# Date 2008-01-16 Time 06:51:47 PST -0800 (1200495107.53 s)
#phil __OFF__

Command line arguments: "../1313.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15567
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1313

-------------------------------------------------------------------------------
  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: (72.0062, 47.8686, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2429 1.99133
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933521

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2429
                             d_min =   1.9913

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: (72.0062, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2429 1.99133
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933521

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2433 -  4.2619 [2200/2229]  1982   218   9.9%
  bin  2:  4.2619 -  3.3951 [2098/2121]  1889   209  10.0%
  bin  3:  3.3951 -  2.9695 [2081/2103]  1867   214  10.3%
  bin  4:  2.9695 -  2.6996 [2071/2090]  1874   197   9.5%
  bin  5:  2.6996 -  2.5071 [2053/2082]  1838   215  10.5%
  bin  6:  2.5071 -  2.3598 [2033/2074]  1837   196   9.6%
  bin  7:  2.3598 -  2.2420 [2027/2063]  1823   204  10.1%
  bin  8:  2.2420 -  2.1447 [2014/2052]  1813   201  10.0%
  bin  9:  2.1447 -  2.0623 [2027/2058]  1821   206  10.2%
  bin 10:  2.0623 -  1.9913 [ 985/2049]   886    99  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1313/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:
        1.13 -     1.89: 4
        1.89 -     2.64: 60
        2.64 -     3.39: 4226
        3.39 -     4.15: 9210
        4.15 -     4.90: 14363
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.134 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.700 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.857 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  1.951 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27858 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_1313/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1313/model_refine_001.geo

