance to " O   GLY A  80 " =    2.462
peak=   -3.381 closest distance to " O   HOH Z  11 " =    1.795
peak=   -3.380 closest distance to " O   HOH Z  88 " =    4.426
peak=   -3.378 closest distance to " O   HOH Z  38 " =    1.533
peak=   -3.375 closest distance to " ND2 ASN A 187 " =    1.462
peak=   -3.374 closest distance to " O   HOH Z 150 " =    2.160
peak=   -3.373 closest distance to " O   HOH Z   6 " =    1.820
peak=   -3.366 closest distance to " O   HOH Z  15 " =    1.580
peak=   -3.365 closest distance to " O   HOH Z  56 " =    1.163
peak=   -3.360 closest distance to " CG1 VAL A 112 " =    2.654
peak=   -3.359 closest distance to " O   ALA A  10 " =    1.652
peak=   -3.355 closest distance to " O   SER A   3 " =    0.973
peak=   -3.353 closest distance to " O   VAL A  67 " =    2.804
peak=   -3.350 closest distance to " NH2 ARG A  66 " =    1.648
peak=   -3.349 closest distance to " C   ASN A 148 " =    1.655
peak=   -3.348 closest distance to " O   HOH Z 145 " =    2.161
peak=   -3.347 closest distance to " CZ2 TRP A  92 " =    2.677
peak=   -3.347 closest distance to " O   PRO A 198 " =    1.255
peak=   -3.345 closest distance to " C   SER A 206 " =    1.634
peak=   -3.339 closest distance to " CA  GLY A 203 " =    2.304
peak=   -3.338 closest distance to " O   HOH Z 283 " =    1.612
peak=   -3.335 closest distance to " O   HOH Z 198 " =    1.853
peak=   -3.329 closest distance to " O   ALA A 256 " =    1.439
peak=   -3.328 closest distance to " O   HOH Z  91 " =    2.134
peak=   -3.326 closest distance to " OG  SER A  62 " =    1.357
peak=   -3.322 closest distance to " O   HOH Z 251 " =    1.430
peak=   -3.321 closest distance to " O   HOH Z 377 " =    1.322
peak=   -3.317 closest distance to " O   ASN A  45 " =    1.743
peak=   -3.317 closest distance to " CE  LYS A 166 " =    2.907
peak=   -3.316 closest distance to " O   SER A 135 " =    1.534
peak=   -3.316 closest distance to " O   HOH Z 392 " =    1.521
peak=   -3.316 closest distance to " C   ASN A 285 " =    2.245
peak=   -3.312 closest distance to " O   TYR A  15 " =    1.668
peak=   -3.308 closest distance to " O   GLY A  75 " =    1.678
peak=   -3.307 closest distance to " O   HOH Z 149 " =    1.772
peak=   -3.306 closest distance to " O   HOH Z 265 " =    2.156
peak=   -3.306 closest distance to " CD  GLN A  58 " =    1.172
peak=   -3.304 closest distance to " O   HOH Z 424 " =    3.054
peak=   -3.303 closest distance to " CD2 TYR A 293 " =    1.907
peak=   -3.300 closest distance to " O   ALA A 160 " =    1.547
peak=   -3.296 closest distance to " N   GLN A  58 " =    1.805
peak=   -3.285 closest distance to " CG1BVAL A  72 " =    2.513
peak=   -3.283 closest distance to " CH2 TRP A 179 " =    1.304
peak=   -3.282 closest distance to " O   SER A 210 " =    1.892
peak=   -3.279 closest distance to " OE1 GLN A 183 " =    1.585
peak=   -3.278 closest distance to " NE2 GLN A  58 " =    2.608
peak=   -3.276 closest distance to " O   HOH Z 174 " =    2.245
peak=   -3.276 closest distance to " CD1 PHE A 130 " =    2.243
peak=   -3.273 closest distance to " O   HOH Z 427 " =    1.489
peak=   -3.271 closest distance to " NH1 ARG A  66 " =    0.897
peak=   -3.270 closest distance to " O   HOH Z 311 " =    3.327
peak=   -3.264 closest distance to " NE2 GLN A  88 " =    1.804
peak=   -3.262 closest distance to " CD  GLN A 223 " =    1.766
peak=   -3.259 closest distance to " O   HOH Z 353 " =    2.182
peak=   -3.250 closest distance to " O   HOH Z 109 " =    5.778
peak=   -3.250 closest distance to " CD1 ILE A 109 " =    2.126
