# Date 2008-01-16 Time 06:27:57 PST -0800 (1200493677.78 s)
#phil __OFF__

Command line arguments: "../1151.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8789
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1151

-------------------------------------------------------------------------------
  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: (71.655, 46.93, 87.2539, 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: 2.76, per 1000 atoms: 0.98


================================== 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: (71.655, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.00276
Completeness in resolution range: 0.961612
Completeness with d_max=infinity: 0.958694

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2528
                             d_min =   2.0028

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: (71.655, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.00276
Completeness in resolution range: 0.961612
Completeness with d_max=infinity: 0.958694

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2532 -  4.2859 [2137/2162]  1924   213  10.0%
  bin  2:  4.2859 -  3.4144 [2050/2070]  1845   205  10.0%
  bin  3:  3.4144 -  2.9865 [2040/2059]  1835   205  10.0%
  bin  4:  2.9865 -  2.7151 [2005/2035]  1806   199   9.9%
  bin  5:  2.7151 -  2.5214 [2007/2026]  1810   197   9.8%
  bin  6:  2.5214 -  2.3733 [1984/2009]  1778   206  10.4%
  bin  7:  2.3733 -  2.2549 [1972/2000]  1776   196   9.9%
  bin  8:  2.2549 -  2.1570 [1973/2009]  1776   197  10.0%
  bin  9:  2.1570 -  2.0742 [1971/2013]  1778   193   9.8%
  bin 10:  2.0742 -  2.0028 [1450/1988]  1302   148  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1151/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: 0.12 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:
        1.81 -     2.42: 8
        2.42 -     3.04: 2168
        3.04 -     3.66: 4591
        3.66 -     4.28: 8912
        4.28 -     4.90: 12240
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.866 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.246 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27914 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_1151/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1151/model_refine_001.geo