CPU time processing inputs: 8.20


============================ 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 = 72.00625 47.8686 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4511   r_free= 0.4326   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.262229                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.7539 0.99   1422  159 0.3542 0.3727       6.518      6.5082|
|  2:  4.7539 -  3.7924 0.99   1374  146 0.3855 0.3908      6.8073      6.7735|
|  3:  3.7924 -  3.3187 0.99   1348  158 0.4231 0.3731      6.6493      6.5874|
|  4:  3.3187 -  3.0178 0.99   1341  147 0.4440 0.4298      6.4939      6.4998|
|  5:  3.0178 -  2.8029 0.99   1308  148 0.4693 0.4677      6.3406       6.358|
|  6:  2.8029 -  2.6386 0.98   1333  146 0.4909 0.4634       6.257       6.187|
|  7:  2.6386 -  2.5071 0.99   1324  149 0.4916 0.4334      6.2346      6.1535|
|  8:  2.5071 -  2.3984 0.99   1296  142 0.4947 0.4481      6.1369      6.1694|
|  9:  2.3984 -  2.3063 0.98   1322  149 0.5065 0.5001      6.1144      6.0977|
| 10:  2.3063 -  2.2270 0.98   1300  146 0.4944 0.5012      6.0703      6.1062|
| 11:  2.2270 -  2.1576 0.98   1296  138 0.5166 0.4629       6.032       6.011|
| 12:  2.1576 -  2.0961 0.99   1301  143 0.5073 0.4850      5.9479      5.9612|
| 13:  2.0961 -  2.0410 0.95   1253  147 0.4865 0.4537      5.8627      5.8208|
| 14:  2.0410 -  1.9913 0.31    412   41 0.4863 0.4828      5.8042      5.7397|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.7539  1422   159  0.72  32.50   0.82     0.75      65014.09|
|  2:  4.7539 -  3.7924  1374   146  0.74  31.89   0.91     0.81      87743.69|
|  3:  3.7924 -  3.3187  1348   158  0.64  40.76   0.89     0.79      97548.96|
|  4:  3.3187 -  3.0178  1341   147  0.55  47.97   0.89     0.71      90597.15|
|  5:  3.0178 -  2.8029  1308   148  0.46  55.34   0.88     0.63      77151.80|
|  6:  2.8029 -  2.6386  1333   146  0.45  56.20   0.89     0.61      62641.92|
|  7:  2.6386 -  2.5071  1324   149  0.47  54.35   0.91     0.62      54605.42|
|  8:  2.5071 -  2.3984  1296   142  0.44  56.96   0.87     0.62      51556.16|
|  9:  2.3984 -  2.3063  1322   149  0.41  59.34   0.91     0.59      49663.14|
| 10:  2.3063 -  2.2270  1300   146  0.41  59.47   0.93     0.58      46969.45|
| 11:  2.2270 -  2.1576  1296   138  0.40  59.89   0.91     0.59      42870.76|
| 12:  2.1576 -  2.0961  1301   143  0.41  59.55   0.92     0.62      38420.24|
| 13:  2.0961 -  2.0410  1253   147  0.43  57.87   0.91     0.63      31395.28|
| 14:  2.0410 -  1.9913   412    41  0.46  54.96   0.94     0.63      23629.05|
|alpha:            min =        0.58 max =            0.81 mean =         0.66|
|beta:             min =    23629.05 max =        97548.96 mean =     60740.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.53|
|phase err.(test): min =        0.00 max =           89.85 mean =        51.33|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.145259              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.493   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.185899              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.567   (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 |  1.134 -  1.510:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.510 -  1.887:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.887 -  2.264:        8 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.264 -  2.640:       52 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.640 -  3.017:     1946 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.017 -  3.393:     2280 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.393 -  3.770:     3906 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.770 -  4.147:     5304 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.147 -  4.523:     6393 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.523 -  4.900:     7970 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.134 |       0.305 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.354)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4511   r_free= 0.4326   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.262229                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4417   r_free= 0.4234   ksol= 0.28   Bsol= 33.91   scale= 0.933   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.55,3.61,-1.98,0.00,-0.00,-0.00); trace/3= 1.06                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255177                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.988318              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.447   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.091397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.301   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4417      final r-factor (work) = 0.3479          |
| start r-factor (free) = 0.4234      final r-factor (free) = 0.3791          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.0198 = 6.99 * 0.50 * 6.2523 + 1.00 * 0.1732                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.5189 = 6.99 * 0.50 * 6.1252 + 1.00 * 0.1164                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3479      final r-factor (work) = 0.3155          |
| start r-factor (free) = 0.3791      final r-factor (free) = 0.3875          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6911 = 1.09 * 1.00 * 6.1252 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6077 = 1.09 * 1.00 * 6.0382 + 1.00 * 0.0176                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.354)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.33  18.42    None  None   None       |
|    all(noH): 2823   0      0.00    107.33  18.42    None  None   None       |
|    Sol.    : 438    0      0.00    107.33  38.04    None  None   None       |
|    Mac.    : 2385   0      0.00    87.53   14.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.733: 1072   |   5:    53.663 -  64.395:   65        |
|      1:    10.733 -  21.465:  907   |   6:    64.395 -  75.128:   40        |
|      2:    21.465 -  32.198:  413   |   7:    75.128 -  85.860:   10        |
|      3:    32.198 -  42.930:  205   |   8:    85.860 -  96.593:    5        |
|      4:    42.930 -  53.663:  105   |   9:    96.593 - 107.325:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3155 r_free = 0.3875             target_work(ml) = 6.043         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3154 r_free = 0.3880             target_work(ml) = 6.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3154   r_free= 0.3880   ksol= 0.28   Bsol= 33.91   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.55,3.61,-1.98,0.00,-0.00,-0.00); trace/3= 1.06                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.042443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3147   r_free= 0.3869   ksol= 0.32   Bsol= 65.73   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.23,1.89,-0.67,0.00,-0.00,-0.00); trace/3= 0.48                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.043398                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.902826              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.367   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.589208              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.581  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3147      final r-factor (work) = 0.2414          |
| start r-factor (free) = 0.3869      final r-factor (free) = 0.2971          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.9982 = 8.90 * 0.50 * 6.0389 + 1.00 * 0.1167                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.5669 = 8.90 * 0.50 * 5.9445 + 1.00 * 0.1055                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2414      final r-factor (work) = 0.2183          |
| start r-factor (free) = 0.2971      final r-factor (free) = 0.2739          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5203 = 0.59 * 1.00 * 5.9445 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4039 = 0.59 * 1.00 * 5.7551 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.354)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.34   18.13    None  None   None       |
|    all(noH): 2823   0      0.00    96.34   18.13    None  None   None       |
|    Sol.    : 438    0      1.63    96.34   41.70    None  None   None       |
|    Mac.    : 2385   0      0.00    93.77   13.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.635: 1026   |   5:    48.172 -  57.807:   98        |
|      1:     9.635 -  19.269:  954   |   6:    57.807 -  67.441:   56        |
|      2:    19.269 -  28.903:  346   |   7:    67.441 -  77.076:   28        |
|      3:    28.903 -  38.538:  171   |   8:    77.076 -  86.710:   15        |
|      4:    38.538 -  48.172:  121   |   9:    86.710 -  96.345:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2183 r_free = 0.2739             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2180 r_free = 0.2735             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2180   r_free= 0.2735   ksol= 0.32   Bsol= 65.73   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.23,1.89,-0.67,0.00,-0.00,-0.00); trace/3= 0.48                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.720581                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2174   r_free= 0.2724   ksol= 0.33   Bsol= 74.58   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,0.29,-0.72,0.00,-0.00,-0.00); trace/3= -0.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.719045                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.206912              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.633   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335616              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.398  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2174      final r-factor (work) = 0.1778          |
| start r-factor (free) = 0.2724      final r-factor (free) = 0.2262          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3354 = 3.21 * 0.50 * 5.7563 + 1.00 * 0.1055                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0925 = 3.21 * 0.50 * 5.6332 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1778      final r-factor (work) = 0.1683          |
| start r-factor (free) = 0.2262      final r-factor (free) = 0.2143          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9035 = 0.34 * 1.00 * 5.6332 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8613 = 0.34 * 1.00 * 5.5131 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.354)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.89   17.53    None  None   None       |
|    all(noH): 2823   0      0.00    96.89   17.53    None  None   None       |
|    Sol.    : 438    0      3.63    94.27   42.31    None  None   None       |
|    Mac.    : 2385   0      0.00    96.89   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.689: 1096   |   5:    48.447 -  58.136:   94        |
|      1:     9.689 -  19.379:  996   |   6:    58.136 -  67.825:   64        |
|      2:    19.379 -  29.068:  272   |   7:    67.825 -  77.515:   22        |
|      3:    29.068 -  38.757:  133   |   8:    77.515 -  87.204:   13        |