peak=   -3.249 closest distance to " O   HOH Z  18 " =    1.563
peak=   -3.249 closest distance to " OD1 ASN A 148 " =    1.557
peak=   -3.249 closest distance to " CB  PRO A 163 " =    2.755
peak=   -3.247 closest distance to " O   MET A  40 " =    2.627
peak=   -3.245 closest distance to " O   HOH Z 191 " =    5.893
peak=   -3.238 closest distance to " C   ALA A 158 " =    1.273
peak=   -3.237 closest distance to " CB  ALA A 291 " =    2.365
peak=   -3.237 closest distance to " CG  ASP A 132 " =    2.257
peak=   -3.233 closest distance to " O   SER A  95 " =    1.670
peak=   -3.217 closest distance to " CB  ALA A 131 " =    2.308
peak=   -3.216 closest distance to " CB  SER A 210 " =    1.342
peak=   -3.214 closest distance to " O   HOH Z  39 " =    1.118
peak=   -3.205 closest distance to " CE3 TRP A 150 " =    2.341
peak=   -3.202 closest distance to " O   HOH Z  52 " =    1.714
peak=   -3.201 closest distance to " O   HOH Z 384 " =    1.841
peak=   -3.201 closest distance to " O   HOH Z 166 " =    1.491
peak=   -3.199 closest distance to " OD2 ASP A 191 " =    1.551
peak=   -3.193 closest distance to " CA  TYR A  68 " =    2.796
peak=   -3.193 closest distance to " NE2 GLN A 103 " =    1.656
peak=   -3.190 closest distance to " CG1 VAL A  78 " =    2.850
peak=   -3.188 closest distance to " O   HOH Z 126 " =    1.955
peak=   -3.181 closest distance to " O   HOH Z 196 " =    1.897
peak=   -3.178 closest distance to " C   ALA A 242 " =    1.889
peak=   -3.177 closest distance to " C   GLY A 133 " =    1.212
peak=   -3.177 closest distance to " O   HOH Z 174 " =    4.187
peak=   -3.176 closest distance to " CG  GLN A  11 " =    1.554
peak=   -3.174 closest distance to " O   LYS A 117 " =    1.694
peak=   -3.174 closest distance to " CD1 ILE A 106 " =    2.092
peak=   -3.167 closest distance to " O   GLN A 194 " =    1.515
peak=   -3.165 closest distance to " CG2 VAL A 189 " =    2.253
peak=   -3.162 closest distance to " O   MET A  47 " =    2.372
peak=   -3.159 closest distance to " O   HOH Z 426 " =    1.744
peak=   -3.139 closest distance to " CG  PRO A 243 " =    1.573
peak=   -3.134 closest distance to " O   HOH Z  78 " =    1.735
peak=   -3.125 closest distance to " O   HOH Z 111 " =    3.409
peak=   -3.125 closest distance to " N   ASP A 272 " =    1.171
peak=   -3.124 closest distance to " O   HOH Z 360 " =    2.566
peak=   -3.122 closest distance to " NH2BARG A 275 " =    1.803
peak=   -3.121 closest distance to " C   GLN A 144 " =    0.853
peak=   -3.115 closest distance to " CE1 TYR A 169 " =    2.113
peak=   -3.110 closest distance to " O   HOH Z 414 " =    2.510
peak=   -3.106 closest distance to " O   HOH Z 380 " =    4.439
peak=   -3.105 closest distance to " NH1 ARG A 195 " =    2.606
peak=   -3.092 closest distance to " O   HOH Z 378 " =    1.132
peak=   -3.081 closest distance to " CB  PRO A 213 " =    1.478
peak=   -3.077 closest distance to " O   HOH Z 428 " =    1.204
peak=   -3.074 closest distance to " N   VAL A 189 " =    1.685
peak=   -3.067 closest distance to " C   THR A 264 " =    1.414
peak=   -3.066 closest distance to " O   HOH Z 369 " =    2.214
peak=   -3.056 closest distance to " O   HOH Z 280 " =    2.245
peak=   -3.047 closest distance to " O   HOH Z 222 " =    1.303
peak=   -3.042 closest distance to " OG BSER A 134 " =    1.741
peak=   -3.032 closest distance to " O   HOH Z 397 " =    1.217
peak=   -3.024 closest distance to " O   HOH Z 411 " =    3.478
peak=   -3.017 closest distance to " O   HOH Z 393 " =    1.265

