# Date 2008-01-16 Time 05:16:11 PST -0800 (1200489371.69 s)
#phil __OFF__

Command line arguments: "../660.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12615
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 660

-------------------------------------------------------------------------------
  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: (70.25, 46.93, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.9513
Completeness in resolution range: 0.940332
Completeness with d_max=infinity: 0.937497

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9513

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: (70.25, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.9513
Completeness in resolution range: 0.940332
Completeness with d_max=infinity: 0.937497

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1759 [2195/2224]  1977   218   9.9%
  bin  2:  4.1759 -  3.3267 [2089/2112]  1881   208  10.0%
  bin  3:  3.3267 -  2.9098 [2067/2089]  1856   211  10.2%
  bin  4:  2.9098 -  2.6453 [2065/2084]  1865   200   9.7%
  bin  5:  2.6453 -  2.4566 [2052/2081]  1842   210  10.2%
  bin  6:  2.4566 -  2.3124 [2028/2070]  1827   201   9.9%
  bin  7:  2.3124 -  2.1969 [2016/2052]  1815   201  10.0%
  bin  8:  2.1969 -  2.1016 [2003/2040]  1803   200  10.0%
  bin  9:  2.1016 -  2.0209 [2008/2040]  1802   206  10.3%
  bin 10:  2.0209 -  1.9513 [1066/2040]   962   104   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_660/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.56 -     2.23: 26
        2.23 -     2.90: 1398
        2.90 -     3.57: 4508
        3.57 -     4.23: 9326
        4.23 -     4.90: 13439
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.563 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.579 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.773 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.832 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28692 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_660/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_660/model_refine_001.geo