CPU time processing inputs: 7.75


============================ 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 = 71.655 46.93 87.2539 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: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3383   r_free= 0.3302   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.074935                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.7805 0.99   1390  155 0.2884 0.2667      6.3594       6.273|
|  2:  4.7805 -  3.8140 0.99   1336  150 0.2712 0.2536      6.5014       6.426|
|  3:  3.8140 -  3.3376 0.99   1316  141 0.2938 0.2770      6.3678      6.3973|
|  4:  3.3376 -  3.0351 0.99   1304  151 0.3025 0.3165      6.2507       6.224|
|  5:  3.0351 -  2.8190 0.99   1296  144 0.3515 0.3484      6.1516      6.2094|
|  6:  2.8190 -  2.6537 0.99   1296  137 0.3457 0.3379      6.0563      5.9959|
|  7:  2.6537 -  2.5214 0.99   1282  141 0.3725 0.3749      6.0587      6.1503|
|  8:  2.5214 -  2.4121 0.98   1273  148 0.3771 0.3372      6.0194      5.9466|
|  9:  2.4121 -  2.3196 0.98   1258  145 0.3788 0.3686      5.9532      5.9468|
| 10:  2.3196 -  2.2398 1.00   1292  138 0.3814 0.3597      5.9369      5.9169|
| 11:  2.2398 -  2.1700 0.97   1266  138 0.4003 0.4244      5.9147      5.9939|
| 12:  2.1700 -  2.1081 0.98   1249  141 0.3900 0.4149      5.8348      5.9181|
| 13:  2.1081 -  2.0527 0.99   1280  140 0.4082 0.3777      5.7517      5.6731|
| 14:  2.0527 -  2.0028 0.62    792   90 0.3765 0.3986      5.6764      5.6975|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.7805  1390   155  0.80  24.94   0.85     0.82      38859.40|
|  2:  4.7805 -  3.8140  1336   150  0.84  21.77   0.96     0.90      44772.84|
|  3:  3.8140 -  3.3376  1316   141  0.79  26.85   0.97     0.91      46883.68|
|  4:  3.3376 -  3.0351  1304   151  0.76  29.93   0.97     0.89      43063.58|
|  5:  3.0351 -  2.8190  1296   144  0.69  36.67   0.97     0.85      38176.90|
|  6:  2.8190 -  2.6537  1296   137  0.68  37.39   0.98     0.84      32652.11|
|  7:  2.6537 -  2.5214  1282   141  0.67  37.88   0.97     0.83      30406.24|
|  8:  2.5214 -  2.4121  1273   148  0.68  37.29   0.97     0.86      27676.90|
|  9:  2.4121 -  2.3196  1258   145  0.67  38.71   1.00     0.86      26437.48|
| 10:  2.3196 -  2.2398  1292   138  0.64  40.93   1.02     0.84      25611.01|
| 11:  2.2398 -  2.1700  1266   138  0.62  42.87   1.01     0.82      25777.48|
| 12:  2.1700 -  2.1081  1249   141  0.62  42.55   1.01     0.84      24208.62|
| 13:  2.1081 -  2.0527  1280   140  0.61  43.30   0.99     0.85      20220.58|
| 14:  2.0527 -  2.0028   792    90  0.66  39.14   1.02     0.84      14798.80|
|alpha:            min =        0.82 max =            0.91 mean =         0.85|
|beta:             min =    14798.80 max =        46883.68 mean =     32020.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           90.00 mean =        35.48|
|phase err.(test): min =        0.00 max =           89.98 mean =        34.92|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.025282              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.752   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.750535              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.816   (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 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      173 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1995 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1823 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2768 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4587 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4325 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5574 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6666 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.141 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.260)------------------------------------------|
|    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: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3383   r_free= 0.3302   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.074935                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3246   r_free= 0.3196   ksol= 0.30   Bsol= 50.00   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.56,-3.32,0.18,-0.00,0.00,0.00); trace/3= -0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.054439                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.292929              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.891   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.435334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.476   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3246      final r-factor (work) = 0.1774          |
| start r-factor (free) = 0.3196      final r-factor (free) = 0.2012          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2210 = 6.29 * 0.50 * 6.0574 + 1.00 * 0.1616                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2317 = 6.29 * 0.50 * 5.7695 + 1.00 * 0.0780                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1774      final r-factor (work) = 0.1606          |
| start r-factor (free) = 0.2012      final r-factor (free) = 0.2043          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5180 = 0.44 * 1.00 * 5.7695 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3742 = 0.44 * 1.00 * 5.4317 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.260)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.33   17.45    None  None   None       |
|    all(noH): 2823   0      0.00    75.33   17.45    None  None   None       |
|    Sol.    : 438    0      3.87    75.33   40.64    None  None   None       |
|    Mac.    : 2385   0      0.00    70.28   13.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.533:  450   |   5:    37.664 -  45.197:  105        |
|      1:     7.533 -  15.066: 1356   |   6:    45.197 -  52.730:   88        |
|      2:    15.066 -  22.598:  443   |   7:    52.730 -  60.262:   77        |
|      3:    22.598 -  30.131:  161   |   8:    60.262 -  67.795:   35        |
|      4:    30.131 -  37.664:   94   |   9:    67.795 -  75.328:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1606 r_free = 0.2043             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1602 r_free = 0.2039             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1602   r_free= 0.2039   ksol= 0.30   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.56,-3.32,0.18,-0.00,0.00,0.00); trace/3= -0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.437640                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1574   r_free= 0.1998   ksol= 0.33   Bsol= 68.11   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-3.20,-1.04,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.427967                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.838366              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.176  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218405              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.573  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1574      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1998      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5238 = 3.84 * 0.50 * 5.4426 + 1.00 * 0.0784                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2984 = 3.84 * 0.50 * 5.3267 + 1.00 * 0.0754                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1239      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1730 = 0.22 * 1.00 * 5.3267 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1468 = 0.22 * 1.00 * 5.2138 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.260)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    79.28   17.18    None  None   None       |
|    all(noH): 2823   0      1.16    79.28   17.18    None  None   None       |
|    Sol.    : 438    0      6.43    79.28   39.33    None  None   None       |
|    Mac.    : 2385   0      1.16    75.09   13.12    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:     1.159 -   8.971:  684   |   5:    40.218 -  48.030:   97        |
|      1:     8.971 -  16.783: 1290   |   6:    48.030 -  55.842:   87        |
|      2:    16.783 -  24.595:  343   |   7:    55.842 -  63.654:   53        |
|      3:    24.595 -  32.407:  127   |   8:    63.654 -  71.466:   16        |
|      4:    32.407 -  40.218:  119   |   9:    71.466 -  79.278:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1637             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1196 r_free = 0.1635             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1635   ksol= 0.33   Bsol= 68.11   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-3.20,-1.04,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.194581                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1625   ksol= 0.33   Bsol= 68.11   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.96,-1.30,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.191535                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.809255              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.171  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.195248              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.509  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3983 = 2.81 * 0.50 * 5.2134 + 1.00 * 0.0754                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3380 = 2.81 * 0.50 * 5.1713 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0177 = 0.20 * 1.00 * 5.1713 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0154 = 0.20 * 1.00 * 5.1616 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.260)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    80.38   16.96    None  None   None       |
|    all(noH): 2823   0      1.54    80.38   16.96    None  None   None       |
|    Sol.    : 438    0      6.13    80.38   38.44    None  None   None       |
|    Mac.    : 2385   0      1.54    75.04   13.02    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:     1.535 -   9.420:  822   |   5:    40.959 -  48.844:  102        |
|      1:     9.420 -  17.305: 1216   |   6:    48.844 -  56.729:   85        |
|      2:    17.305 -  25.190:  299   |   7:    56.729 -  64.614:   31        |
|      3:    25.190 -  33.074:  128   |   8:    64.614 -  72.499:   14        |