|      4:    38.757 -  48.447:  127   |   9:    87.204 -  96.893:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1683 r_free = 0.2143             target_work(ml) = 5.492         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1683 r_free = 0.2142             target_work(ml) = 5.492         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1683   r_free= 0.2142   ksol= 0.33   Bsol= 74.58   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,0.29,-0.72,0.00,-0.00,-0.00); trace/3= -0.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.491595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1687   r_free= 0.2144   ksol= 0.33   Bsol= 75.72   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-0.58,-0.99,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.493650                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.570045              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.475  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.464388              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.303  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1687      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.2144      final r-factor (free) = 0.1861          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1490 = 2.57 * 0.50 * 5.5167 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0218 = 2.57 * 0.50 * 5.4141 + 1.00 * 0.0646                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1410      final r-factor (work) = 0.1347          |
| start r-factor (free) = 0.1861      final r-factor (free) = 0.1816          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5252 = 0.46 * 1.00 * 5.4141 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4806 = 0.46 * 1.00 * 5.3172 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.354)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.84  17.31    None  None   None       |
|    all(noH): 2823   0      0.00    100.84  17.31    None  None   None       |
|    Sol.    : 438    0      4.28    97.20   42.91    None  None   None       |
|    Mac.    : 2385   0      0.00    100.84  12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.085: 1185   |   5:    50.423 -  60.507:   91        |
|      1:    10.085 -  20.169:  996   |   6:    60.507 -  70.592:   62        |
|      2:    20.169 -  30.254:  210   |   7:    70.592 -  80.676:   20        |
|      3:    30.254 -  40.338:  127   |   8:    80.676 -  90.761:    9        |
|      4:    40.338 -  50.423:  116   |   9:    90.761 - 100.845:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1347 r_free = 0.1816             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1346 r_free = 0.1814             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1814   ksol= 0.33   Bsol= 75.72   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-0.58,-0.99,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.304862                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1350   r_free= 0.1814   ksol= 0.33   Bsol= 72.06   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-0.84,-0.76,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306620                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.069804              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.785  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.911  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1350      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1745          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5684 = 2.07 * 0.50 * 5.3182 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5259 = 2.07 * 0.50 * 5.2787 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4925 = 0.66 * 1.00 * 5.2787 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4730 = 0.66 * 1.00 * 5.2485 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.354)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.74  17.09    None  None   None       |
|    all(noH): 2823   0      0.00    104.74  17.09    None  None   None       |
|    Sol.    : 438    0      4.23    100.76  42.73    None  None   None       |
|    Mac.    : 2385   0      0.00    104.74  12.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.474: 1282   |   5:    52.370 -  62.843:   93        |
|      1:    10.474 -  20.948:  945   |   6:    62.843 -  73.317:   41        |
|      2:    20.948 -  31.422:  192   |   7:    73.317 -  83.791:   22        |
|      3:    31.422 -  41.896:  130   |   8:    83.791 -  94.265:    5        |
|      4:    41.896 -  52.370:  105   |   9:    94.265 - 104.739:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1238 r_free = 0.1743             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1743             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1743   ksol= 0.33   Bsol= 72.06   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-0.84,-0.76,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247726                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.7539 0.99   1422  159 0.1022 0.1321      5.4147      5.5615|
|  2:  4.7539 -  3.7924 0.99   1374  146 0.0877 0.1116      5.4511      5.6568|
|  3:  3.7924 -  3.3187 0.99   1348  158 0.1116 0.1644      5.5131      5.8961|
|  4:  3.3187 -  3.0178 0.99   1341  147 0.1378 0.1706      5.5521        5.69|
|  5:  3.0178 -  2.8029 0.99   1308  148 0.1540 0.2073      5.4685      5.6674|
|  6:  2.8029 -  2.6386 0.98   1333  146 0.1456 0.2061      5.3423      5.5465|
|  7:  2.6386 -  2.5071 0.99   1324  149 0.1370 0.1997      5.2636      5.5119|
|  8:  2.5071 -  2.3984 0.99   1296  142 0.1334 0.1853      5.1695      5.3921|
|  9:  2.3984 -  2.3063 0.98   1322  149 0.1349 0.2070      5.1514      5.3997|
| 10:  2.3063 -  2.2270 0.98   1300  146 0.1284 0.1842      5.0895      5.2978|
| 11:  2.2270 -  2.1576 0.98   1296  138 0.1260 0.2051      5.0329      5.4012|
| 12:  2.1576 -  2.0961 0.99   1301  143 0.1271 0.1986      4.9772      5.2085|
| 13:  2.0961 -  2.0410 0.95   1253  147 0.1286 0.1890      4.8863      5.1095|
| 14:  2.0410 -  1.9913 0.31    412   41 0.1196 0.1766      4.7604      4.9811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.7539  1422   159  0.94   9.43   0.96     0.93       7641.66|
|  2:  4.7539 -  3.7924  1374   146  0.95   8.41   1.00     0.98       9258.51|
|  3:  3.7924 -  3.3187  1348   158  0.93  12.17   1.02     1.01      11358.38|
|  4:  3.3187 -  3.0178  1341   147  0.90  15.85   1.00     0.98      12669.73|
|  5:  3.0178 -  2.8029  1308   148  0.87  19.28   0.99     0.97      11500.51|
|  6:  2.8029 -  2.6386  1333   146  0.88  18.73   0.99     0.96       9113.11|
|  7:  2.6386 -  2.5071  1324   149  0.89  17.49   0.99     0.95       7719.81|
|  8:  2.5071 -  2.3984  1296   142  0.88  18.10   0.99     0.95       6721.34|
|  9:  2.3984 -  2.3063  1322   149  0.88  18.24   0.99     0.93       6266.73|
| 10:  2.3063 -  2.2270  1300   146  0.89  17.82   0.98     0.94       5792.58|
| 11:  2.2270 -  2.1576  1296   138  0.88  18.39   0.98     0.93       5322.72|
| 12:  2.1576 -  2.0961  1301   143  0.89  17.85   0.98     0.97       4949.51|
| 13:  2.0961 -  2.0410  1253   147  0.88  18.42   0.97     0.96       4140.16|
| 14:  2.0410 -  1.9913   412    41  0.88  18.12   0.96     0.93       3223.21|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3223.21 max =        12669.73 mean =      7809.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.12|
|phase err.(test): min =        0.00 max =           89.29 mean =        15.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1743   ksol= 0.33   Bsol= 72.06   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-1.00,-0.79,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247697                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1743   ksol= 0.33   Bsol= 72.06   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-1.00,-0.79,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247697                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.7539 0.99   1422  159 0.1022 0.1321      5.4146      5.5614|
|  2:  4.7539 -  3.7924 0.99   1374  146 0.0878 0.1116      5.4512      5.6572|
|  3:  3.7924 -  3.3187 0.99   1348  158 0.1116 0.1645      5.5134      5.8966|
|  4:  3.3187 -  3.0178 0.99   1341  147 0.1378 0.1706      5.5522      5.6898|
|  5:  3.0178 -  2.8029 0.99   1308  148 0.1540 0.2073      5.4684      5.6675|
|  6:  2.8029 -  2.6386 0.98   1333  146 0.1456 0.2058       5.342      5.5458|
|  7:  2.6386 -  2.5071 0.99   1324  149 0.1370 0.1997      5.2634      5.5118|
|  8:  2.5071 -  2.3984 0.99   1296  142 0.1333 0.1854      5.1694      5.3922|
|  9:  2.3984 -  2.3063 0.98   1322  149 0.1348 0.2071      5.1512      5.3998|
| 10:  2.3063 -  2.2270 0.98   1300  146 0.1284 0.1842      5.0897      5.2982|
| 11:  2.2270 -  2.1576 0.98   1296  138 0.1259 0.2049      5.0326      5.4008|
| 12:  2.1576 -  2.0961 0.99   1301  143 0.1271 0.1987      4.9773      5.2089|
| 13:  2.0961 -  2.0410 0.95   1253  147 0.1286 0.1890      4.8863      5.1096|
| 14:  2.0410 -  1.9913 0.31    412   41 0.1195 0.1763        4.76      4.9796|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.7539  1422   159  0.94   9.43   0.96     0.93       7640.91|
|  2:  4.7539 -  3.7924  1374   146  0.95   8.41   1.00     0.98       9260.58|
|  3:  3.7924 -  3.3187  1348   158  0.93  12.17   1.01     1.01      11368.39|
|  4:  3.3187 -  3.0178  1341   147  0.90  15.85   1.00     0.97      12671.79|
|  5:  3.0178 -  2.8029  1308   148  0.87  19.27   0.99     0.97      11496.95|
|  6:  2.8029 -  2.6386  1333   146  0.88  18.71   0.98     0.96       9105.93|
|  7:  2.6386 -  2.5071  1324   149  0.89  17.48   0.98     0.95       7715.96|
|  8:  2.5071 -  2.3984  1296   142  0.88  18.10   0.99     0.95       6723.43|
|  9:  2.3984 -  2.3063  1322   149  0.88  18.24   0.99     0.93       6269.87|
| 10:  2.3063 -  2.2270  1300   146  0.89  17.82   0.98     0.94       5796.52|
| 11:  2.2270 -  2.1576  1296   138  0.88  18.39   0.97     0.92       5323.07|
| 12:  2.1576 -  2.0961  1301   143  0.89  17.85   0.98     0.96       4951.22|
| 13:  2.0961 -  2.0410  1253   147  0.88  18.41   0.97     0.96       4137.47|
| 14:  2.0410 -  1.9913   412    41  0.88  18.11   0.96     0.92       3219.70|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3219.70 max =        12671.79 mean =      7809.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.12|
|phase err.(test): min =        0.00 max =           89.29 mean =        15.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.354)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.74  17.09    None  None   None       |
|    all(noH): 2823   0      0.00    104.74  17.09    None  None   None       |
|    Sol.    : 438    0      4.23    100.77  42.73    None  None   None       |
|    Mac.    : 2385   0      0.00    104.74  12.39    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:     0.003 -  10.477: 1282   |   5:    52.372 -  62.846:   93        |
|      1:    10.477 -  20.951:  945   |   6:    62.846 -  73.320:   41        |
|      2:    20.951 -  31.425:  192   |   7:    73.320 -  83.794:   22        |
|      3:    31.425 -  41.899:  130   |   8:    83.794 -  94.268:    5        |
|      4:    41.899 -  52.372:  105   |   9:    94.268 - 104.742:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 350         
Filter by distance & map next to the model:
   mapped sites are within: 0.643 - 5.964
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 350
   mapped sites are within: 0.718 - 5.964