CPU time processing inputs: 9.43


============================ 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 = 70.25 46.93 84.23025 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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3566   r_free= 0.3572   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.141526                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6579 0.99   1419  158 0.3057 0.3099      6.4255      6.4344|
|  2:  4.6579 -  3.7160 0.99   1366  147 0.2925 0.2665      6.5783      6.5069|
|  3:  3.7160 -  3.2519 0.99   1339  157 0.3153 0.3319       6.465      6.6348|
|  4:  3.2519 -  2.9571 0.99   1339  145 0.3282 0.3350      6.3336      6.3492|
|  5:  2.9571 -  2.7466 0.99   1313  146 0.3617 0.3324      6.2114       6.191|
|  6:  2.7466 -  2.5855 0.98   1319  145 0.3785 0.3842      6.1281      6.0887|
|  7:  2.5855 -  2.4566 0.99   1326  149 0.3734 0.3115      6.1052      6.0425|
|  8:  2.4566 -  2.3501 0.99   1289  145 0.3845 0.4071      6.0312      6.0839|
|  9:  2.3501 -  2.2600 0.98   1322  149 0.3852 0.3984      6.0111       6.004|
| 10:  2.2600 -  2.1822 0.98   1282  144 0.3948 0.4404      5.9862      6.0479|
| 11:  2.1822 -  2.1142 0.98   1285  137 0.4122 0.4562      5.9421      6.0228|
| 12:  2.1142 -  2.0539 0.99   1293  145 0.3923 0.3868      5.8589      5.8848|
| 13:  2.0539 -  2.0000 0.97   1288  144 0.4196 0.4321      5.7923      5.7764|
| 14:  2.0000 -  1.9513 0.34    450   48 0.5150 0.5105      5.8515      5.7272|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6579  1419   158  0.76  28.54   0.86     0.78      49695.11|
|  2:  4.6579 -  3.7160  1366   147  0.79  26.71   0.96     0.89      63818.52|
|  3:  3.7160 -  3.2519  1339   157  0.74  31.68   0.98     0.92      66476.05|
|  4:  3.2519 -  2.9571  1339   145  0.69  36.57   1.00     0.90      58870.51|
|  5:  2.9571 -  2.7466  1313   146  0.64  40.82   0.96     0.85      48179.76|
|  6:  2.7466 -  2.5855  1319   145  0.63  41.62   0.97     0.84      40759.24|
|  7:  2.5855 -  2.4566  1326   149  0.64  40.97   1.00     0.84      37228.85|
|  8:  2.4566 -  2.3501  1289   145  0.61  43.65   0.97     0.83      34704.99|
|  9:  2.3501 -  2.2600  1322   149  0.58  45.35   1.02     0.80      33519.37|
| 10:  2.2600 -  2.1822  1282   144  0.56  47.70   1.04     0.77      33666.66|
| 11:  2.1822 -  2.1142  1285   137  0.54  49.28   1.02     0.77      32201.89|
| 12:  2.1142 -  2.0539  1293   145  0.53  49.83   1.04     0.81      30658.38|
| 13:  2.0539 -  2.0000  1288   144  0.51  51.26   1.02     0.77      26375.98|
| 14:  2.0000 -  1.9513   450    48  0.47  54.30   0.96     0.65      23253.19|
|alpha:            min =        0.65 max =            0.92 mean =         0.82|
|beta:             min =    23253.19 max =        66476.05 mean =     42517.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.22|
|phase err.(test): min =        0.00 max =           89.99 mean =        41.20|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.768232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.710   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.052934              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.825   (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 |  1.563 -  1.897:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.897 -  2.231:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.231 -  2.564:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.564 -  2.898:     1359 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.898 -  3.232:     1939 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.232 -  3.565:     2569 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.565 -  3.899:     4741 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.899 -  4.233:     4585 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.233 -  4.566:     6085 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.566 -  4.900:     7354 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.563 |       0.426 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3566   r_free= 0.3572   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.141526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3377   r_free= 0.3382   ksol= 0.31   Bsol= 24.96   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,-2.91,3.76,-0.00,0.00,0.00); trace/3= -0.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.124761                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.806726              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.796   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514390              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.813   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3377      final r-factor (work) = 0.2510          |
| start r-factor (free) = 0.3382      final r-factor (free) = 0.2809          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8318 = 3.81 * 0.50 * 6.1230 + 1.00 * 0.1774                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3710 = 3.81 * 0.50 * 5.9301 + 1.00 * 0.0839                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2510      final r-factor (work) = 0.2306          |
| start r-factor (free) = 0.2809      final r-factor (free) = 0.2874          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0564 = 0.51 * 1.00 * 5.9301 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9835 = 0.51 * 1.00 * 5.7793 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.92   17.49    None  None   None       |
|    all(noH): 2823   0      0.00    75.92   17.49    None  None   None       |
|    Sol.    : 438    0      3.17    73.08   38.51    None  None   None       |
|    Mac.    : 2385   0      0.00    75.92   13.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.592:  544   |   5:    37.958 -  45.549:  135        |
|      1:     7.592 -  15.183: 1161   |   6:    45.549 -  53.141:   68        |
|      2:    15.183 -  22.775:  479   |   7:    53.141 -  60.732:   53        |
|      3:    22.775 -  30.366:  199   |   8:    60.732 -  68.324:   32        |