|      4:    33.074 -  40.959:  122   |   9:    72.499 -  80.384:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1594             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1594             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1594   ksol= 0.33   Bsol= 68.11   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.96,-1.30,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157243                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1594   ksol= 0.32   Bsol= 58.84   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.73,-1.26,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.335956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.955  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.184647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.605  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1025 = 2.34 * 0.50 * 5.1612 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0921 = 2.34 * 0.50 * 5.1572 + 1.00 * 0.0685                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9598 = 0.18 * 1.00 * 5.1572 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9603 = 0.18 * 1.00 * 5.1608 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.260)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    80.40   16.78    None  None   None       |
|    all(noH): 2823   0      1.53    80.40   16.78    None  None   None       |
|    Sol.    : 438    0      6.28    80.40   38.03    None  None   None       |
|    Mac.    : 2385   0      1.53    75.17   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:     1.531 -   9.418:  853   |   5:    40.968 -  48.855:   97        |
|      1:     9.418 -  17.305: 1196   |   6:    48.855 -  56.743:   86        |
|      2:    17.305 -  25.193:  296   |   7:    56.743 -  64.630:   27        |
|      3:    25.193 -  33.080:  124   |   8:    64.630 -  72.517:   14        |
|      4:    33.080 -  40.968:  126   |   9:    72.517 -  80.405:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1602             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1603             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1603   ksol= 0.32   Bsol= 58.84   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.73,-1.26,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1602   ksol= 0.32   Bsol= 58.84   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.59,-1.16,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160784                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.302066              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.865  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.393695              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.463  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0090 = 2.30 * 0.50 * 5.1610 + 1.00 * 0.0685                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0065 = 2.30 * 0.50 * 5.1593 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0385 = 0.39 * 1.00 * 5.1593 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0393 = 0.39 * 1.00 * 5.1591 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.260)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.97    80.88   16.71    None  None   None       |
|    all(noH): 2823   0      0.97    80.88   16.71    None  None   None       |
|    Sol.    : 438    0      5.83    80.88   38.29    None  None   None       |
|    Mac.    : 2385   0      0.97    76.36   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.973 -   8.963:  806   |   5:    40.926 -  48.917:  101        |
|      1:     8.963 -  16.954: 1222   |   6:    48.917 -  56.908:   86        |
|      2:    16.954 -  24.945:  306   |   7:    56.908 -  64.899:   31        |
|      3:    24.945 -  32.936:  128   |   8:    64.899 -  72.890:   13        |
|      4:    32.936 -  40.926:  125   |   9:    72.890 -  80.880:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1619             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1619             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1619   ksol= 0.32   Bsol= 58.84   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.59,-1.16,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162795                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.7805 0.99   1390  155 0.1018 0.1335      5.4216      5.5594|
|  2:  4.7805 -  3.8140 0.99   1336  150 0.0872 0.1156      5.4607      5.6548|
|  3:  3.8140 -  3.3376 0.99   1316  141 0.1049 0.1515      5.4802      5.8816|
|  4:  3.3376 -  3.0351 0.99   1304  151 0.1206 0.1623      5.4686      5.5935|
|  5:  3.0351 -  2.8190 0.99   1296  144 0.1368 0.1823        5.36      5.6123|
|  6:  2.8190 -  2.6537 0.99   1296  137 0.1224 0.1962      5.2359       5.508|
|  7:  2.6537 -  2.5214 0.99   1282  141 0.1301 0.1616      5.2014      5.3747|
|  8:  2.5214 -  2.4121 0.98   1273  148 0.1133 0.1752      5.0659      5.3624|
|  9:  2.4121 -  2.3196 0.98   1258  145 0.1160 0.1798      5.0418        5.31|
| 10:  2.3196 -  2.2398 1.00   1292  138 0.1121 0.1813      4.9607      5.2601|
| 11:  2.2398 -  2.1700 0.97   1266  138 0.1127 0.1785      4.9568      5.2748|
| 12:  2.1700 -  2.1081 0.98   1249  141 0.1087 0.1722      4.8962       5.177|
| 13:  2.1081 -  2.0527 0.99   1280  140 0.1125 0.1826      4.8028      5.1038|
| 14:  2.0527 -  2.0028 0.62    792   90 0.1040 0.1687      4.6795      4.9181|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.7805  1390   155  0.94   9.59   0.97     0.94       7865.25|
|  2:  4.7805 -  3.8140  1336   150  0.95   8.22   1.00     0.98       9601.10|
|  3:  3.8140 -  3.3376  1316   141  0.93  11.47   1.01     1.00      10637.33|
|  4:  3.3376 -  3.0351  1304   151  0.91  14.18   0.99     0.97      10873.40|
|  5:  3.0351 -  2.8190  1296   144  0.89  16.56   0.98     0.96       9078.76|
|  6:  2.8190 -  2.6537  1296   137  0.89  16.88   0.97     0.95       7665.45|
|  7:  2.6537 -  2.5214  1282   141  0.90  16.11   0.98     0.95       6676.07|
|  8:  2.5214 -  2.4121  1273   148  0.91  15.37   0.98     0.95       5428.07|
|  9:  2.4121 -  2.3196  1258   145  0.91  15.48   0.98     0.94       5097.69|
| 10:  2.3196 -  2.2398  1292   138  0.90  15.83   0.99     0.95       4504.27|
| 11:  2.2398 -  2.1700  1266   138  0.90  16.53   0.97     0.92       4487.20|
| 12:  2.1700 -  2.1081  1249   141  0.91  15.42   0.99     0.98       4233.93|
| 13:  2.1081 -  2.0527  1280   140  0.89  16.96   0.97     0.95       3563.18|
| 14:  2.0527 -  2.0028   792    90  0.91  14.77   0.95     0.91       2688.57|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2688.57 max =        10873.40 mean =      6749.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.46|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1618   ksol= 0.32   Bsol= 58.80   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.33,-0.94,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162899                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1618   ksol= 0.32   Bsol= 58.80   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.33,-0.94,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162899                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.7805 0.99   1390  155 0.1018 0.1336      5.4221      5.5603|
|  2:  4.7805 -  3.8140 0.99   1336  150 0.0872 0.1156      5.4608      5.6544|
|  3:  3.8140 -  3.3376 0.99   1316  141 0.1049 0.1515      5.4799      5.8815|
|  4:  3.3376 -  3.0351 0.99   1304  151 0.1206 0.1623      5.4686      5.5935|
|  5:  3.0351 -  2.8190 0.99   1296  144 0.1368 0.1823        5.36      5.6123|
|  6:  2.8190 -  2.6537 0.99   1296  137 0.1224 0.1963      5.2361      5.5082|
|  7:  2.6537 -  2.5214 0.99   1282  141 0.1301 0.1616      5.2015      5.3745|
|  8:  2.5214 -  2.4121 0.98   1273  148 0.1132 0.1752      5.0659      5.3626|
|  9:  2.4121 -  2.3196 0.98   1258  145 0.1160 0.1798       5.042      5.3102|
| 10:  2.3196 -  2.2398 1.00   1292  138 0.1121 0.1812      4.9607      5.2591|
| 11:  2.2398 -  2.1700 0.97   1266  138 0.1127 0.1786      4.9569       5.275|
| 12:  2.1700 -  2.1081 0.98   1249  141 0.1088 0.1722      4.8961      5.1769|
| 13:  2.1081 -  2.0527 0.99   1280  140 0.1125 0.1827      4.8029      5.1037|
| 14:  2.0527 -  2.0028 0.62    792   90 0.1040 0.1688        4.68      4.9189|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.7805  1390   155  0.94   9.60   0.97     0.94       7876.27|
|  2:  4.7805 -  3.8140  1336   150  0.95   8.23   1.00     0.99       9605.07|
|  3:  3.8140 -  3.3376  1316   141  0.93  11.47   1.01     1.00      10631.44|
|  4:  3.3376 -  3.0351  1304   151  0.91  14.18   1.00     0.97      10873.12|
|  5:  3.0351 -  2.8190  1296   144  0.89  16.57   0.99     0.96       9080.76|
|  6:  2.8190 -  2.6537  1296   137  0.89  16.88   0.98     0.95       7666.18|
|  7:  2.6537 -  2.5214  1282   141  0.90  16.11   0.98     0.95       6675.63|
|  8:  2.5214 -  2.4121  1273   148  0.91  15.37   0.98     0.96       5428.25|
|  9:  2.4121 -  2.3196  1258   145  0.91  15.48   0.99     0.95       5097.28|
| 10:  2.3196 -  2.2398  1292   138  0.90  15.83   0.99     0.96       4503.30|
| 11:  2.2398 -  2.1700  1266   138  0.90  16.53   0.98     0.93       4485.39|
| 12:  2.1700 -  2.1081  1249   141  0.91  15.42   1.00     0.99       4232.46|
| 13:  2.1081 -  2.0527  1280   140  0.89  16.96   0.98     0.96       3564.19|
| 14:  2.0527 -  2.0028   792    90  0.91  14.78   0.96     0.92       2692.40|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2692.40 max =        10873.12 mean =      6750.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.47|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.260)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.94    80.85   16.68    None  None   None       |
|    all(noH): 2823   0      0.94    80.85   16.68    None  None   None       |
|    Sol.    : 438    0      5.80    80.85   38.26    None  None   None       |
|    Mac.    : 2385   0      0.94    76.33   12.72    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:     0.939 -   8.930:  806   |   5:    40.893 -  48.884:  101        |
|      1:     8.930 -  16.921: 1222   |   6:    48.884 -  56.874:   86        |
|      2:    16.921 -  24.911:  306   |   7:    56.874 -  64.865:   31        |
|      3:    24.911 -  32.902:  128   |   8:    64.865 -  72.856:   13        |
|      4:    32.902 -  40.893:  125   |   9:    72.856 -  80.847:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.571 - 4.784
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 282 from: 288
   mapped sites are within: 0.712 - 4.784