peak=    5.846 closest distance to " CB  GLN A 223 " =    1.462
peak=    5.505 closest distance to " CB  SER A  63 " =    1.376
peak=    5.370 closest distance to " O   HOH Z 111 " =    1.924
peak=    5.108 closest distance to " CG  PRO A  54 " =    1.288
peak=    5.092 closest distance to " O   HOH Z 232 " =    2.223
peak=    4.981 closest distance to " CG  PRO A 213 " =    1.334
peak=    4.958 closest distance to " CG  PRO A 280 " =    0.857
peak=    4.905 closest distance to " O   PRO A 198 " =    1.515
peak=    4.757 closest distance to " CA  TYR A  30 " =    0.986
peak=    4.727 closest distance to " CG  PRO A 198 " =    1.242
peak=    4.600 closest distance to " CB  GLU A 128 " =    1.159
peak=    4.577 closest distance to " O   HOH Z 210 " =    1.165
peak=    4.525 closest distance to " O   HOH Z 433 " =    1.763
peak=    4.496 closest distance to " O   HOH Z 425 " =    1.561
peak=    4.431 closest distance to " O   HOH Z 134 " =    1.752
peak=    4.421 closest distance to " O   HOH Z 126 " =    1.586
peak=    4.406 closest distance to " CG1 ILE A  33 " =    1.293
peak=    4.404 closest distance to " CB  PRO A  54 " =    0.838
peak=    4.384 closest distance to " O   HOH Z  15 " =    2.123
peak=    4.335 closest distance to " O   HOH Z 298 " =    2.065
peak=    4.332 closest distance to " CB  ARG A 190 " =    1.774
peak=    4.293 closest distance to " O   HOH Z 133 " =    2.379
peak=    4.290 closest distance to " O   HOH Z  67 " =    2.066
peak=    4.232 closest distance to " CG2 THR A 221 " =    1.019
peak=    4.230 closest distance to " O   HOH Z  40 " =    1.994
peak=    4.227 closest distance to " CD  ARG A 269 " =    0.926
peak=    4.220 closest distance to " O   HOH Z  97 " =    2.012
peak=    4.219 closest distance to " CB  LEU A 228 " =    1.073
peak=    4.218 closest distance to " CG2BVAL A  41 " =    0.937
peak=    4.210 closest distance to " O   HOH Z 196 " =    1.525
peak=    4.207 closest distance to " CZ  PHE A 218 " =    1.174
peak=    4.189 closest distance to " O   HOH Z  20 " =    2.100
peak=    4.182 closest distance to " CB  TRP A 266 " =    0.978
peak=    4.178 closest distance to " O   HOH Z 369 " =    2.079
peak=    4.170 closest distance to " CB  ARG A 275 " =    0.826
peak=    4.165 closest distance to " O   HOH Z 271 " =    2.615
peak=    4.164 closest distance to " NE2 HIS A 115 " =    1.053
peak=    4.158 closest distance to " CG  PRO A 243 " =    1.168
peak=    4.092 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.090 closest distance to " O   HOH Z 234 " =    3.886
peak=    4.087 closest distance to " CA  ALA A 160 " =    0.986
peak=    4.066 closest distance to " CB  ASN A 148 " =    1.381
peak=    4.063 closest distance to " CZ  PHE A 192 " =    0.951
peak=    4.056 closest distance to " O   HOH Z 411 " =    3.379
peak=    4.044 closest distance to " O   HOH Z 247 " =    1.498
peak=    4.040 closest distance to " O   HOH Z 112 " =    1.484
peak=    4.032 closest distance to " CB  VAL A 202 " =    1.547
peak=    4.026 closest distance to " CD  ARG A 159 " =    0.844
peak=    3.993 closest distance to " CA  GLU A 152 " =    0.917
peak=    3.985 closest distance to " CD1 LEU A 300 " =    1.264
peak=    3.973 closest distance to " OD1 ASN A 217 " =    1.628
peak=    3.959 closest distance to " CB  TRP A 179 " =    1.501
peak=    3.956 closest distance to " O   HOH Z  47 " =    1.655
peak=    3.954 closest distance to " O   HOH Z  80 " =    2.026
peak=    3.950 closest distance to " O   HOH Z  78 " =    2.257
peak=    3.949 closest distance to " CB  GLU A 152 " =    1.198
peak=    3.949 closest distance to " CA  ASP A 191 " =    0.832
peak=    3.943 closest distance to " OE1 GLN A  11 " =    1.945
peak=    3.943 closest distance to " O   HOH Z 118 " =    1.685
peak=    3.940 closest distance to " CD BLYS A 290 " =    0.974
peak=    3.937 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.927 closest distance to " CB  ASP A 124 " =    0.835
peak=    3.925 closest distance to " CA  ALA A  51 " =    0.959
peak=    3.905 closest distance to " NH2BARG A 102 " =    1.089
peak=    3.896 closest distance to " O   HOH Z 374 " =    2.770
peak=    3.888 closest distance to " O   HOH Z  21 " =    1.876
peak=    3.882 closest distance to " O   HOH Z 214 " =    1.325
peak=    3.876 closest distance to " CA  GLY A 196 " =    1.015
peak=    3.859 closest distance to " O   HOH Z 404 " =    1.530
peak=    3.856 closest distance to " CG1 VAL A 153 " =    1.085
peak=    3.853 closest distance to " O   HOH Z 394 " =    1.656
peak=    3.843 closest distance to " CD2 LEU A 255 " =    1.521
peak=    3.839 closest distance to " O   HOH Z 132 " =    2.729
peak=    3.834 closest distance to " O   HOH Z  22 " =    2.686
peak=    3.832 closest distance to " CA  ALA A  21 " =    1.387
peak=    3.827 closest distance to " NH2 ARG A 156 " =    1.242
peak=    3.826 closest distance to " OE1 GLN A  88 " =    0.845
peak=    3.812 closest distance to " CD2 LEU A 297 " =    1.037
peak=    3.805 closest distance to " O   HOH Z 418 " =    1.557
peak=    3.804 closest distance to " CB  SER A 141 " =    1.038
peak=    3.802 closest distance to " O   HOH Z  43 " =    2.005
peak=    3.772 closest distance to " O   HOH Z 131 " =    2.450
peak=    3.766 closest distance to " N   HIS A 108 " =    1.889
peak=    3.762 closest distance to " O   HOH Z 209 " =    2.398
peak=    3.755 closest distance to " CA  GLU A  46 " =    0.824
peak=    3.753 closest distance to " O   THR A 251 " =    1.294
peak=    3.752 closest distance to " O   HOH Z 227 " =    1.772
peak=    3.748 closest distance to " O   HOH Z 383 " =    2.124
peak=    3.744 closest distance to " N   ASN A  39 " =    1.264
peak=    3.741 closest distance to " O   HOH Z 368 " =    1.996
peak=    3.735 closest distance to " N   ILE A  33 " =    1.073
peak=    3.733 closest distance to " O   HOH Z 389 " =    1.968
peak=    3.733 closest distance to " O   HOH Z  61 " =    1.771
peak=    3.731 closest distance to " O   HOH Z 245 " =    1.342
peak=    3.730 closest distance to " CB  PRO A 198 " =    0.998
peak=    3.729 closest distance to " O   SER A  87 " =    2.377
peak=    3.728 closest distance to " NZ  LYS A 117 " =    3.184
peak=    3.716 closest distance to " CB  ALA A 100 " =    1.550
peak=    3.701 closest distance to " CG2 VAL A  78 " =    0.946
peak=    3.694 closest distance to " O   HOH Z 402 " =    1.575
peak=    3.677 closest distance to " O   HOH Z 373 " =    1.645
peak=    3.673 closest distance to " O   HOH Z 189 " =    2.636
peak=    3.669 closest distance to " O   HOH Z 163 " =    1.833
peak=    3.666 closest distance to " CD  ARG A  56 " =    1.306
peak=    3.654 closest distance to " O   HOH Z 135 " =    2.057
peak=    3.651 closest distance to " CD  ARG A  66 " =    2.548
peak=    3.647 closest distance to " CB  GLU A 277 " =    3.880
peak=    3.647 closest distance to " O   HOH Z 279 " =    2.387
peak=    3.645 closest distance to " O   HOH Z 432 " =    1.763
peak=    3.644 closest distance to " O   HOH Z 287 " =    2.014
peak=    3.643 closest distance to " O   ASP A 124 " =    1.186
peak=    3.642 closest distance to " O   HOH Z  30 " =    1.783
peak=    3.636 closest distance to " CB  ASP A 140 " =    0.865
peak=    3.635 closest distance to " O   HOH Z 437 " =    1.555
peak=    3.633 closest distance to " CB  TYR A 169 " =    0.840
peak=    3.633 closest distance to " C   GLY A  80 " =    1.193
peak=    3.626 closest distance to " O   HOH Z 193 " =    1.971
peak=    3.624 closest distance to " CB  ASN A 187 " =    1.103
peak=    3.622 closest distance to " CB  ILE A 199 " =    1.069
peak=    3.620 closest distance to " O   HOH Z  48 " =    1.680
peak=    3.605 closest distance to " O   HOH Z 433 " =    2.181
peak=    3.599 closest distance to " O   HOH Z 362 " =    3.250
peak=    3.595 closest distance to " CB  PRO A  54 " =    1.326
peak=    3.594 closest distance to " O   HOH Z 180 " =    2.202
peak=    3.591 closest distance to " CD1 TRP A 266 " =    1.102
peak=    3.591 closest distance to " ND1 HIS A  81 " =    1.706
peak=    3.588 closest distance to " CG AARG A 275 " =    1.201
peak=    3.582 closest distance to " O   HOH Z 265 " =    1.941
peak=    3.580 closest distance to " O   HOH Z 128 " =    2.305
peak=    3.579 closest distance to " O   HOH Z 171 " =    3.803
peak=    3.568 closest distance to " O   HOH Z 387 " =    2.805
peak=    3.566 closest distance to " CB  ARG A  79 " =    1.397
peak=    3.563 closest distance to " O   HOH Z 128 " =    2.200
peak=    3.562 closest distance to " CD  LYS A 166 " =    1.383
peak=    3.555 closest distance to " O   HOH Z 116 " =    1.880
peak=    3.543 closest distance to " CA  ARG A  36 " =    1.175
peak=    3.542 closest distance to " OG  SER A  97 " =    3.552
peak=    3.537 closest distance to " O   HOH Z  19 " =    2.322
peak=    3.534 closest distance to " CG  GLU A  37 " =    1.025
peak=    3.530 closest distance to " CB  PHE A 204 " =    1.053
peak=    3.526 closest distance to " O   HOH Z  88 " =    3.625
peak=    3.523 closest distance to " OD1 ASN A  69 " =    2.550
peak=    3.516 closest distance to " O   HOH Z 243 " =    1.107
peak=    3.513 closest distance to " NH1 ARG A  56 " =    1.274
peak=    3.512 closest distance to " O   HOH Z 391 " =    3.013
peak=    3.509 closest distance to " CA  MET A  40 " =    1.161
peak=    3.506 closest distance to " O   HOH Z 426 " =    1.510
peak=    3.495 closest distance to " O   HOH Z 303 " =    2.217
peak=    3.491 closest distance to " CB  ALA A 291 " =    1.260
peak=    3.489 closest distance to " CB  SER A   3 " =    1.488
peak=    3.487 closest distance to " CE2 TYR A 186 " =    0.891
peak=    3.486 closest distance to " CA  GLN A 223 " =    0.940
peak=    3.486 closest distance to " O   HOH Z 104 " =    2.789
peak=    3.484 closest distance to " CD  ARG A 195 " =    1.011
peak=    3.483 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.478 closest distance to " O   HOH Z 395 " =    1.446
peak=    3.478 closest distance to " CB  SER A 216 " =    0.862
peak=    3.474 closest distance to " CB  ALA A   9 " =    1.610
peak=    3.471 closest distance to " CA  GLY A 241 " =    0.792
peak=    3.469 closest distance to " O   ALA A 165 " =    1.399
peak=    3.464 closest distance to " NH1AARG A 145 " =    1.112
peak=    3.459 closest distance to " O   HOH Z 325 " =    2.247
peak=    3.457 closest distance to " CB  ALA A 256 " =    1.416
peak=    3.451 closest distance to " CB  VAL A 265 " =    1.220
peak=    3.449 closest distance to " O   HOH Z 271 " =    2.513
peak=    3.443 closest distance to " CG BARG A 275 " =    1.477
peak=    3.440 closest distance to " CB  ALA A 248 " =    1.056
peak=    3.437 closest distance to " O   HOH Z 102 " =    1.324
peak=    3.436 closest distance to " CZ3 TRP A  85 " =    0.916
peak=    3.435 closest distance to " O   HOH Z 174 " =    2.010
peak=    3.431 closest distance to " CB  ASN A 142 " =    1.113
peak=    3.425 closest distance to " CB  ARG A 139 " =    1.071
peak=    3.418 closest distance to " NZ  LYS A  76 " =    1.555