================= 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    :  0.4671 0.4614   6.273721e+00   6.265187e+00
   1_bss:  0.4595 0.4520   6.266494e+00   6.252714e+00
   1_xyz:  0.3573 0.3800   6.106154e+00   6.142760e+00
   1_adp:  0.3208 0.3849   6.050667e+00   6.159617e+00
   1_occ:  0.3205 0.3851   6.049963e+00   6.159448e+00
   2_bss:  0.3196 0.3822   6.048221e+00   6.158331e+00
   2_xyz:  0.2460 0.3015   5.818162e+00   5.979892e+00
   2_adp:  0.2241 0.2814   5.751309e+00   5.925019e+00
   2_occ:  0.2238 0.2815   5.750839e+00   5.924643e+00
   3_bss:  0.2235 0.2810   5.749459e+00   5.922108e+00
   3_xyz:  0.1636 0.2123   5.467566e+00   5.671704e+00
   3_adp:  0.1454 0.1949   5.366487e+00   5.584946e+00
   3_occ:  0.1453 0.1949   5.366155e+00   5.585006e+00
   4_bss:  0.1453 0.1937   5.366255e+00   5.582879e+00
   4_xyz:  0.1275 0.1773   5.261375e+00   5.491141e+00
   4_adp:  0.1229 0.1728   5.229989e+00   5.462812e+00
   4_occ:  0.1229 0.1726   5.229511e+00   5.462505e+00
   5_bss:  0.1228 0.1727   5.229783e+00   5.462668e+00
   5_xyz:  0.1189 0.1676   5.200071e+00   5.434796e+00
   5_adp:  0.1178 0.1660   5.191071e+00   5.425658e+00
   5_occ:  0.1178 0.1660   5.190841e+00   5.425817e+00
   5_bss:  0.1180 0.1658   5.192009e+00   5.426197e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000  -1.135   3.431  -0.010   0.000  -0.000  -0.000
   1_xyz:  0.300  20.000  -1.135   3.431  -0.010   0.000  -0.000  -0.000
   1_adp:  0.300  20.000  -1.135   3.431  -0.010   0.000  -0.000  -0.000
   1_occ:  0.300  20.000  -1.135   3.431  -0.010   0.000  -0.000  -0.000
   2_bss:  0.306  35.906  -1.535   2.079  -0.176   0.000  -0.000  -0.000
   2_xyz:  0.306  35.906  -1.535   2.079  -0.176   0.000  -0.000  -0.000
   2_adp:  0.306  35.906  -1.535   2.079  -0.176   0.000  -0.000  -0.000
   2_occ:  0.306  35.906  -1.535   2.079  -0.176   0.000  -0.000  -0.000
   3_bss:  0.316  42.321  -1.968   0.472  -0.722   0.000  -0.000  -0.000
   3_xyz:  0.316  42.321  -1.968   0.472  -0.722   0.000  -0.000  -0.000
   3_adp:  0.316  42.321  -1.968   0.472  -0.722   0.000  -0.000  -0.000
   3_occ:  0.316  42.321  -1.968   0.472  -0.722   0.000  -0.000  -0.000
   4_bss:  0.307  48.482  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   4_xyz:  0.307  48.482  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   4_adp:  0.307  48.482  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   4_occ:  0.307  48.482  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   5_bss:  0.319  50.639  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   5_xyz:  0.319  50.639  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   5_adp:  0.319  50.639  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   5_occ:  0.319  50.639  -2.772  -0.840  -1.425  -0.000  -0.000  -0.000
   5_bss:  0.321  50.966  -2.646  -0.955  -1.240  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.796 0.4349  0.5882    67497.768
   1_bss:  55.671 0.4478  0.6233    63969.314
   1_xyz:  42.440 0.6130  0.8274    41496.489
   1_adp:  43.510 0.5994  0.8201    43272.295
   1_occ:  43.518 0.5993  0.8188    43222.488
   2_bss:  43.199 0.6031  0.8085    42680.089
   2_xyz:  32.563 0.7270  0.9491    24809.028
   2_adp:  29.568 0.7618  0.9639    21559.804
   2_occ:  29.545 0.7621  0.9636    21526.432
   3_bss:  29.378 0.7638  0.9369    21293.367
   3_xyz:  20.899 0.8521  1.0079    11511.033
   3_adp:  18.577 0.8748  1.0126     9641.204
   3_occ:  18.574 0.8749  1.0127     9647.888
   4_bss:  18.473 0.8757  0.9797     9557.628
   4_xyz:  16.464 0.8939  0.9854     7885.846