peak=    5.697 closest distance to " O   HOH Z 111 " =    2.181
peak=    5.495 closest distance to " CB  GLN A 223 " =    1.449
peak=    5.341 closest distance to " CG  PRO A  54 " =    1.331
peak=    5.186 closest distance to " O   HOH Z 232 " =    2.304
peak=    4.874 closest distance to " O   HOH Z 126 " =    1.895
peak=    4.821 closest distance to " CB  SER A  63 " =    1.237
peak=    4.804 closest distance to " NE2 GLN A  11 " =    1.160
peak=    4.684 closest distance to " CB  ARG A  79 " =    1.325
peak=    4.641 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.583 closest distance to " CG  PRO A 213 " =    1.195
peak=    4.579 closest distance to " CG  PRO A 198 " =    1.256
peak=    4.579 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.544 closest distance to " CB  PRO A  54 " =    0.932
peak=    4.515 closest distance to " CB  LEU A 228 " =    1.082
peak=    4.506 closest distance to " CB  ARG A 190 " =    1.619
peak=    4.474 closest distance to " O   HOH Z  78 " =    1.671
peak=    4.473 closest distance to " O   HOH Z 298 " =    1.975
peak=    4.472 closest distance to " O   HOH Z 369 " =    2.079
peak=    4.447 closest distance to " O   HOH Z  15 " =    2.145
peak=    4.403 closest distance to " C   PRO A 198 " =    1.527
peak=    4.364 closest distance to " CB  ASN A 148 " =    1.433
peak=    4.287 closest distance to " CZ  PHE A 218 " =    1.067
peak=    4.269 closest distance to " CD  ARG A 159 " =    0.804
peak=    4.245 closest distance to " CA  TYR A  30 " =    0.965
peak=    4.228 closest distance to " CG2 VAL A 257 " =    0.961
peak=    4.195 closest distance to " O   HOH Z 303 " =    2.138
peak=    4.188 closest distance to " O   HOH Z 250 " =    1.559
peak=    4.187 closest distance to " CB  GLU A 152 " =    1.178
peak=    4.127 closest distance to " O   HOH Z 234 " =    3.904
peak=    4.085 closest distance to " CB  TRP A 266 " =    0.976
peak=    4.051 closest distance to " CB  ASP A 124 " =    0.732
peak=    4.038 closest distance to " NH2 ARG A 156 " =    1.188
peak=    4.033 closest distance to " NH1AARG A 145 " =    1.311
peak=    4.033 closest distance to " O   HOH Z 189 " =    2.740
peak=    4.017 closest distance to " ND2 ASN A 187 " =    1.467
peak=    3.992 closest distance to " CB  VAL A 265 " =    1.254
peak=    3.991 closest distance to " CA  ALA A  51 " =    0.906
peak=    3.989 closest distance to " CE  LYS A  76 " =    0.866
peak=    3.987 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.986 closest distance to " O   HOH Z 236 " =    2.196
peak=    3.963 closest distance to " CB  GLU A 128 " =    0.986
peak=    3.963 closest distance to " O   HOH Z 261 " =    1.923
peak=    3.959 closest distance to " CB  TYR A 169 " =    0.761
peak=    3.947 closest distance to " CB  VAL A 202 " =    1.635
peak=    3.939 closest distance to " O   HOH Z 193 " =    1.997
peak=    3.923 closest distance to " CG  PRO A 243 " =    1.106
peak=    3.921 closest distance to " CB  GLU A 277 " =    3.704
peak=    3.915 closest distance to " O   HOH Z  21 " =    1.815
peak=    3.913 closest distance to " O   HOH Z  54 " =    2.429
peak=    3.904 closest distance to " O   HOH Z  78 " =    2.137
peak=    3.901 closest distance to " O   HOH Z 158 " =    3.041
peak=    3.892 closest distance to " CB  ASN A 187 " =    1.349
peak=    3.885 closest distance to " OD1 ASN A  69 " =    2.650
peak=    3.881 closest distance to " O   HOH Z 213 " =    2.108
peak=    3.872 closest distance to " O   HOH Z 180 " =    2.103
peak=    3.865 closest distance to " O   HOH Z 142 " =    1.678
peak=    3.860 closest distance to " O   HOH Z 368 " =    2.122
peak=    3.859 closest distance to " CD1 LEU A 300 " =    1.214
peak=    3.859 closest distance to " CA  ARG A 195 " =    1.233
peak=    3.848 closest distance to " NZ  LYS A 117 " =    3.317
peak=    3.838 closest distance to " O   HOH Z 423 " =    1.869
peak=    3.812 closest distance to " O   HOH Z 214 " =    2.024
peak=    3.801 closest distance to " CA  ASN A 215 " =    1.184
peak=    3.795 closest distance to " CB  SER A 212 " =    1.148
peak=    3.785 closest distance to " O   HOH Z 197 " =    3.060
peak=    3.780 closest distance to " O   HOH Z 346 " =    1.567
peak=    3.777 closest distance to " O   THR A 251 " =    1.259
peak=    3.776 closest distance to " CD  ARG A 269 " =    0.909
peak=    3.775 closest distance to " CB  ALA A 104 " =    0.717
peak=    3.768 closest distance to " O   HOH Z 126 " =    1.965
peak=    3.768 closest distance to " O   HOH Z 427 " =    3.107
peak=    3.765 closest distance to " CA  PRO A  54 " =    1.370
peak=    3.765 closest distance to " CB  ASN A  39 " =    0.927
peak=    3.758 closest distance to " CD ALYS A 290 " =    0.997
peak=    3.749 closest distance to " O   HOH Z 411 " =    3.961
peak=    3.742 closest distance to " CB  ASP A 140 " =    0.978
peak=    3.738 closest distance to " O   HOH Z 272 " =    1.878
peak=    3.716 closest distance to " CD  ARG A  66 " =    2.297
peak=    3.714 closest distance to " O   HOH Z  53 " =    2.569
peak=    3.712 closest distance to " CB  MET A  40 " =    0.790
peak=    3.711 closest distance to " O   HOH Z 133 " =    2.380
peak=    3.710 closest distance to " CD  ARG A  66 " =    2.256
peak=    3.703 closest distance to " NE2 HIS A 207 " =    1.347
peak=    3.701 closest distance to " CB  SER A 216 " =    0.830
peak=    3.701 closest distance to " CA  THR A 264 " =    0.859
peak=    3.694 closest distance to " CG  LEU A 167 " =    1.295
peak=    3.693 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.686 closest distance to " CB  SER A   3 " =    1.357
peak=    3.677 closest distance to " CG2 THR A 221 " =    0.995
peak=    3.672 closest distance to " O   HOH Z 313 " =    1.908
peak=    3.664 closest distance to " O  BHOH Z 338 " =    2.365
peak=    3.658 closest distance to " O   HOH Z 403 " =    1.692
peak=    3.657 closest distance to " CG1 VAL A 153 " =    0.967
peak=    3.640 closest distance to " O   HOH Z 209 " =    2.294
peak=    3.632 closest distance to " CB  ASN A 142 " =    0.971
peak=    3.631 closest distance to " CB  GLN A  88 " =    1.280
peak=    3.618 closest distance to " O   HOH Z  10 " =    1.813
peak=    3.616 closest distance to " CA  THR A 221 " =    1.001
peak=    3.609 closest distance to " ND1 HIS A  86 " =    1.711
peak=    3.607 closest distance to " O   HOH Z   1 " =    2.087
peak=    3.603 closest distance to " CD  LYS A 166 " =    1.261
peak=    3.595 closest distance to " O   HOH Z 171 " =    3.882
peak=    3.590 closest distance to " CG1 ILE A  33 " =    1.276
peak=    3.578 closest distance to " N   ASN A 127 " =    1.256
peak=    3.576 closest distance to " CA  MET A  40 " =    1.182
peak=    3.569 closest distance to " O   HOH Z 406 " =    1.619
peak=    3.568 closest distance to " OD2 ASP A 286 " =    2.911
peak=    3.558 closest distance to " O   HOH Z 291 " =    1.627
peak=    3.554 closest distance to " O   HOH Z 148 " =    3.398
peak=    3.553 closest distance to " CA  SER A  87 " =    0.992
peak=    3.553 closest distance to " CA  ARG A  36 " =    1.126
peak=    3.552 closest distance to " O   HOH Z  88 " =    3.668
peak=    3.546 closest distance to " CB  TYR A 116 " =    0.800
peak=    3.546 closest distance to " O   HOH Z 166 " =    3.693
peak=    3.542 closest distance to " CD  ARG A 219 " =    1.107
peak=    3.542 closest distance to " O   TYR A 116 " =    1.296
peak=    3.539 closest distance to " O   MET A 105 " =    1.886
peak=    3.531 closest distance to " CG2AVAL A  72 " =    1.721
peak=    3.529 closest distance to " O   HOH Z 316 " =    3.120
peak=    3.528 closest distance to " O   HOH Z 193 " =    1.750
peak=    3.525 closest distance to " N   ARG A 156 " =    1.360
peak=    3.523 closest distance to " CB  ALA A  34 " =    0.984
peak=    3.522 closest distance to " CB  SER A 210 " =    0.772
peak=    3.518 closest distance to " CD2 TRP A 179 " =    1.299
peak=    3.507 closest distance to " CZ  PHE A 192 " =    0.944
peak=    3.492 closest distance to " CD1 ILE A 106 " =    0.798
peak=    3.489 closest distance to " O   HOH Z 344 " =    3.213
peak=    3.486 closest distance to " O   HOH Z 371 " =    3.090
peak=    3.485 closest distance to " CB  ILE A 120 " =    1.229
peak=    3.483 closest distance to " CB  LEU A  83 " =    0.798
peak=    3.479 closest distance to " O   HOH Z  68 " =    2.132
peak=    3.478 closest distance to " O   HOH Z 329 " =    3.926
peak=    3.473 closest distance to " O   HOH Z 368 " =    3.673
peak=    3.473 closest distance to " CB  ALA A   1 " =    4.784
peak=    3.459 closest distance to " ND2 ASN A 249 " =    1.929
peak=    3.457 closest distance to " O   HOH Z 147 " =    1.810
peak=    3.450 closest distance to " CA  TYR A  30 " =    1.058
peak=    3.450 closest distance to " O   HOH Z 403 " =    1.426
peak=    3.445 closest distance to " O   HOH Z  20 " =    1.856
peak=    3.442 closest distance to " O   THR A 220 " =    1.262
peak=    3.441 closest distance to " O   HOH Z 285 " =    2.582