peak=    3.417 closest distance to " CA  ILE A  33 " =    1.649
peak=    3.413 closest distance to " NH2AARG A 190 " =    1.458
peak=    3.408 closest distance to " O   HOH Z 174 " =    1.256
peak=    3.400 closest distance to " O   HOH Z 344 " =    3.260
peak=    3.397 closest distance to " O   HOH Z 176 " =    1.786
peak=    3.392 closest distance to " CB  MET A  47 " =    1.015
peak=    3.390 closest distance to " N   ASN A 127 " =    1.271
peak=    3.388 closest distance to " O   HOH Z 301 " =    1.272
peak=    3.387 closest distance to " O   HOH Z 272 " =    1.932
peak=    3.386 closest distance to " O   HOH Z 357 " =    2.010
peak=    3.383 closest distance to " CA  ILE A 263 " =    0.988
peak=    3.367 closest distance to " O   HOH Z 313 " =    2.033
peak=    3.366 closest distance to " CB  SER A 212 " =    1.209
peak=    3.363 closest distance to " CB  PHE A  16 " =    0.923
peak=    3.362 closest distance to " CA  ARG A 102 " =    1.256
peak=    3.353 closest distance to " OE1 GLN A 278 " =    0.911
peak=    3.350 closest distance to " CB  GLN A 103 " =    0.999
peak=    3.342 closest distance to " NH2BARG A 145 " =    2.058
peak=    3.336 closest distance to " O   HOH Z  49 " =    1.207
peak=    3.335 closest distance to " O   HOH Z 223 " =    1.015
peak=    3.333 closest distance to " CB  ALA A  71 " =    1.249
peak=    3.332 closest distance to " O   HOH Z 128 " =    1.776
peak=    3.330 closest distance to " N   TYR A  15 " =    0.760
peak=    3.324 closest distance to " CB  ARG A 259 " =    1.883
peak=    3.322 closest distance to " CA  THR A 221 " =    0.903
peak=    3.319 closest distance to " NZ  LYS A 117 " =    1.535
peak=    3.316 closest distance to " CB  TRP A 150 " =    1.043
peak=    3.315 closest distance to " CB  MET A  40 " =    0.772
peak=    3.310 closest distance to " CD  PRO A 280 " =    0.932
peak=    3.310 closest distance to " OG1 THR A 294 " =    2.519
peak=    3.308 closest distance to " O   HOH Z 134 " =    2.357
peak=    3.307 closest distance to " O   HOH Z 371 " =    3.360
peak=    3.307 closest distance to " CD1 ILE A 106 " =    0.888
peak=    3.307 closest distance to " CB  GLU A 175 " =    1.387
peak=    3.306 closest distance to " CG1 ILE A 120 " =    1.045
peak=    3.306 closest distance to " O   HOH Z 403 " =    1.762
peak=    3.304 closest distance to " NE2 GLN A  11 " =    1.018
peak=    3.303 closest distance to " OG BSER A 164 " =    2.444
peak=    3.299 closest distance to " CD  ARG A 219 " =    1.055
peak=    3.298 closest distance to " CA  VAL A  41 " =    0.909
peak=    3.298 closest distance to " O   HOH Z  64 " =    2.066
peak=    3.297 closest distance to " O   HOH Z 423 " =    3.147
peak=    3.297 closest distance to " O   HOH Z 298 " =    2.477
peak=    3.296 closest distance to " CE3 TRP A  85 " =    1.092
peak=    3.296 closest distance to " NH1 ARG A 269 " =    0.718
peak=    3.296 closest distance to " O   HOH Z 139 " =    4.776
peak=    3.295 closest distance to " CB  MET A 105 " =    1.166
peak=    3.295 closest distance to " CA  TRP A 274 " =    0.950
peak=    3.293 closest distance to " CG  GLN A  58 " =    2.426
peak=    3.284 closest distance to " CZ  PHE A 208 " =    1.140
peak=    3.281 closest distance to " O   HOH Z 126 " =    2.084
peak=    3.281 closest distance to " O   HOH Z   1 " =    2.785
peak=    3.278 closest distance to " O   HOH Z 420 " =    2.130
peak=    3.277 closest distance to " CD  LYS A 119 " =    1.322
peak=    3.277 closest distance to " CG  LEU A 167 " =    1.074
peak=    3.276 closest distance to " CA  LEU A  83 " =    1.468
peak=    3.272 closest distance to " O   TRP A 274 " =    1.584
peak=    3.272 closest distance to " O   HOH Z 139 " =    3.290
peak=    3.271 closest distance to " O   HOH Z 248 " =    1.658
peak=    3.271 closest distance to " O   HOH Z 316 " =    3.117
peak=    3.267 closest distance to " O   HOH Z  54 " =    1.362
peak=    3.264 closest distance to " ND2 ASN A 301 " =    1.058
peak=    3.263 closest distance to " CB  TRP A 123 " =    1.141
peak=    3.262 closest distance to " CB  ALA A 242 " =    0.977
peak=    3.262 closest distance to " O   HOH Z 377 " =    1.340
peak=    3.260 closest distance to " CG2 THR A  42 " =    0.956
peak=    3.258 closest distance to " O   HOH Z 185 " =    1.949
peak=    3.257 closest distance to " O   HOH Z 261 " =    1.743
peak=    3.256 closest distance to " CG2 ILE A 151 " =    0.771
peak=    3.255 closest distance to " ND2 ASN A 209 " =    1.401
peak=    3.253 closest distance to " CD2 TRP A 179 " =    1.366
peak=    3.252 closest distance to " O   HOH Z 386 " =    2.258
peak=    3.245 closest distance to " CB  SER A  62 " =    0.778
peak=    3.244 closest distance to " CA  ASP A 124 " =    0.823
peak=    3.242 closest distance to " O   HOH Z  66 " =    2.029
peak=    3.242 closest distance to " CA  GLN A  88 " =    1.340
peak=    3.241 closest distance to " CB  ALA A 248 " =    1.260
peak=    3.239 closest distance to " N   ARG A 190 " =    1.056
peak=    3.239 closest distance to " ND2 ASN A 110 " =    1.549
peak=    3.238 closest distance to " CG2 ILE A  20 " =    1.191
peak=    3.236 closest distance to " CD  ARG A  66 " =    2.439
peak=    3.236 closest distance to " O   HOH Z 327 " =    1.796
peak=    3.233 closest distance to " CE2 TYR A 293 " =    0.950
peak=    3.233 closest distance to " O   HOH Z 258 " =    2.168
peak=    3.232 closest distance to " O   GLY A  91 " =    1.182
peak=    3.230 closest distance to " O   HOH Z 298 " =    5.964
peak=    3.226 closest distance to " CD1 LEU A  96 " =    0.735
peak=    3.226 closest distance to " O   HOH Z 167 " =    1.718
peak=    3.226 closest distance to " CG2 VAL A 197 " =    1.177
peak=    3.223 closest distance to " OD2 ASP A 286 " =    3.022
peak=    3.219 closest distance to " N   ASP A 132 " =    1.159
peak=    3.219 closest distance to " CG  LYS A  76 " =    1.104
peak=    3.219 closest distance to " O   GLY A  57 " =    2.624
peak=    3.218 closest distance to " O   HOH Z  42 " =    1.582
peak=    3.217 closest distance to " CA  THR A 294 " =    1.680
peak=    3.215 closest distance to " O   HOH Z  32 " =    1.662
peak=    3.214 closest distance to " O   HOH Z 109 " =    2.209
peak=    3.214 closest distance to " O   HOH Z  88 " =    1.740
peak=    3.211 closest distance to " CG  ASP A 231 " =    1.027
peak=    3.211 closest distance to " CE  LYS A 119 " =    1.092
peak=    3.211 closest distance to " CA  SER A  87 " =    0.900
peak=    3.211 closest distance to " O   HOH Z 120 " =    0.954
peak=    3.208 closest distance to " O   HOH Z 142 " =    1.521
peak=    3.207 closest distance to " CG  GLN A  11 " =    1.543
peak=    3.207 closest distance to " CG2 THR A  29 " =    1.488
peak=    3.207 closest distance to " N   SER A 164 " =    1.108
peak=    3.205 closest distance to " O   HOH Z 413 " =    1.878
peak=    3.204 closest distance to " O   HOH Z 406 " =    1.492
peak=    3.203 closest distance to " CD1 LEU A 222 " =    0.751
peak=    3.202 closest distance to " O   HOH Z 423 " =    1.676
peak=    3.202 closest distance to " CG1 ILE A  49 " =    1.653
peak=    3.201 closest distance to " O   HOH Z 155 " =    1.444
peak=    3.198 closest distance to " CB  THR A 235 " =    0.942
peak=    3.198 closest distance to " CA  ASP A 162 " =    1.259
peak=    3.198 closest distance to " OG  SER A 245 " =    1.675
peak=    3.197 closest distance to " CG2 VAL A 257 " =    0.940
peak=    3.195 closest distance to " CA  CYS A 201 " =    1.821
peak=    3.194 closest distance to " O   HOH Z 327 " =    2.362
peak=    3.193 closest distance to " CZ  PHE A  38 " =    1.381
peak=    3.191 closest distance to " CB  ALA A  51 " =    0.751
peak=    3.191 closest distance to " CD  ARG A  14 " =    1.273
peak=    3.191 closest distance to " CB  ASN A 127 " =    0.921
peak=    3.191 closest distance to " O   THR A 220 " =    1.153
peak=    3.188 closest distance to " CB  GLU A 277 " =    0.724
peak=    3.185 closest distance to " CA  ALA A 295 " =    1.073
peak=    3.185 closest distance to " O   HOH Z 184 " =    1.667
peak=    3.182 closest distance to " O   HOH Z  61 " =    1.555
peak=    3.180 closest distance to " OD1 ASN A 301 " =    1.533
peak=    3.179 closest distance to " O   HOH Z 145 " =    2.243
peak=    3.179 closest distance to " CG2AVAL A 121 " =    2.253
peak=    3.176 closest distance to " NZ  LYS A 166 " =    3.209
peak=    3.173 closest distance to " O   HOH Z 294 " =    1.649
peak=    3.173 closest distance to " N   CYS A 260 " =    0.760
peak=    3.170 closest distance to " CB  GLN A  89 " =    1.107
peak=    3.165 closest distance to " O   HOH Z   6 " =    2.175
peak=    3.159 closest distance to " CB  ASN A 148 " =    1.698
peak=    3.158 closest distance to " CB  PHE A  16 " =    1.184
peak=    3.158 closest distance to " CG2 VAL A 296 " =    1.000
peak=    3.157 closest distance to " N   ARG A 156 " =    1.408
peak=    3.157 closest distance to " CB  LEU A  83 " =    0.840
peak=    3.157 closest distance to " CB  ALA A 154 " =    1.183
peak=    3.152 closest distance to " CE  LYS A  76 " =    0.831
peak=    3.146 closest distance to " O   HOH Z  50 " =    3.609
peak=    3.146 closest distance to " O   HOH Z 346 " =    1.635
peak=    3.145 closest distance to " CB  GLU A 236 " =    1.111
peak=    3.144 closest distance to " OD1 ASN A 252 " =    1.237
peak=    3.143 closest distance to " O   HOH Z 417 " =    3.106
peak=    3.142 closest distance to " CB  ARG A 156 " =    0.845
peak=    3.135 closest distance to " O   HOH Z 166 " =    3.612
peak=    3.133 closest distance to " NZ ALYS A 290 " =    1.108
peak=    3.125 closest distance to " CE1 PHE A 225 " =    0.936
peak=    3.121 closest distance to " O   HOH Z 256 " =    1.884
peak=    3.118 closest distance to " CB  LEU A 237 " =    0.719
peak=    3.118 closest distance to " OH  TYR A 186 " =    1.032
peak=    3.117 closest distance to " CB  ALA A  34 " =    0.743
peak=    3.117 closest distance to " CB  PHE A  61 " =    0.719
peak=    3.117 closest distance to " N   LYS A 166 " =    0.904
peak=    3.115 closest distance to " CB  ILE A 120 " =    1.355
peak=    3.109 closest distance to " CB  SER A 210 " =    0.962
peak=    3.106 closest distance to " ND2 ASN A 187 " =    1.449
peak=    3.106 closest distance to " OE1 GLN A  58 " =    1.051
peak=    3.105 closest distance to " O   HOH Z 147 " =    1.707
peak=    3.093 closest distance to " N   VAL A 126 " =    1.527
peak=    3.079 closest distance to " CZ3 TRP A  92 " =    1.574
peak=    3.063 closest distance to " OD2 ASP A 298 " =    3.842
peak=    3.061 closest distance to " CB  LEU A 300 " =    1.063
peak=    3.059 closest distance to " CD  ARG A 139 " =    1.372
peak=    3.059 closest distance to " OD2 ASP A 200 " =    1.366
peak=    3.040 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.031 closest distance to " CB  PRO A 243 " =    1.123
peak=    3.031 closest distance to " CG  GLN A  77 " =    0.774
peak=    3.017 closest distance to " CB  ALA A  43 " =    0.913
peak=    3.015 closest distance to " O   HOH Z  48 " =    1.781