   4_adp:  15.750 0.9005  0.9797     7496.346
   4_occ:  15.739 0.9006  0.9797     7489.867
   5_bss:  15.746 0.9006  0.9798     7500.040
   5_xyz:  15.089 0.9061  0.9831     7035.052
   5_adp:  14.857 0.9083  0.9776     6946.019
   5_occ:  14.856 0.9083  0.9776     6944.122
   5_bss:  14.863 0.9082  0.9790     6954.414
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.0463e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.0463e-01
   1_xyz:   1.495  0.011  0.087 15.436  0.006  4.105   1.1783e-01
   1_adp:   1.495  0.011  0.087 15.436  0.006  4.105   1.1783e-01
   1_occ:   1.495  0.011  0.087 15.436  0.006  4.105   1.1783e-01
   2_bss:   1.495  0.011  0.087 15.436  0.006  4.105   1.1783e-01
   2_xyz:   1.320  0.009  0.084 15.008  0.006  4.107   9.2039e-02
   2_adp:   1.320  0.009  0.084 15.008  0.006  4.107   9.2039e-02
   2_occ:   1.320  0.009  0.084 15.008  0.006  4.107   9.2039e-02
   3_bss:   1.320  0.009  0.084 15.008  0.006  4.107   9.2039e-02
   3_xyz:   1.129  0.009  0.071 14.760  0.005  4.117   7.3591e-02
   3_adp:   1.129  0.009  0.071 14.760  0.005  4.117   7.3591e-02
   3_occ:   1.129  0.009  0.071 14.760  0.005  4.117   7.3591e-02
   4_bss:   1.129  0.009  0.071 14.760  0.005  4.117   7.3591e-02
   4_xyz:   1.025  0.006  0.070 14.632  0.004  4.110   5.9400e-02
   4_adp:   1.025  0.006  0.070 14.632  0.004  4.110   5.9400e-02
   4_occ:   1.025  0.006  0.070 14.632  0.004  4.110   5.9400e-02
   5_bss:   1.025  0.006  0.070 14.632  0.004  4.110   5.9400e-02
   5_xyz:   0.954  0.006  0.068 14.429  0.004  4.112   5.3242e-02
   5_adp:   0.954  0.006  0.068 14.429  0.004  4.112   5.3242e-02
   5_occ:   0.954  0.006  0.068 14.429  0.004  4.112   5.3242e-02
   5_bss:   0.954  0.006  0.068 14.429  0.004  4.112   5.3242e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.215   2.4155e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.215   2.4155e-01
   1_xyz:   8.977  0.059  0.380 84.666  0.027  2.065   9.7750e-02
   1_adp:   8.977  0.059  0.380 84.666  0.027  2.065   9.7750e-02
   1_occ:   8.977  0.059  0.380 84.666  0.027  2.065   9.7750e-02
   2_bss:   8.977  0.059  0.380 84.666  0.027  2.065   9.7750e-02
   2_xyz:   8.184  0.050  0.330 82.357  0.046  2.250   1.1484e-01
   2_adp:   8.184  0.050  0.330 82.357  0.046  2.250   1.1484e-01
   2_occ:   8.184  0.050  0.330 82.357  0.046  2.250   1.1484e-01
   3_bss:   8.184  0.050  0.330 82.357  0.046  2.250   1.1484e-01
   3_xyz:   7.239  0.064  0.223 79.892  0.039  2.150   8.9621e-02
   3_adp:   7.239  0.064  0.223 79.892  0.039  2.150   8.9621e-02
   3_occ:   7.239  0.064  0.223 79.892  0.039  2.150   8.9621e-02
   4_bss:   7.239  0.064  0.223 79.892  0.039  2.150   8.9621e-02
   4_xyz:   6.822  0.043  0.219 82.508  0.033  2.327   4.4344e-02
   4_adp:   6.822  0.043  0.219 82.508  0.033  2.327   4.4344e-02
   4_occ:   6.822  0.043  0.219 82.508  0.033  2.327   4.4344e-02
   5_bss:   6.822  0.043  0.219 82.508  0.033  2.327   4.4344e-02
   5_xyz:   6.757  0.041  0.220 81.515  0.033  2.333   3.3776e-02
   5_adp:   6.757  0.041  0.220 81.515  0.033  2.333   3.3776e-02
   5_occ:   6.757  0.041  0.220 81.515  0.033  2.333   3.3776e-02
   5_bss:   6.757  0.041  0.220 81.515  0.033  2.333   3.3776e-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: 102.75   0.00  19.96  92.00   0.00  16.45 102.75   0.00  39.09
   1_occ: 102.75   0.00  19.96  92.00   0.00  16.45 102.75   0.00  39.09
   2_bss: 102.75   0.00  19.96  92.00   0.00  16.45 102.75   0.00  39.09
   2_xyz: 102.75   0.00  19.96  92.00   0.00  16.45 102.75   0.00  39.09