peak=    3.441 closest distance to " O   SER A  87 " =    2.238
peak=    3.437 closest distance to " O   HOH Z 132 " =    2.785
peak=    3.436 closest distance to " O   HOH Z 426 " =    1.620
peak=    3.425 closest distance to " CA  ALA A 154 " =    0.970
peak=    3.423 closest distance to " CA  MET A 105 " =    1.022
peak=    3.419 closest distance to " O   HOH Z 172 " =    3.410
peak=    3.417 closest distance to " O   HOH Z 411 " =    1.730
peak=    3.416 closest distance to " CA  ALA A 158 " =    1.187
peak=    3.410 closest distance to " N   PHE A 130 " =    1.239
peak=    3.407 closest distance to " CB  ASN A 110 " =    1.162
peak=    3.406 closest distance to " CA  ALA A 233 " =    1.371
peak=    3.402 closest distance to " CB  MET A  47 " =    1.009
peak=    3.400 closest distance to " CB  THR A  82 " =    1.399
peak=    3.391 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.390 closest distance to " CA  TYR A 116 " =    1.407
peak=    3.388 closest distance to " CG BARG A 275 " =    1.473
peak=    3.385 closest distance to " O   HOH Z 108 " =    2.782
peak=    3.377 closest distance to " NH2BARG A 145 " =    2.174
peak=    3.377 closest distance to " CA  ALA A 295 " =    1.029
peak=    3.370 closest distance to " O   HOH Z 383 " =    2.130
peak=    3.368 closest distance to " CB  GLN A 103 " =    0.882
peak=    3.366 closest distance to " N   ASN A  39 " =    1.330
peak=    3.364 closest distance to " O   HOH Z 345 " =    1.776
peak=    3.361 closest distance to " O   HOH Z 188 " =    2.169
peak=    3.356 closest distance to " O   HOH Z 248 " =    1.767
peak=    3.354 closest distance to " O   HOH Z 135 " =    1.706
peak=    3.349 closest distance to " NE  ARG A  79 " =    1.170
peak=    3.348 closest distance to " O   HOH Z 185 " =    1.886
peak=    3.347 closest distance to " ND2 ASN A 110 " =    1.755
peak=    3.346 closest distance to " CB  ALA A 248 " =    0.935
peak=    3.345 closest distance to " CB  ALA A   9 " =    1.584
peak=    3.337 closest distance to " CG2 ILE A 120 " =    1.075
peak=    3.335 closest distance to " O   HOH Z 245 " =    1.231
peak=    3.335 closest distance to " O   HOH Z 273 " =    2.767
peak=    3.331 closest distance to " CA  ALA A  21 " =    1.194
peak=    3.328 closest distance to " O   HOH Z 258 " =    1.675
peak=    3.327 closest distance to " N   VAL A 126 " =    1.393
peak=    3.326 closest distance to " CZ  PHE A  38 " =    1.256
peak=    3.321 closest distance to " O   HOH Z 280 " =    2.998
peak=    3.321 closest distance to " CD1 LEU A  96 " =    0.734
peak=    3.318 closest distance to " O   ALA A 165 " =    1.495
peak=    3.308 closest distance to " CD2 LEU A 297 " =    0.826
peak=    3.305 closest distance to " CG  ARG A 159 " =    0.925
peak=    3.303 closest distance to " O   HOH Z 218 " =    4.643
peak=    3.301 closest distance to " CB  LYS A 193 " =    1.020
peak=    3.299 closest distance to " O   HOH Z  62 " =    1.933
peak=    3.290 closest distance to " O   HOH Z 128 " =    2.372
peak=    3.289 closest distance to " CA  GLY A 241 " =    0.729
peak=    3.288 closest distance to " O   HOH Z 133 " =    1.700
peak=    3.288 closest distance to " OG  SER A  22 " =    2.800
peak=    3.287 closest distance to " CB  ALA A 291 " =    1.209
peak=    3.281 closest distance to " O   HOH Z 227 " =    1.738
peak=    3.276 closest distance to " CA  GLY A 267 " =    1.166
peak=    3.275 closest distance to " NH2AARG A 275 " =    3.641
peak=    3.270 closest distance to " O   HOH Z 359 " =    1.466
peak=    3.268 closest distance to " N   GLY A  98 " =    1.140
peak=    3.256 closest distance to " CE1 TYR A 186 " =    1.334
peak=    3.249 closest distance to " CG2 ILE A 234 " =    0.822
peak=    3.249 closest distance to " O   HOH Z 421 " =    1.982
peak=    3.247 closest distance to " CG  MET A 185 " =    1.214
peak=    3.246 closest distance to " CB  ALA A 242 " =    0.824
peak=    3.245 closest distance to " CE2 TYR A 293 " =    0.956
peak=    3.245 closest distance to " NH1 ARG A 138 " =    1.090
peak=    3.244 closest distance to " O   HOH Z 281 " =    4.095
peak=    3.244 closest distance to " OH  TYR A 214 " =    1.197
peak=    3.243 closest distance to " OD1 ASN A 217 " =    1.779
peak=    3.236 closest distance to " CG  GLN A  11 " =    1.568
peak=    3.236 closest distance to " CA  GLU A  46 " =    0.900
peak=    3.235 closest distance to " CA  ALA A 291 " =    0.857
peak=    3.233 closest distance to " O   HOH Z 425 " =    2.082
peak=    3.233 closest distance to " ND2 ASN A 249 " =    0.829
peak=    3.231 closest distance to " CB  PRO A  90 " =    1.173
peak=    3.225 closest distance to " O   HOH Z 128 " =    2.197
peak=    3.222 closest distance to " O   HOH Z 294 " =    1.549
peak=    3.220 closest distance to " CD2 LEU A 255 " =    1.566
peak=    3.220 closest distance to " OD1 ASP A 231 " =    1.900
peak=    3.217 closest distance to " CB  ASN A 224 " =    1.030
peak=    3.216 closest distance to " CG1 ILE A 151 " =    1.034
peak=    3.215 closest distance to " C   TYR A 214 " =    1.550
peak=    3.212 closest distance to " O   HOH Z 109 " =    2.666
peak=    3.205 closest distance to " OD1BASN A 224 " =    2.416
peak=    3.202 closest distance to " CA  ILE A 234 " =    0.927
peak=    3.201 closest distance to " O   HOH Z 319 " =    2.270
peak=    3.200 closest distance to " O   HOH Z 327 " =    1.995
peak=    3.198 closest distance to " O   HOH Z 384 " =    2.973
peak=    3.196 closest distance to " O   HOH Z 409 " =    2.891
peak=    3.193 closest distance to " O   HOH Z  44 " =    3.006
peak=    3.191 closest distance to " O   HOH Z 419 " =    1.947
peak=    3.183 closest distance to " CG  GLN A  88 " =    1.069
peak=    3.182 closest distance to " CB  ASP A 298 " =    1.193
peak=    3.180 closest distance to " CB  ALA A 291 " =    0.764
peak=    3.179 closest distance to " OD1 ASP A 171 " =    1.229
peak=    3.178 closest distance to " CB  ARG A 138 " =    1.033
peak=    3.175 closest distance to " O   HOH Z 305 " =    3.662
peak=    3.173 closest distance to " CA  TRP A  92 " =    0.974
peak=    3.170 closest distance to " CA  LYS A 117 " =    1.202
peak=    3.169 closest distance to " CA  ASN A 217 " =    1.291
peak=    3.168 closest distance to " O   HOH Z  59 " =    2.118
peak=    3.166 closest distance to " O   HOH Z 156 " =    2.998
peak=    3.164 closest distance to " O   HOH Z 391 " =    2.924
peak=    3.164 closest distance to " CG1 VAL A 189 " =    2.127
peak=    3.162 closest distance to " NZ  LYS A  76 " =    1.551
peak=    3.162 closest distance to " ND1 HIS A  81 " =    1.680
peak=    3.161 closest distance to " O   HOH Z 302 " =    2.018
peak=    3.155 closest distance to " O   ASN A 209 " =    1.268
peak=    3.155 closest distance to " N   SER A 146 " =    1.713
peak=    3.154 closest distance to " O   HOH Z 234 " =    1.712
peak=    3.150 closest distance to " CB  ARG A 139 " =    0.952
peak=    3.149 closest distance to " CB  HIS A 108 " =    0.780
peak=    3.148 closest distance to " CD1AILE A 234 " =    0.933
peak=    3.145 closest distance to " N   SER A 135 " =    1.312
peak=    3.139 closest distance to " O   HOH Z 271 " =    2.332
peak=    3.130 closest distance to " O   HOH Z 203 " =    1.863
peak=    3.125 closest distance to " O   HOH Z  49 " =    2.961
peak=    3.125 closest distance to " OG  SER A 206 " =    1.228
peak=    3.125 closest distance to " O   HOH Z 285 " =    1.781
peak=    3.124 closest distance to " CG2 ILE A 106 " =    0.839
peak=    3.122 closest distance to " CG  LYS A  76 " =    0.950
peak=    3.120 closest distance to " CB  LYS A 117 " =    1.188
peak=    3.115 closest distance to " OG BSER A 164 " =    2.328
peak=    3.115 closest distance to " O   HOH Z 353 " =    2.694
peak=    3.114 closest distance to " CA  ASP A 191 " =    0.890
peak=    3.111 closest distance to " CG2BVAL A  41 " =    0.817
peak=    3.110 closest distance to " O   HOH Z  97 " =    2.806
peak=    3.110 closest distance to " O   HOH Z 327 " =    2.435
peak=    3.110 closest distance to " N   TYR A  15 " =    0.712
peak=    3.109 closest distance to " O   HOH Z  97 " =    1.981
peak=    3.108 closest distance to " CG BARG A 102 " =    1.890
peak=    3.108 closest distance to " CG2 ILE A 151 " =    0.817
peak=    3.106 closest distance to " O   HOH Z 116 " =    1.852
peak=    3.106 closest distance to " CB  PRO A 243 " =    1.250
peak=    3.104 closest distance to " O   ALA A 158 " =    1.323
peak=    3.102 closest distance to " O   TRP A 274 " =    1.746
peak=    3.082 closest distance to " O   HOH Z 310 " =    2.170
peak=    3.082 closest distance to " O   GLN A 278 " =    1.561
peak=    3.082 closest distance to " CA  GLY A 211 " =    1.282
peak=    3.081 closest distance to " O   HOH Z  66 " =    2.141
peak=    3.078 closest distance to " O   SER A 164 " =    1.341
peak=    3.066 closest distance to " CB  ALA A 114 " =    1.057
peak=    3.043 closest distance to " CB  ALA A 227 " =    0.923
peak=    3.015 closest distance to " CB  TYR A 169 " =    1.221