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.810 - 5.825
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 222 from: 222
   mapped sites are within: 0.810 - 5.825

peak=   -4.515 closest distance to " O   HOH Z 266 " =    4.877
peak=   -4.492 closest distance to " NH2 ARG A  66 " =    1.445
peak=   -4.401 closest distance to " CD  GLN A  88 " =    0.863
peak=   -4.357 closest distance to " O   HOH Z 155 " =    1.632
peak=   -4.313 closest distance to " O   HOH Z 166 " =    1.558
peak=   -4.183 closest distance to " O   HOH Z  19 " =    1.970
peak=   -4.177 closest distance to " C   ASN A 285 " =    2.584
peak=   -4.099 closest distance to " O   PRO A 198 " =    1.303
peak=   -4.065 closest distance to " O   HOH Z 109 " =    3.645
peak=   -4.059 closest distance to " CD2 LEU A 237 " =    2.658
peak=   -4.019 closest distance to " CD1 PHE A  59 " =    1.895
peak=   -3.973 closest distance to " CD  GLN A 223 " =    1.537
peak=   -3.965 closest distance to " CD2 LEU A 143 " =    2.607
peak=   -3.925 closest distance to " CA  GLY A 241 " =    3.134
peak=   -3.911 closest distance to " CB  GLU A 277 " =    1.252
peak=   -3.909 closest distance to " O   HOH Z   5 " =    1.605
peak=   -3.880 closest distance to " O   HOH Z 185 " =    2.506
peak=   -3.877 closest distance to " O   HOH Z  43 " =    1.230
peak=   -3.876 closest distance to " CA  GLY A 203 " =    2.273
peak=   -3.869 closest distance to " O   HOH Z 184 " =    1.335
peak=   -3.857 closest distance to " O   HOH Z 275 " =    1.780
peak=   -3.852 closest distance to " O   HOH Z 377 " =    1.928
peak=   -3.848 closest distance to " CG  ARG A 269 " =    2.418
peak=   -3.843 closest distance to " O   HOH Z 290 " =    1.172
peak=   -3.842 closest distance to " O   HOH Z 308 " =    1.660
peak=   -3.842 closest distance to " O   HOH Z  71 " =    1.460
peak=   -3.838 closest distance to " O   VAL A  67 " =    2.680
peak=   -3.836 closest distance to " OD1 ASN A 148 " =    1.618
peak=   -3.829 closest distance to " CG  MET A 105 " =    0.909
peak=   -3.827 closest distance to " O   HOH Z 418 " =    1.301
peak=   -3.825 closest distance to " OG1 THR A  82 " =    1.778
peak=   -3.797 closest distance to " OG  SER A  97 " =    2.245
peak=   -3.791 closest distance to " O   HOH Z 231 " =    2.256
peak=   -3.789 closest distance to " O   HOH Z  38 " =    0.839
peak=   -3.787 closest distance to " O   ILE A 109 " =    2.693
peak=   -3.765 closest distance to " CD  ARG A 156 " =    2.150
peak=   -3.750 closest distance to " OD2 ASP A 171 " =    1.954
peak=   -3.738 closest distance to " CE2 TYR A  30 " =    2.662
peak=   -3.737 closest distance to " CE  MET A  93 " =    1.454
peak=   -3.736 closest distance to " CA  TYR A  68 " =    2.708
peak=   -3.731 closest distance to " O   HOH Z 210 " =    1.025
peak=   -3.717 closest distance to " N   ALA A  43 " =    2.654
peak=   -3.716 closest distance to " O   HOH Z 351 " =    1.521
peak=   -3.714 closest distance to " O   HOH Z 103 " =    1.883
peak=   -3.709 closest distance to " CB  ALA A   9 " =    2.749
peak=   -3.699 closest distance to " CB  ALA A  10 " =    2.006
peak=   -3.695 closest distance to " CZ3 TRP A 179 " =    1.162
peak=   -3.694 closest distance to " CD2 PHE A  59 " =    2.449
peak=   -3.691 closest distance to " OE1 GLN A 223 " =    2.371
peak=   -3.683 closest distance to " O   PRO A 163 " =    2.248
peak=   -3.682 closest distance to " CA  GLY A 241 " =    2.299
peak=   -3.679 closest distance to " CG1 VAL A 112 " =    2.584
peak=   -3.670 closest distance to " O   HOH Z 275 " =    1.649
peak=   -3.663 closest distance to " O   HOH Z  52 " =    1.654
peak=   -3.654 closest distance to " C   SER A 206 " =    1.430
peak=   -3.653 closest distance to " CB  PRO A 243 " =    2.674
peak=   -3.651 closest distance to " O   ALA A  10 " =    1.825
peak=   -3.646 closest distance to " C   ALA A 158 " =    1.187
peak=   -3.645 closest distance to " OD1 ASP A 191 " =    1.710
peak=   -3.643 closest distance to " CD  ARG A  14 " =    3.470
peak=   -3.636 closest distance to " O   HOH Z 150 " =    1.301
peak=   -3.635 closest distance to " SG  CYS A 168 " =    1.041
peak=   -3.631 closest distance to " O   HOH Z 111 " =    2.123
peak=   -3.622 closest distance to " CG  ARG A  66 " =    2.457
peak=   -3.604 closest distance to " O   HOH Z 348 " =    2.319
peak=   -3.603 closest distance to " O   HOH Z 407 " =    0.862
peak=   -3.594 closest distance to " C   SER A 271 " =    1.242
peak=   -3.588 closest distance to " O   HOH Z  91 " =    2.005
peak=   -3.586 closest distance to " OXT GLY A 302 " =    2.977
peak=   -3.580 closest distance to " O   HOH Z 426 " =    1.793
peak=   -3.579 closest distance to " CG1 VAL A 125 " =    2.061
peak=   -3.574 closest distance to " O   HOH Z 292 " =    4.526
peak=   -3.541 closest distance to " OH  TYR A 169 " =    0.999
peak=   -3.533 closest distance to " CD  GLN A 223 " =    1.025
peak=   -3.530 closest distance to " CH2 TRP A 177 " =    1.954
peak=   -3.530 closest distance to " OE2 GLU A   2 " =    1.642
peak=   -3.527 closest distance to " CA  GLY A 133 " =    2.340
peak=   -3.513 closest distance to " CG  GLU A  53 " =    1.294
peak=   -3.503 closest distance to " CG  ASP A 231 " =    0.903
peak=   -3.498 closest distance to " O   HOH Z 117 " =    4.480
peak=   -3.492 closest distance to " OG  SER A  87 " =    1.633
peak=   -3.491 closest distance to " CD1 LEU A 167 " =    2.117
peak=   -3.478 closest distance to " O   HOH Z 234 " =    4.426
peak=   -3.472 closest distance to " CB  ALA A 291 " =    2.359
peak=   -3.471 closest distance to " O   HOH Z 251 " =    1.920
peak=   -3.468 closest distance to " CD2 PHE A  61 " =    1.831
peak=   -3.466 closest distance to " CB  ALA A 291 " =    2.367
peak=   -3.464 closest distance to " O   HOH Z  94 " =    1.927
peak=   -3.461 closest distance to " OD1 ASN A 249 " =    1.367
peak=   -3.453 closest distance to " CG1 VAL A  78 " =    2.562
peak=   -3.452 closest distance to " O   HOH Z 377 " =    1.096
peak=   -3.451 closest distance to " O   HOH Z 312 " =    1.506
peak=   -3.448 closest distance to " CA  VAL A  67 " =    3.024
peak=   -3.446 closest distance to " ND2 ASN A  45 " =    1.962
peak=   -3.444 closest distance to " OD2 ASP A 171 " =    2.380
peak=   -3.443 closest distance to " O   HOH Z 380 " =    4.721
peak=   -3.430 closest distance to " O   HOH Z 414 " =    1.434
peak=   -3.428 closest distance to " O   PHE A 218 " =    1.444
peak=   -3.415 closest distance to " ND2 ASN A  45 " =    1.100
peak=   -3.405 closest distance to " CB  ALA A 131 " =    2.430
peak=   -3.401 closest distance to " O   HOH Z 166 " =    1.815
peak=   -3.400 closest distance to " OE1 GLN A  88 " =    1.022
peak=   -3.398 closest distance to " O   HOH Z 150 " =    2.089
peak=   -3.398 closest distance to " O   ALA A   1 " =    2.069
peak=   -3.396 closest distance to " CB  TYR A  15 " =    2.300
peak=   -3.395 closest distance to " CB  SER A 146 " =    2.219
peak=   -3.393 closest distance to " CB  CYS A 254 " =    2.313
peak=   -3.391 closest distance to " CA  ASN A 127 " =    1.117
peak=   -3.380 closest distance to " O   HOH Z 283 " =    2.288
peak=   -3.377 closest distance to " O   HOH Z  17 " =    1.411