   2_adp:  96.27   0.00  18.53  95.44   0.00  14.65  96.27   3.03  39.67
   2_occ:  96.27   0.00  18.53  95.44   0.00  14.65  96.27   3.03  39.67
   3_bss:  96.27   0.00  18.53  95.44   0.00  14.65  96.27   3.03  39.67
   3_xyz:  96.27   0.00  18.53  95.44   0.00  14.65  96.27   3.03  39.67
   3_adp:  96.71   0.00  18.22  96.07   0.00  13.56  96.71   4.83  43.60
   3_occ:  96.71   0.00  18.22  96.07   0.00  13.56  96.71   4.83  43.60
   4_bss:  96.71   0.00  18.22  96.07   0.00  13.56  96.71   4.83  43.60
   4_xyz:  96.71   0.00  18.22  96.07   0.00  13.56  96.71   4.83  43.60
   4_adp: 103.71   1.06  17.94 103.71   1.10  13.17  96.12   1.06  43.91
   4_occ: 103.71   1.06  17.94 103.71   1.10  13.17  96.12   1.06  43.91
   5_bss: 103.71   1.06  17.94 103.71   1.10  13.17  96.12   1.06  43.91
   5_xyz: 103.71   1.06  17.94 103.71   1.10  13.17  96.12   1.06  43.91
   5_adp: 109.14   0.96  17.45 109.14   0.96  12.88  98.06   1.60  42.30
   5_occ: 109.14   0.96  17.45 109.14   0.96  12.88  98.06   1.60  42.30
   5_bss: 109.10   0.93  17.41 109.10   0.93  12.85  98.03   1.57  42.27
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.809    0.019    0.326
   1_adp:    2.809    0.019    0.326
   1_occ:    2.809    0.019    0.326
   2_bss:    2.809    0.019    0.326
   2_xyz:    2.145    0.037    0.566
   2_adp:    2.145    0.037    0.566
   2_occ:    2.145    0.037    0.566
   3_bss:    2.145    0.037    0.566
   3_xyz:    2.089    0.081    0.710
   3_adp:    2.089    0.081    0.710
   3_occ:    2.089    0.081    0.710
   4_bss:    2.089    0.081    0.710
   4_xyz:    1.942    0.101    0.755
   4_adp:    1.942    0.101    0.755
   4_occ:    1.942    0.101    0.755
   5_bss:    1.942    0.101    0.755
   5_xyz:    1.962    0.086    0.774
   5_adp:    1.962    0.086    0.774
   5_occ:    1.962    0.086    0.774
   5_bss:    1.962    0.086    0.774
------------------------------------------------------------------------

CPU time actual refinement: 285.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_222/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_222/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_222/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_222/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_222/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 285.71 
  Macro-tasks:
    bulk solvent and scale       = 38.03  
    individual site refinement   = 111.96 
    weights calculation          = 24.42  
    collect and process          = 5.42   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 179.92 
  Micro-tasks:
    mask                            = 2.01   
    f_calc                          = 91.10  
    alpha_beta                      = 6.86   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 97.06  
    fmodel                         = 5.99   
    r_factors                      = 0.19   
    phase_errors                   = 8.63   
    foms                           = 0.30   
    TOTAL for micro-tasks          = 213.13 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.103 micro seconds
Total CPU time: 4.95 minutes
from_scatterers_fft:    639 calls, 90.69 s
gradients_fft:          584 calls, 86.24 s

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

# Date 2008-01-16 Time 04:18:09 PST -0800 (1200485889.03 s)
Start R-work = 0.4671, R-free = 0.4614 (no bulk solvent and anisotropic scale)
Final R-work = 0.1399, R-free = 0.1840 (no bulk solvent and anisotropic scale)

Start R-work = 0.4595, R-free = 0.4520
Final R-work = 0.1180, R-free = 0.1658