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.506 - 5.545
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 210
   mapped sites are within: 0.760 - 5.545

peak=   -4.631 closest distance to " CG1 VAL A 112 " =    2.645
peak=   -4.485 closest distance to " CB  PRO A 243 " =    2.639
peak=   -4.266 closest distance to " CD  ARG A  14 " =    3.375
peak=   -4.252 closest distance to " CD  ARG A 156 " =    2.070
peak=   -4.215 closest distance to " CZ3 TRP A 179 " =    1.132
peak=   -4.208 closest distance to " CD  GLN A  58 " =    0.912
peak=   -4.122 closest distance to " O   HOH Z 266 " =    5.310
peak=   -4.091 closest distance to " O   VAL A  67 " =    2.770
peak=   -4.089 closest distance to " CE2 TYR A  30 " =    2.797
peak=   -4.046 closest distance to " O   HOH Z  73 " =    2.100
peak=   -4.044 closest distance to " O   HOH Z 290 " =    1.232
peak=   -4.034 closest distance to " O   PRO A 198 " =    1.281
peak=   -4.030 closest distance to " N   ALA A  43 " =    2.534
peak=   -4.029 closest distance to " CG1 VAL A 112 " =    2.920
peak=   -4.004 closest distance to " OE1 GLN A 223 " =    1.935
peak=   -3.974 closest distance to " O   HOH Z 231 " =    2.199
peak=   -3.921 closest distance to " O   HOH Z  10 " =    1.561
peak=   -3.898 closest distance to " O   HOH Z 377 " =    2.033
peak=   -3.885 closest distance to " O   ILE A 109 " =    2.621
peak=   -3.880 closest distance to " O   HOH Z  38 " =    1.315
peak=   -3.866 closest distance to " OG BSER A 134 " =    1.277
peak=   -3.858 closest distance to " O   HOH Z 389 " =    2.003
peak=   -3.853 closest distance to " O   HOH Z 372 " =    2.452
peak=   -3.840 closest distance to " CB  ALA A  43 " =    2.631
peak=   -3.835 closest distance to " CD2 TYR A 293 " =    2.014
peak=   -3.820 closest distance to " NH2AARG A 275 " =    5.545
peak=   -3.815 closest distance to " OG  SER A  97 " =    2.238
peak=   -3.814 closest distance to " CD1 PHE A  59 " =    1.939
peak=   -3.802 closest distance to " C   HIS A 108 " =    1.128
peak=   -3.795 closest distance to " CG  ARG A 269 " =    2.440
peak=   -3.787 closest distance to " O   HOH Z 394 " =    1.496
peak=   -3.768 closest distance to " CA  GLY A 203 " =    2.422
peak=   -3.759 closest distance to " CG1 VAL A 250 " =    2.722
peak=   -3.754 closest distance to " CD  GLN A 223 " =    0.775
peak=   -3.750 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.741 closest distance to " O   HOH Z 351 " =    1.495
peak=   -3.736 closest distance to " O   HOH Z 198 " =    2.175
peak=   -3.735 closest distance to " O   HOH Z 114 " =    3.406
peak=   -3.734 closest distance to " N   THR A 157 " =    1.629
peak=   -3.715 closest distance to " O   HOH Z 435 " =    2.834
peak=   -3.694 closest distance to " OXT GLY A 302 " =    2.947
peak=   -3.682 closest distance to " CE2 PHE A  61 " =    2.626
peak=   -3.681 closest distance to " O   HOH Z  60 " =    2.460
peak=   -3.672 closest distance to " O   VAL A 189 " =    2.644
peak=   -3.672 closest distance to " CA  GLY A 241 " =    3.130
peak=   -3.668 closest distance to " CD  ARG A 139 " =    1.571
peak=   -3.665 closest distance to " O   GLY A 211 " =    1.427
peak=   -3.645 closest distance to " NE2 GLN A 194 " =    1.815
peak=   -3.635 closest distance to " CD2 LEU A 237 " =    2.911
peak=   -3.630 closest distance to " O   HOH Z  52 " =    1.347
peak=   -3.626 closest distance to " CD1 LEU A 101 " =    2.418
peak=   -3.623 closest distance to " O   HOH Z 426 " =    1.644
peak=   -3.621 closest distance to " C   LEU A 222 " =    0.793
peak=   -3.614 closest distance to " O   HOH Z 407 " =    3.321
peak=   -3.606 closest distance to " O   HOH Z  43 " =    1.556
peak=   -3.603 closest distance to " O   HOH Z 196 " =    2.078
peak=   -3.588 closest distance to " ND2 ASN A 249 " =    2.436
peak=   -3.581 closest distance to " CB  ALA A 291 " =    2.300
peak=   -3.576 closest distance to " ND2 ASN A  45 " =    1.102
peak=   -3.576 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.574 closest distance to " ND2 ASN A  45 " =    1.843
peak=   -3.571 closest distance to " OD1 ASN A 148 " =    1.532
peak=   -3.565 closest distance to " CG2 ILE A 263 " =    2.402
peak=   -3.558 closest distance to " C   ASN A 285 " =    2.506
peak=   -3.554 closest distance to " CB  PHE A 192 " =    2.069
peak=   -3.553 closest distance to " CG  PHE A 283 " =    2.836
peak=   -3.538 closest distance to " CB  ASN A  39 " =    2.305
peak=   -3.533 closest distance to " CA  SER A 135 " =    1.321
peak=   -3.528 closest distance to " O   HOH Z 176 " =    0.864
peak=   -3.527 closest distance to " N   MET A 188 " =    1.892
peak=   -3.523 closest distance to " O   HOH Z 198 " =    1.318
peak=   -3.521 closest distance to " CE  MET A 105 " =    2.320
peak=   -3.519 closest distance to " CA  GLY A 241 " =    2.348
peak=   -3.514 closest distance to " O   HOH Z   6 " =    1.453
peak=   -3.505 closest distance to " NH2 ARG A  79 " =    1.518
peak=   -3.496 closest distance to " CD1 ILE A 151 " =    2.446
peak=   -3.496 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.494 closest distance to " O   PRO A 163 " =    2.148
peak=   -3.492 closest distance to " CE3 TRP A 150 " =    2.036
peak=   -3.487 closest distance to " O   HOH Z 185 " =    2.349
peak=   -3.484 closest distance to " CE BMET A  47 " =    1.921
peak=   -3.479 closest distance to " CD1 LEU A 228 " =    2.450
peak=   -3.478 closest distance to " O   HOH Z 353 " =    2.142
peak=   -3.472 closest distance to " CG2 ILE A  20 " =    2.873
peak=   -3.472 closest distance to " ND2 ASN A  45 " =    1.306
peak=   -3.468 closest distance to " CG1 VAL A 197 " =    2.328
peak=   -3.449 closest distance to " O   HOH Z  11 " =    1.687
peak=   -3.437 closest distance to " O   HOH Z 313 " =    1.999
peak=   -3.437 closest distance to " O   HOH Z 298 " =    2.550
peak=   -3.428 closest distance to " O   HOH Z  51 " =    1.598
peak=   -3.425 closest distance to " O   GLY A 203 " =    2.336
peak=   -3.416 closest distance to " CG2 ILE A  49 " =    2.689
peak=   -3.409 closest distance to " C   MET A 188 " =    1.327
peak=   -3.398 closest distance to " O   GLY A  17 " =    1.239
peak=   -3.390 closest distance to " C   ALA A 158 " =    1.404
peak=   -3.385 closest distance to " O   HOH Z 114 " =    1.458
peak=   -3.384 closest distance to " CB  PRO A 163 " =    2.563
peak=   -3.382 closest distance to " O   VAL A  67 " =    2.881
peak=   -3.381 closest distance to " CA  GLY A 241 " =    2.849
peak=   -3.376 closest distance to " CG  HIS A  86 " =    1.087
peak=   -3.373 closest distance to " O   HOH Z 111 " =    2.068
peak=   -3.358 closest distance to " OD1 ASP A 171 " =    1.620