peak=   -3.377 closest distance to " O   HOH Z 385 " =    4.078
peak=   -3.376 closest distance to " CB  ASP A 132 " =    2.432
peak=   -3.373 closest distance to " C   THR A 279 " =    1.181
peak=   -3.365 closest distance to " CD2 TYR A 293 " =    1.860
peak=   -3.362 closest distance to " O   HOH Z 198 " =    1.668
peak=   -3.360 closest distance to " CE  MET A  93 " =    2.535
peak=   -3.359 closest distance to " CE  LYS A  76 " =    2.679
peak=   -3.357 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.352 closest distance to " O   ALA A   7 " =    1.625
peak=   -3.345 closest distance to " CZ  PHE A  38 " =    2.007
peak=   -3.345 closest distance to " O   HOH Z  37 " =    1.469
peak=   -3.339 closest distance to " CD  LYS A 289 " =    2.354
peak=   -3.334 closest distance to " CD2 PHE A 225 " =    1.268
peak=   -3.332 closest distance to " O   GLY A 118 " =    2.114
peak=   -3.328 closest distance to " O   HOH Z 399 " =    2.157
peak=   -3.324 closest distance to " O   HOH Z 396 " =    1.689
peak=   -3.319 closest distance to " O   HOH Z 191 " =    2.374
peak=   -3.316 closest distance to " O   HOH Z 118 " =    1.685
peak=   -3.312 closest distance to " O   HOH Z 111 " =    1.305
peak=   -3.310 closest distance to " N   GLN A  58 " =    1.520
peak=   -3.310 closest distance to " OG ASER A 134 " =    1.176
peak=   -3.309 closest distance to " CG  GLN A  58 " =    1.141
peak=   -3.309 closest distance to " O   HOH Z 200 " =    1.333
peak=   -3.305 closest distance to " CB  TRP A  85 " =    2.533
peak=   -3.304 closest distance to " CB  ALA A 131 " =    2.180
peak=   -3.297 closest distance to " C   HIS A 108 " =    1.099
peak=   -3.295 closest distance to " O   HOH Z   6 " =    1.700
peak=   -3.288 closest distance to " O   HOH Z  58 " =    1.001
peak=   -3.288 closest distance to " O   HOH Z 389 " =    2.142
peak=   -3.281 closest distance to " CD1 ILE A 263 " =    2.202
peak=   -3.271 closest distance to " O   HOH Z 128 " =    4.243
peak=   -3.271 closest distance to " O   SER A 276 " =    1.792
peak=   -3.271 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.268 closest distance to " N   THR A 157 " =    1.735
peak=   -3.259 closest distance to " O   HOH Z 189 " =    1.990
peak=   -3.258 closest distance to " O   HOH Z 177 " =    1.776
peak=   -3.257 closest distance to " O   HOH Z 151 " =    1.565
peak=   -3.256 closest distance to " NE  ARG A 138 " =    2.127
peak=   -3.255 closest distance to " O   HOH Z  38 " =    1.381
peak=   -3.252 closest distance to " OH  TYR A 247 " =    1.696
peak=   -3.251 closest distance to " ND2BASN A 224 " =    1.933
peak=   -3.250 closest distance to " NE2 HIS A  86 " =    1.113
peak=   -3.249 closest distance to " CD1 TYR A 247 " =    2.276
peak=   -3.249 closest distance to " O   TYR A 186 " =    2.541
peak=   -3.242 closest distance to " OG1 THR A  82 " =    1.434
peak=   -3.239 closest distance to " CD1 LEU A   5 " =    2.565
peak=   -3.238 closest distance to " SG ACYS A 201 " =    2.145
peak=   -3.235 closest distance to " CD  ARG A 139 " =    1.554
peak=   -3.235 closest distance to " O   ASP A 171 " =    1.093
peak=   -3.233 closest distance to " NH1 ARG A 195 " =    2.319
peak=   -3.228 closest distance to " CB  ARG A 219 " =    2.540
peak=   -3.226 closest distance to " O   HOH Z 370 " =    2.295
peak=   -3.226 closest distance to " C   LEU A 143 " =    1.409
peak=   -3.222 closest distance to " O   HOH Z 136 " =    1.896
peak=   -3.220 closest distance to " O   GLY A  80 " =    2.237
peak=   -3.218 closest distance to " O   GLY A 262 " =    2.463
peak=   -3.217 closest distance to " CG2 THR A   4 " =    1.967
peak=   -3.216 closest distance to " O   HOH Z 190 " =    2.244
peak=   -3.216 closest distance to " CB  ALA A  43 " =    2.624
peak=   -3.213 closest distance to " CG  LYS A 193 " =    2.570
peak=   -3.211 closest distance to " O   GLN A 194 " =    1.356
peak=   -3.210 closest distance to " CE3 TRP A 150 " =    2.102
peak=   -3.210 closest distance to " O   HOH Z 423 " =    1.927
peak=   -3.209 closest distance to " OD1 ASN A 173 " =    1.584
peak=   -3.206 closest distance to " O   HOH Z 174 " =    1.962
peak=   -3.204 closest distance to " O   TYR A  15 " =    1.605
peak=   -3.198 closest distance to " O   HOH Z 430 " =    5.825
peak=   -3.196 closest distance to " CD  GLU A 236 " =    1.100
peak=   -3.193 closest distance to " CG  TRP A 266 " =    1.829
peak=   -3.193 closest distance to " ND2 ASN A 127 " =    1.732
peak=   -3.193 closest distance to " CG2 THR A 221 " =    2.207
peak=   -3.190 closest distance to " ND2 ASN A 215 " =    2.286
peak=   -3.189 closest distance to " O   HOH Z 113 " =    2.105
peak=   -3.185 closest distance to " CZ  TYR A 169 " =    1.827
peak=   -3.184 closest distance to " O   HOH Z 390 " =    2.373
peak=   -3.181 closest distance to " CD2 TRP A 274 " =    2.400
peak=   -3.174 closest distance to " N   SER A 134 " =    1.230
peak=   -3.172 closest distance to " O   GLY A 196 " =    1.114
peak=   -3.170 closest distance to " O   SER A 210 " =    2.059
peak=   -3.165 closest distance to " CD  ARG A 195 " =    4.979
peak=   -3.162 closest distance to " CG  PRO A 243 " =    1.632
peak=   -3.157 closest distance to " CG  LEU A 281 " =    1.804
peak=   -3.154 closest distance to " O   HOH Z 298 " =    2.805
peak=   -3.153 closest distance to " C   GLN A 240 " =    2.366
peak=   -3.150 closest distance to " N   ALA A 226 " =    2.192
peak=   -3.150 closest distance to " O   HOH Z  70 " =    2.316
peak=   -3.144 closest distance to " CB  ARG A  79 " =    2.517
peak=   -3.143 closest distance to " O   HOH Z 252 " =    4.153
peak=   -3.140 closest distance to " O   HOH Z  38 " =    0.958
peak=   -3.131 closest distance to " CG2 ILE A  49 " =    2.803
peak=   -3.130 closest distance to " O   HOH Z 350 " =    1.725
peak=   -3.126 closest distance to " OE1 GLN A  88 " =    1.152
peak=   -3.117 closest distance to " CA  VAL A 232 " =    2.402
peak=   -3.115 closest distance to " C   ASN A 187 " =    1.829
peak=   -3.111 closest distance to " O   ASP A  27 " =    1.960
peak=   -3.110 closest distance to " OD1 ASN A 187 " =    1.490
peak=   -3.108 closest distance to " CG2 VAL A 257 " =    1.921
peak=   -3.107 closest distance to " O   HOH Z  39 " =    0.896
peak=   -3.105 closest distance to " O   HOH Z 283 " =    5.671
peak=   -3.105 closest distance to " ND2 ASN A  60 " =    1.933
peak=   -3.103 closest distance to " OG BSER A 134 " =    1.956
peak=   -3.101 closest distance to " CG2BVAL A  41 " =    1.593
peak=   -3.097 closest distance to " O   HOH Z  48 " =    0.810
peak=   -3.090 closest distance to " O   HOH Z 417 " =    2.914
peak=   -3.075 closest distance to " O   HOH Z 186 " =    0.965
peak=   -3.071 closest distance to " O   SER A 271 " =    2.238
peak=   -3.062 closest distance to " CZ  PHE A 218 " =    1.225
peak=   -3.060 closest distance to " CD1 PHE A  16 " =    2.644
peak=   -3.051 closest distance to " O   HOH Z  41 " =    2.226
peak=   -3.044 closest distance to " CD1 LEU A 101 " =    2.812
peak=   -3.044 closest distance to " O   HOH Z 301 " =    2.427
peak=   -3.034 closest distance to " O   HOH Z 265 " =    2.289