peak=   -3.356 closest distance to " O   HOH Z 241 " =    1.220
peak=   -3.355 closest distance to " N   ALA A 248 " =    1.656
peak=   -3.347 closest distance to " O   HOH Z 350 " =    1.864
peak=   -3.343 closest distance to " NH2 ARG A 159 " =    2.379
peak=   -3.340 closest distance to " O   HOH Z 166 " =    1.869
peak=   -3.339 closest distance to " O   TRP A  70 " =    1.453
peak=   -3.338 closest distance to " O   HOH Z 174 " =    2.605
peak=   -3.337 closest distance to " CD  ARG A 195 " =    5.126
peak=   -3.329 closest distance to " CB  TRP A  85 " =    2.447
peak=   -3.322 closest distance to " OG BSER A 134 " =    1.785
peak=   -3.319 closest distance to " CG  ARG A  66 " =    2.173
peak=   -3.316 closest distance to " O   HOH Z 275 " =    1.575
peak=   -3.314 closest distance to " ND2 ASN A  60 " =    1.335
peak=   -3.312 closest distance to " O   HOH Z 417 " =    2.942
peak=   -3.311 closest distance to " CG  PRO A 243 " =    1.790
peak=   -3.310 closest distance to " ND2BASN A 224 " =    1.746
peak=   -3.303 closest distance to " O   HOH Z 232 " =    1.717
peak=   -3.301 closest distance to " O   HOH Z 393 " =    1.386
peak=   -3.299 closest distance to " O   PHE A 218 " =    1.609
peak=   -3.297 closest distance to " CB  PHE A 225 " =    2.227
peak=   -3.297 closest distance to " CD  GLN A  88 " =    0.770
peak=   -3.292 closest distance to " CG  LEU A  83 " =    1.935
peak=   -3.291 closest distance to " CZ BARG A 275 " =    1.794
peak=   -3.288 closest distance to " O   HOH Z 207 " =    2.186
peak=   -3.287 closest distance to " O   SER A  62 " =    2.253
peak=   -3.282 closest distance to " CG  ASP A 231 " =    0.760
peak=   -3.281 closest distance to " O   GLN A 240 " =    2.177
peak=   -3.276 closest distance to " OE1 GLN A  88 " =    1.194
peak=   -3.268 closest distance to " O   HOH Z 281 " =    2.644
peak=   -3.267 closest distance to " N   THR A  52 " =    1.685
peak=   -3.264 closest distance to " O   HOH Z 211 " =    1.566
peak=   -3.260 closest distance to " O   HOH Z 243 " =    2.011
peak=   -3.259 closest distance to " CB  ALA A 114 " =    2.578
peak=   -3.258 closest distance to " CB  ALA A   9 " =    2.552
peak=   -3.254 closest distance to " CG  TRP A 266 " =    1.773
peak=   -3.242 closest distance to " CG  GLU A 277 " =    1.153
peak=   -3.236 closest distance to " CG  PRO A 163 " =    2.477
peak=   -3.233 closest distance to " CB  ASP A 286 " =    2.071
peak=   -3.233 closest distance to " CB  ASN A 252 " =    1.580
peak=   -3.232 closest distance to " O   HOH Z  37 " =    1.840
peak=   -3.232 closest distance to " O   ALA A  10 " =    1.704
peak=   -3.232 closest distance to " CZ  PHE A  59 " =    1.638
peak=   -3.228 closest distance to " O   HOH Z 174 " =    3.035
peak=   -3.227 closest distance to " CD2 PHE A  61 " =    2.070
peak=   -3.226 closest distance to " O   HOH Z 311 " =    3.830
peak=   -3.225 closest distance to " ND2 ASN A 249 " =    2.180
peak=   -3.223 closest distance to " NH2 ARG A 219 " =    1.706
peak=   -3.223 closest distance to " CB  ALA A 248 " =    2.541
peak=   -3.222 closest distance to " CG1 VAL A 125 " =    1.925
peak=   -3.220 closest distance to " OD2 ASP A 171 " =    1.882
peak=   -3.220 closest distance to " CZ  TYR A 169 " =    1.661
peak=   -3.214 closest distance to " OG  SER A 206 " =    1.911
peak=   -3.214 closest distance to " CB  PRO A  54 " =    2.507
peak=   -3.213 closest distance to " SG ACYS A 201 " =    1.993
peak=   -3.211 closest distance to " CB  PHE A 208 " =    2.290
peak=   -3.206 closest distance to " O   HOH Z 322 " =    1.258
peak=   -3.204 closest distance to " CB  ASP A 132 " =    2.286
peak=   -3.201 closest distance to " O   ALA A  34 " =    2.175
peak=   -3.200 closest distance to " N   SER A   3 " =    1.996
peak=   -3.197 closest distance to " CD2 PHE A  59 " =    2.557
peak=   -3.196 closest distance to " O   HOH Z 359 " =    3.137
peak=   -3.189 closest distance to " CH2 TRP A 177 " =    2.267
peak=   -3.187 closest distance to " ND2 ASN A  60 " =    1.962
peak=   -3.186 closest distance to " CD1 ILE A 239 " =    2.107
peak=   -3.180 closest distance to " O   HOH Z 377 " =    1.183
peak=   -3.179 closest distance to " O   HOH Z 134 " =    2.795
peak=   -3.171 closest distance to " CE3 TRP A 274 " =    2.493
peak=   -3.171 closest distance to " O   HOH Z 264 " =    1.713
peak=   -3.169 closest distance to " O   HOH Z 292 " =    1.803
peak=   -3.169 closest distance to " CB  CYS A 254 " =    2.319
peak=   -3.168 closest distance to " C   LEU A 143 " =    1.280
peak=   -3.166 closest distance to " O   HOH Z 106 " =    1.956
peak=   -3.165 closest distance to " O   HOH Z  76 " =    1.970
peak=   -3.160 closest distance to " O   HOH Z 111 " =    1.342
peak=   -3.159 closest distance to " O   ALA A 292 " =    2.084
peak=   -3.158 closest distance to " O   GLN A 240 " =    2.513
peak=   -3.156 closest distance to " CE  LYS A  76 " =    2.644
peak=   -3.156 closest distance to " CE  LYS A  76 " =    2.621
peak=   -3.153 closest distance to " CA  GLY A  98 " =    1.975
peak=   -3.151 closest distance to " C   GLY A  13 " =    0.934
peak=   -3.150 closest distance to " OD1 ASN A 187 " =    1.593
peak=   -3.145 closest distance to " C   PHE A  59 " =    1.345
peak=   -3.144 closest distance to " N   LYS A 166 " =    1.991
peak=   -3.142 closest distance to " C   SER A 206 " =    1.451
peak=   -3.139 closest distance to " OH  TYR A 247 " =    2.158
peak=   -3.136 closest distance to " CG2 THR A 178 " =    2.321
peak=   -3.128 closest distance to " O   GLY A 196 " =    1.264
peak=   -3.126 closest distance to " O   HOH Z 189 " =    1.880
peak=   -3.123 closest distance to " CG2 VAL A 189 " =    2.091
peak=   -3.109 closest distance to " O   HOH Z 259 " =    2.153
peak=   -3.108 closest distance to " NE2 GLN A  88 " =    1.885
peak=   -3.106 closest distance to " O   HOH Z 128 " =    2.576
peak=   -3.098 closest distance to " CD2 TYR A 247 " =    2.457
peak=   -3.096 closest distance to " N   SER A 212 " =    2.046
peak=   -3.093 closest distance to " O   HOH Z 409 " =    4.620
peak=   -3.091 closest distance to " CE3 TRP A  70 " =    1.796
peak=   -3.079 closest distance to " CD2 LEU A 222 " =    2.217
peak=   -3.074 closest distance to " N   SER A 276 " =    1.348
peak=   -3.073 closest distance to " O   HOH Z 266 " =    5.064
peak=   -3.064 closest distance to " CB  ALA A 248 " =    2.121
peak=   -3.054 closest distance to " SD  MET A 188 " =    2.313
peak=   -3.048 closest distance to " O   HOH Z 193 " =    1.759
peak=   -3.048 closest distance to " O   PRO A 198 " =    1.365
peak=   -3.044 closest distance to " SD BMET A  47 " =    0.946
peak=   -3.031 closest distance to " O   HOH Z 139 " =    2.952

================= 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    :  0.3383 0.3302   6.074935e+00   6.068589e+00
   1_bss:  0.3246 0.3196   6.054439e+00   6.045725e+00
   1_xyz:  0.1774 0.2012   5.501853e+00   5.601795e+00
   1_adp:  0.1606 0.2043   5.439636e+00   5.622616e+00
   1_occ:  0.1602 0.2039   5.437640e+00   5.621487e+00
   2_bss:  0.1574 0.1998   5.427967e+00   5.611246e+00
   2_xyz:  0.1239 0.1690   5.229418e+00   5.455445e+00
   2_adp:  0.1197 0.1637   5.195007e+00   5.423313e+00
   2_occ:  0.1196 0.1635   5.194581e+00   5.423286e+00
   3_bss:  0.1195 0.1625   5.191535e+00   5.418647e+00
   3_xyz:  0.1136 0.1606   5.163668e+00   5.405500e+00
   3_adp:  0.1132 0.1594   5.157352e+00   5.399046e+00
   3_occ:  0.1131 0.1594   5.157243e+00   5.399168e+00
   4_bss:  0.1130 0.1594   5.156972e+00   5.398993e+00
   4_xyz:  0.1132 0.1603   5.161375e+00   5.405350e+00
   4_adp:  0.1132 0.1602   5.160737e+00   5.404893e+00
   4_occ:  0.1131 0.1603   5.160746e+00   5.405102e+00
   5_bss:  0.1131 0.1602   5.160784e+00   5.405048e+00
   5_xyz:  0.1127 0.1611   5.162819e+00   5.410897e+00
   5_adp:  0.1122 0.1619   5.162587e+00   5.415084e+00
   5_occ:  0.1121 0.1619   5.162795e+00   5.415508e+00
   5_bss:  0.1120 0.1618   5.162899e+00   5.415540e+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  50.000   1.562  -3.318   0.184  -0.000   0.000   0.000
   1_xyz:  0.300  50.000   1.562  -3.318   0.184  -0.000   0.000   0.000
   1_adp:  0.300  50.000   1.562  -3.318   0.184  -0.000   0.000   0.000
   1_occ:  0.300  50.000   1.562  -3.318   0.184  -0.000   0.000   0.000
   2_bss:  0.335  68.112  -1.233  -3.200  -1.038  -0.000  -0.000  -0.000
   2_xyz:  0.335  68.112  -1.233  -3.200  -1.038  -0.000  -0.000  -0.000
   2_adp:  0.335  68.112  -1.233  -3.200  -1.038  -0.000  -0.000  -0.000
   2_occ:  0.335  68.112  -1.233  -3.200  -1.038  -0.000  -0.000  -0.000
   3_bss:  0.332  68.112  -2.066  -2.963  -1.301  -0.000  -0.000  -0.000
   3_xyz:  0.332  68.112  -2.066  -2.963  -1.301  -0.000  -0.000  -0.000
   3_adp:  0.332  68.112  -2.066  -2.963  -1.301  -0.000  -0.000  -0.000
   3_occ:  0.332  68.112  -2.066  -2.963  -1.301  -0.000  -0.000  -0.000
   4_bss:  0.318  58.836  -2.245  -2.734  -1.255  -0.000  -0.000  -0.000
   4_xyz:  0.318  58.836  -2.245  -2.734  -1.255  -0.000  -0.000  -0.000
   4_adp:  0.318  58.836  -2.245  -2.734  -1.255  -0.000  -0.000  -0.000
   4_occ:  0.318  58.836  -2.245  -2.734  -1.255  -0.000  -0.000  -0.000
   5_bss:  0.318  58.836  -2.241  -2.586  -1.161  -0.000  -0.000  -0.000
   5_xyz:  0.318  58.836  -2.241  -2.586  -1.161  -0.000  -0.000  -0.000
   5_adp:  0.318  58.836  -2.241  -2.586  -1.161  -0.000  -0.000  -0.000
   5_occ:  0.318  58.836  -2.241  -2.586  -1.161  -0.000  -0.000  -0.000
   5_bss:  0.318  58.802  -2.037  -2.325  -0.940  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.427 0.6990  0.8541    32019.107
   1_bss:  34.455 0.7089  0.8568    29782.443
   1_xyz:  18.674 0.8753  1.0043    10109.658
   1_adp:  19.274 0.8690  1.0066    10449.371
   1_occ:  19.234 0.8693  1.0063    10392.751
   2_bss:  18.960 0.8720  0.9629    10156.072
   2_xyz:  15.494 0.9024  0.9781     7307.780
   2_adp:  14.726 0.9091  0.9773     6876.363
   2_occ:  14.724 0.9091  0.9771     6865.709
   3_bss:  14.646 0.9096  0.9670     6772.306
   3_xyz:  14.287 0.9129  0.9683     6590.375
   3_adp:  14.112 0.9144  0.9651     6518.686
   3_occ:  14.118 0.9143  0.9651     6517.082
   4_bss:  14.118 0.9143  0.9658     6503.609
   4_xyz:  14.248 0.9133  0.9645     6616.132
   4_adp:  14.219 0.9136  0.9597     6614.611
   4_occ:  14.226 0.9136  0.9596     6615.178
   5_bss:  14.226 0.9136  0.9623     6613.824
   5_xyz:  14.317 0.9129  0.9620     6709.670
   5_adp:  14.406 0.9122  0.9551     6746.000
   5_occ:  14.413 0.9121  0.9550     6749.664
   5_bss:  14.417 0.9121  0.9616     6750.468
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6164e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6164e-01
   1_xyz:   1.190  0.010  0.078 15.347  0.005  4.131   7.8026e-02
   1_adp:   1.190  0.010  0.078 15.347  0.005  4.131   7.8026e-02
   1_occ:   1.190  0.010  0.078 15.347  0.005  4.131   7.8026e-02
   2_bss:   1.190  0.010  0.078 15.347  0.005  4.131   7.8026e-02
   2_xyz:   1.113  0.010  0.083 15.015  0.004  4.131   7.5404e-02
   2_adp:   1.113  0.010  0.083 15.015  0.004  4.131   7.5404e-02
   2_occ:   1.113  0.010  0.083 15.015  0.004  4.131   7.5404e-02
   3_bss:   1.113  0.010  0.083 15.015  0.004  4.131   7.5404e-02
   3_xyz:   1.098  0.011  0.083 14.997  0.004  4.137   7.4303e-02
   3_adp:   1.098  0.011  0.083 14.997  0.004  4.137   7.4303e-02
   3_occ:   1.098  0.011  0.083 14.997  0.004  4.137   7.4303e-02
   4_bss:   1.098  0.011  0.083 14.997  0.004  4.137   7.4303e-02
   4_xyz:   1.057  0.010  0.081 14.852  0.004  4.139   6.8526e-02
   4_adp:   1.057  0.010  0.081 14.852  0.004  4.139   6.8526e-02
   4_occ:   1.057  0.010  0.081 14.852  0.004  4.139   6.8526e-02
   5_bss:   1.057  0.010  0.081 14.852  0.004  4.139   6.8526e-02
   5_xyz:   1.055  0.010  0.080 14.811  0.004  4.140   6.8033e-02
   5_adp:   1.055  0.010  0.080 14.811  0.004  4.140   6.8033e-02
   5_occ:   1.055  0.010  0.080 14.811  0.004  4.140   6.8033e-02
   5_bss:   1.055  0.010  0.080 14.811  0.004  4.140   6.8033e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4347e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4347e-01
   1_xyz:   9.786  0.049  0.220 84.583  0.046  2.327   7.6685e-02
   1_adp:   9.786  0.049  0.220 84.583  0.046  2.327   7.6685e-02
   1_occ:   9.786  0.049  0.220 84.583  0.046  2.327   7.6685e-02
   2_bss:   9.786  0.049  0.220 84.583  0.046  2.327   7.6685e-02
   2_xyz:   7.912  0.046  0.260 81.997  0.036  2.295   5.8782e-02
   2_adp:   7.912  0.046  0.260 81.997  0.036  2.295   5.8782e-02
   2_occ:   7.912  0.046  0.260 81.997  0.036  2.295   5.8782e-02
   3_bss:   7.912  0.046  0.260 81.997  0.036  2.295   5.8782e-02
   3_xyz:   8.034  0.047  0.258 84.149  0.039  2.326   5.4981e-02
   3_adp:   8.034  0.047  0.258 84.149  0.039  2.326   5.4981e-02
   3_occ:   8.034  0.047  0.258 84.149  0.039  2.326   5.4981e-02
   4_bss:   8.034  0.047  0.258 84.149  0.039  2.326   5.4981e-02
   4_xyz:   7.889  0.045  0.248 83.584  0.038  2.362   5.2375e-02
   4_adp:   7.889  0.045  0.248 83.584  0.038  2.362   5.2375e-02
   4_occ:   7.889  0.045  0.248 83.584  0.038  2.362   5.2375e-02
   5_bss:   7.889  0.045  0.248 83.584  0.038  2.362   5.2375e-02
   5_xyz:   7.963  0.046  0.239 83.763  0.038  2.345   4.5553e-02
   5_adp:   7.963  0.046  0.239 83.763  0.038  2.345   4.5553e-02
   5_occ:   7.963  0.046  0.239 83.763  0.038  2.345   4.5553e-02
   5_bss:   7.963  0.046  0.239 83.763  0.038  2.345   4.5553e-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:  75.33   0.00  17.45  70.28   0.00  13.20  75.33   3.87  40.64
   1_occ:  75.33   0.00  17.45  70.28   0.00  13.20  75.33   3.87  40.64
   2_bss:  75.33   0.00  17.45  70.28   0.00  13.20  75.33   3.87  40.64
   2_xyz:  75.33   0.00  17.45  70.28   0.00  13.20  75.33   3.87  40.64
   2_adp:  79.28   1.16  17.18  75.09   1.16  13.12  79.28   6.43  39.33
   2_occ:  79.28   1.16  17.18  75.09   1.16  13.12  79.28   6.43  39.33
   3_bss:  79.28   1.16  17.18  75.09   1.16  13.12  79.28   6.43  39.33
   3_xyz:  79.28   1.16  17.18  75.09   1.16  13.12  79.28   6.43  39.33
   3_adp:  80.38   1.54  16.96  75.04   1.54  13.02  80.38   6.13  38.44
   3_occ:  80.38   1.54  16.96  75.04   1.54  13.02  80.38   6.13  38.44
   4_bss:  80.38   1.54  16.96  75.04   1.54  13.02  80.38   6.13  38.44
   4_xyz:  80.38   1.54  16.96  75.04   1.54  13.02  80.38   6.13  38.44
   4_adp:  80.40   1.53  16.78  75.17   1.53  12.88  80.40   6.28  38.03
   4_occ:  80.40   1.53  16.78  75.17   1.53  12.88  80.40   6.28  38.03
   5_bss:  80.40   1.53  16.78  75.17   1.53  12.88  80.40   6.28  38.03
   5_xyz:  80.40   1.53  16.78  75.17   1.53  12.88  80.40   6.28  38.03
   5_adp:  80.88   0.97  16.71  76.36   0.97  12.75  80.88   5.83  38.29
   5_occ:  80.88   0.97  16.71  76.36   0.97  12.75  80.88   5.83  38.29
   5_bss:  80.85   0.94  16.68  76.33   0.94  12.72  80.85   5.80  38.26
------------------------------------------------------------------------
 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:    0.951    0.005    0.343
   1_adp:    0.951    0.005    0.343
   1_occ:    0.951    0.005    0.343
   2_bss:    0.951    0.005    0.343
   2_xyz:    0.898    0.038    0.388
   2_adp:    0.898    0.038    0.388
   2_occ:    0.898    0.038    0.388
   3_bss:    0.898    0.038    0.388
   3_xyz:    1.073    0.044    0.411
   3_adp:    1.073    0.044    0.411
   3_occ:    1.073    0.044    0.411
   4_bss:    1.073    0.044    0.411
   4_xyz:    1.171    0.038    0.418
   4_adp:    1.171    0.038    0.418
   4_occ:    1.171    0.038    0.418
   5_bss:    1.171    0.038    0.418
   5_xyz:    1.256    0.045    0.424
   5_adp:    1.256    0.045    0.424
   5_occ:    1.256    0.045    0.424
   5_bss:    1.256    0.045    0.424
------------------------------------------------------------------------

CPU time actual refinement: 271.14


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1151/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_1151/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1151/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1151/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1151/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 271.00 
  Macro-tasks:
    bulk solvent and scale       = 30.55  
    individual site refinement   = 113.98 
    weights calculation          = 24.09  
    collect and process          = 5.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 174.19 
  Micro-tasks:
    mask                            = 0.95   
    f_calc                          = 86.43  
    alpha_beta                      = 6.83   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 95.52  
    fmodel                         = 5.35   
    r_factors                      = 0.18   
    phase_errors                   = 9.32   
    foms                           = 0.19   
    TOTAL for micro-tasks          = 205.76 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.802 micro seconds
Total CPU time: 4.71 minutes
from_scatterers_fft:    659 calls, 86.21 s
gradients_fft:          604 calls, 83.11 s

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

# Date 2008-01-16 Time 06:32:39 PST -0800 (1200493959.56 s)
Start R-work = 0.3383, R-free = 0.3302 (no bulk solvent and anisotropic scale)
Final R-work = 0.1350, R-free = 0.1807 (no bulk solvent and anisotropic scale)

Start R-work = 0.3246, R-free = 0.3196
Final R-work = 0.1120, R-free = 0.1618