================= 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    :  0.4511 0.4326   6.262229e+00   6.243106e+00
   1_bss:  0.4417 0.4234   6.255177e+00   6.230852e+00
   1_xyz:  0.3479 0.3791   6.088512e+00   6.149012e+00
   1_adp:  0.3155 0.3875   6.042741e+00   6.156994e+00
   1_occ:  0.3154 0.3880   6.042443e+00   6.157731e+00
   2_bss:  0.3147 0.3869   6.043398e+00   6.157614e+00
   2_xyz:  0.2414 0.2971   5.799441e+00   5.961896e+00
   2_adp:  0.2183 0.2739   5.721396e+00   5.900561e+00
   2_occ:  0.2180 0.2735   5.720581e+00   5.899627e+00
   3_bss:  0.2174 0.2724   5.719045e+00   5.897125e+00
   3_xyz:  0.1778 0.2262   5.535710e+00   5.730538e+00
   3_adp:  0.1683 0.2143   5.491892e+00   5.683575e+00
   3_occ:  0.1683 0.2142   5.491595e+00   5.683093e+00
   4_bss:  0.1687 0.2144   5.493650e+00   5.683113e+00
   4_xyz:  0.1410 0.1861   5.336840e+00   5.547775e+00
   4_adp:  0.1347 0.1816   5.305158e+00   5.524836e+00
   4_occ:  0.1346 0.1814   5.304862e+00   5.524497e+00
   5_bss:  0.1350 0.1814   5.306620e+00   5.524765e+00
   5_xyz:  0.1259 0.1745   5.255539e+00   5.483482e+00
   5_adp:  0.1238 0.1743   5.247666e+00   5.480810e+00
   5_occ:  0.1238 0.1743   5.247726e+00   5.480987e+00
   5_bss:  0.1238 0.1743   5.247697e+00   5.480995e+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:  0.282  33.909   1.548   3.612  -1.984   0.000  -0.000  -0.000
   1_xyz:  0.282  33.909   1.548   3.612  -1.984   0.000  -0.000  -0.000
   1_adp:  0.282  33.909   1.548   3.612  -1.984   0.000  -0.000  -0.000
   1_occ:  0.282  33.909   1.548   3.612  -1.984   0.000  -0.000  -0.000
   2_bss:  0.319  65.731   0.226   1.893  -0.668   0.000  -0.000  -0.000
   2_xyz:  0.319  65.731   0.226   1.893  -0.668   0.000  -0.000  -0.000
   2_adp:  0.319  65.731   0.226   1.893  -0.668   0.000  -0.000  -0.000
   2_occ:  0.319  65.731   0.226   1.893  -0.668   0.000  -0.000  -0.000
   3_bss:  0.329  74.575  -0.498   0.293  -0.719   0.000  -0.000  -0.000
   3_xyz:  0.329  74.575  -0.498   0.293  -0.719   0.000  -0.000  -0.000
   3_adp:  0.329  74.575  -0.498   0.293  -0.719   0.000  -0.000  -0.000
   3_occ:  0.329  74.575  -0.498   0.293  -0.719   0.000  -0.000  -0.000
   4_bss:  0.333  75.717  -1.286  -0.578  -0.985  -0.000  -0.000  -0.000
   4_xyz:  0.333  75.717  -1.286  -0.578  -0.985  -0.000  -0.000  -0.000
   4_adp:  0.333  75.717  -1.286  -0.578  -0.985  -0.000  -0.000  -0.000
   4_occ:  0.333  75.717  -1.286  -0.578  -0.985  -0.000  -0.000  -0.000
   5_bss:  0.330  72.057  -1.261  -0.836  -0.757  -0.000  -0.000  -0.000
   5_xyz:  0.330  72.057  -1.261  -0.836  -0.757  -0.000  -0.000  -0.000
   5_adp:  0.330  72.057  -1.261  -0.836  -0.757  -0.000  -0.000  -0.000
   5_occ:  0.330  72.057  -1.261  -0.836  -0.757  -0.000  -0.000  -0.000
   5_bss:  0.330  72.060  -1.288  -0.996  -0.790  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.506 0.5028  0.6588    60748.996
   1_bss:  50.601 0.5126  0.6974    57804.114
   1_xyz:  42.908 0.6073  0.8092    42546.439
   1_adp:  43.851 0.5952  0.7851    43657.003
   1_occ:  43.941 0.5940  0.7829    43737.085
   2_bss:  43.772 0.5961  0.7733    43576.013
   2_xyz:  31.885 0.7346  0.9268    23850.306
   2_adp:  28.519 0.7731  0.9454    20208.249
   2_occ:  28.473 0.7736  0.9455    20152.685
   3_bss:  28.319 0.7750  0.9218    19935.799
   3_xyz:  22.544 0.8356  0.9639    13291.391
   3_adp:  21.010 0.8516  0.9645    12051.238
   3_occ:  21.007 0.8517  0.9644    12042.128
   4_bss:  21.006 0.8517  0.9434    12046.508
   4_xyz:  17.734 0.8824  0.9634     8891.728
   4_adp:  17.068 0.8890  0.9610     8530.298
   4_occ:  17.059 0.8890  0.9608     8524.056
   5_bss:  17.081 0.8889  0.9608     8542.676
   5_xyz:  16.150 0.8971  0.9646     7833.430
   5_adp:  16.059 0.8980  0.9578     7805.594
   5_occ:  16.064 0.8980  0.9576     7810.654
   5_bss:  16.061 0.8980  0.9554     7811.143
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7322e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7322e-01
   1_xyz:   1.474  0.011  0.093 15.692  0.005  4.111   1.1641e-01
   1_adp:   1.474  0.011  0.093 15.692  0.005  4.111   1.1641e-01
   1_occ:   1.474  0.011  0.093 15.692  0.005  4.111   1.1641e-01
   2_bss:   1.474  0.011  0.093 15.692  0.005  4.111   1.1641e-01
   2_xyz:   1.376  0.011  0.089 15.149  0.006  4.116   1.0549e-01
   2_adp:   1.376  0.011  0.089 15.149  0.006  4.116   1.0549e-01
   2_occ:   1.376  0.011  0.089 15.149  0.006  4.116   1.0549e-01
   3_bss:   1.376  0.011  0.089 15.149  0.006  4.116   1.0549e-01
   3_xyz:   1.002  0.007  0.070 14.625  0.004  4.127   5.9957e-02
   3_adp:   1.002  0.007  0.070 14.625  0.004  4.127   5.9957e-02
   3_occ:   1.002  0.007  0.070 14.625  0.004  4.127   5.9957e-02
   4_bss:   1.002  0.007  0.070 14.625  0.004  4.127   5.9957e-02
   4_xyz:   1.048  0.008  0.077 14.600  0.004  4.117   6.4559e-02
   4_adp:   1.048  0.008  0.077 14.600  0.004  4.117   6.4559e-02
   4_occ:   1.048  0.008  0.077 14.600  0.004  4.117   6.4559e-02
   5_bss:   1.048  0.008  0.077 14.600  0.004  4.117   6.4559e-02
   5_xyz:   1.028  0.009  0.075 14.587  0.004  4.124   6.2935e-02
   5_adp:   1.028  0.009  0.075 14.587  0.004  4.124   6.2935e-02
   5_occ:   1.028  0.009  0.075 14.587  0.004  4.124   6.2935e-02
   5_bss:   1.028  0.009  0.075 14.587  0.004  4.124   6.2935e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.134   2.4474e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.134   2.4474e-01
   1_xyz:  10.247  0.065  0.354 85.587  0.030  1.914   9.9585e-02
   1_adp:  10.247  0.065  0.354 85.587  0.030  1.914   9.9585e-02
   1_occ:  10.247  0.065  0.354 85.587  0.030  1.914   9.9585e-02
   2_bss:  10.247  0.065  0.354 85.587  0.030  1.914   9.9585e-02
   2_xyz:   8.470  0.059  0.265 79.789  0.043  2.181   1.4581e-01
   2_adp:   8.470  0.059  0.265 79.789  0.043  2.181   1.4581e-01
   2_occ:   8.470  0.059  0.265 79.789  0.043  2.181   1.4581e-01
   3_bss:   8.470  0.059  0.265 79.789  0.043  2.181   1.4581e-01
   3_xyz:   8.926  0.049  0.262 80.668  0.035  2.368   4.9784e-02
   3_adp:   8.926  0.049  0.262 80.668  0.035  2.368   4.9784e-02
   3_occ:   8.926  0.049  0.262 80.668  0.035  2.368   4.9784e-02
   4_bss:   8.926  0.049  0.262 80.668  0.035  2.368   4.9784e-02
   4_xyz:   8.406  0.065  0.240 83.937  0.029  2.262   6.1356e-02
   4_adp:   8.406  0.065  0.240 83.937  0.029  2.262   6.1356e-02
   4_occ:   8.406  0.065  0.240 83.937  0.029  2.262   6.1356e-02
   5_bss:   8.406  0.065  0.240 83.937  0.029  2.262   6.1356e-02
   5_xyz:   8.386  0.056  0.237 82.571  0.037  2.333   5.8404e-02
   5_adp:   8.386  0.056  0.237 82.571  0.037  2.333   5.8404e-02
   5_occ:   8.386  0.056  0.237 82.571  0.037  2.333   5.8404e-02
   5_bss:   8.386  0.056  0.237 82.571  0.037  2.333   5.8404e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 107.33   0.00  18.42  87.53   0.00  14.81 107.33   0.00  38.04
   1_occ: 107.33   0.00  18.42  87.53   0.00  14.81 107.33   0.00  38.04
   2_bss: 107.33   0.00  18.42  87.53   0.00  14.81 107.33   0.00  38.04
   2_xyz: 107.33   0.00  18.42  87.53   0.00  14.81 107.33   0.00  38.04
   2_adp:  96.34   0.00  18.13  93.77   0.00  13.80  96.34   1.63  41.70
   2_occ:  96.34   0.00  18.13  93.77   0.00  13.80  96.34   1.63  41.70
   3_bss:  96.34   0.00  18.13  93.77   0.00  13.80  96.34   1.63  41.70
   3_xyz:  96.34   0.00  18.13  93.77   0.00  13.80  96.34   1.63  41.70
   3_adp:  96.89   0.00  17.53  96.89   0.00  12.98  94.27   3.63  42.31
   3_occ:  96.89   0.00  17.53  96.89   0.00  12.98  94.27   3.63  42.31
   4_bss:  96.89   0.00  17.53  96.89   0.00  12.98  94.27   3.63  42.31
   4_xyz:  96.89   0.00  17.53  96.89   0.00  12.98  94.27   3.63  42.31
   4_adp: 100.84   0.00  17.31 100.84   0.00  12.61  97.20   4.28  42.91
   4_occ: 100.84   0.00  17.31 100.84   0.00  12.61  97.20   4.28  42.91
   5_bss: 100.84   0.00  17.31 100.84   0.00  12.61  97.20   4.28  42.91
   5_xyz: 100.84   0.00  17.31 100.84   0.00  12.61  97.20   4.28  42.91
   5_adp: 104.74   0.00  17.09 104.74   0.00  12.38 100.76   4.23  42.73
   5_occ: 104.74   0.00  17.09 104.74   0.00  12.38 100.76   4.23  42.73
   5_bss: 104.74   0.00  17.09 104.74   0.00  12.39 100.77   4.23  42.73
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.473    0.017    0.319
   1_adp:    2.473    0.017    0.319
   1_occ:    2.473    0.017    0.319
   2_bss:    2.473    0.017    0.319
   2_xyz:    1.462    0.029    0.589
   2_adp:    1.462    0.029    0.589
   2_occ:    1.462    0.029    0.589
   3_bss:    1.462    0.029    0.589
   3_xyz:    1.348    0.020    0.659
   3_adp:    1.348    0.020    0.659
   3_occ:    1.348    0.020    0.659
   4_bss:    1.348    0.020    0.659
   4_xyz:    1.444    0.051    0.736
   4_adp:    1.444    0.051    0.736
   4_occ:    1.444    0.051    0.736
   5_bss:    1.444    0.051    0.736
   5_xyz:    1.419    0.069    0.762
   5_adp:    1.419    0.069    0.762
   5_occ:    1.419    0.069    0.762
   5_bss:    1.419    0.069    0.762
------------------------------------------------------------------------

CPU time actual refinement: 295.18


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1313/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_1313/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1313/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1313/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1313/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 295.06 
  Macro-tasks:
    bulk solvent and scale       = 38.11  
    individual site refinement   = 119.08 
    weights calculation          = 25.04  
    collect and process          = 5.32   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 187.63 
  Micro-tasks:
    mask                            = 2.10   
    f_calc                          = 95.60  
    alpha_beta                      = 6.79   
    target                          = 0.93   
    gradients_wrt_atomic_parameters = 101.15 
    fmodel                         = 5.96   
    r_factors                      = 0.21   
    phase_errors                   = 8.65   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 221.63 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.225 micro seconds
Total CPU time: 5.11 minutes
from_scatterers_fft:    631 calls, 95.37 s
gradients_fft:          576 calls, 90.43 s

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

# Date 2008-01-16 Time 06:56:52 PST -0800 (1200495412.83 s)
Start R-work = 0.4511, R-free = 0.4326 (no bulk solvent and anisotropic scale)
Final R-work = 0.1417, R-free = 0.1904 (no bulk solvent and anisotropic scale)

Start R-work = 0.4417, R-free = 0.4234
Final R-work = 0.1238, R-free = 0.1743