|      4:    30.366 -  37.958:  143   |   9:    68.324 -  75.915:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2306 r_free = 0.2874             target_work(ml) = 5.788         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2303 r_free = 0.2879             target_work(ml) = 5.787         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2303   r_free= 0.2879   ksol= 0.31   Bsol= 24.96   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,-2.91,3.76,-0.00,0.00,0.00); trace/3= -0.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.787365                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2276   r_free= 0.2832   ksol= 0.32   Bsol= 38.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.27,0.49,-0.00,0.00,0.00); trace/3= -1.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.777849                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.307755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.585   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222660              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.246  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2276      final r-factor (work) = 0.1603          |
| start r-factor (free) = 0.2832      final r-factor (free) = 0.2096          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5221 = 4.31 * 0.50 * 5.7748 + 1.00 * 0.0839                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2116 = 4.31 * 0.50 * 5.6405 + 1.00 * 0.0627                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1603      final r-factor (work) = 0.1461          |
| start r-factor (free) = 0.2096      final r-factor (free) = 0.1918          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2665 = 0.22 * 1.00 * 5.6405 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2121 = 0.22 * 1.00 * 5.4105 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.68    75.74   17.18    None  None   None       |
|    all(noH): 2823   0      1.68    75.74   17.18    None  None   None       |
|    Sol.    : 438    0      5.22    71.29   38.80    None  None   None       |
|    Mac.    : 2385   0      1.68    75.74   13.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.683 -   9.088:  748   |   5:    38.712 -  46.118:  128        |
|      1:     9.088 -  16.494: 1185   |   6:    46.118 -  53.524:   85        |
|      2:    16.494 -  23.900:  335   |   7:    53.524 -  60.930:   42        |
|      3:    23.900 -  31.306:  140   |   8:    60.930 -  68.335:   26        |
|      4:    31.306 -  38.712:  127   |   9:    68.335 -  75.741:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1461 r_free = 0.1918             target_work(ml) = 5.368         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1458 r_free = 0.1917             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1917   ksol= 0.32   Bsol= 38.89   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.27,0.49,-0.00,0.00,0.00); trace/3= -1.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.367236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1896   ksol= 0.32   Bsol= 38.89   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.45,-1.42,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.358570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.974193              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.663  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.585495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.589  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1896      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8143 = 3.97 * 0.50 * 5.4108 + 1.00 * 0.0625                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5518 = 3.97 * 0.50 * 5.2761 + 1.00 * 0.0676                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0965 = 0.59 * 1.00 * 5.2761 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0306 = 0.59 * 1.00 * 5.1618 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.97   17.28    None  None   None       |
|    all(noH): 2823   0      0.00    87.97   17.28    None  None   None       |
|    Sol.    : 438    0      2.38    75.35   40.18    None  None   None       |
|    Mac.    : 2385   0      0.00    87.97   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.797:  688   |   5:    43.984 -  52.781:  114        |
|      1:     8.797 -  17.594: 1358   |   6:    52.781 -  61.577:   72        |
|      2:    17.594 -  26.390:  291   |   7:    61.577 -  70.374:   30        |
|      3:    26.390 -  35.187:  133   |   8:    70.374 -  79.171:   10        |
|      4:    35.187 -  43.984:  124   |   9:    79.171 -  87.968:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1590             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1588             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1588   ksol= 0.32   Bsol= 38.89   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.45,-1.42,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147791                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1591   ksol= 0.32   Bsol= 41.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.45,-1.91,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148541                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.932706              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.406  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.342422              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.948  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0560 = 1.93 * 0.50 * 5.1620 + 1.00 * 0.0676                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0233 = 1.93 * 0.50 * 5.1417 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7690 = 0.34 * 1.00 * 5.1417 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7654 = 0.34 * 1.00 * 5.1316 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    88.58   17.15    None  None   None       |
|    all(noH): 2823   0      2.09    88.58   17.15    None  None   None       |
|    Sol.    : 438    0      3.67    75.43   39.83    None  None   None       |
|    Mac.    : 2385   0      2.09    88.58   12.99    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:     2.089 -  10.739: 1186   |   5:    45.336 -  53.985:  107        |
|      1:    10.739 -  19.388:  968   |   6:    53.985 -  62.635:   60        |
|      2:    19.388 -  28.037:  218   |   7:    62.635 -  71.284:   27        |
|      3:    28.037 -  36.687:  126   |   8:    71.284 -  79.933:    8        |
|      4:    36.687 -  45.336:  120   |   9:    79.933 -  88.582:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1565             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1565             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1565   ksol= 0.32   Bsol= 41.16   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.45,-1.91,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130521                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1565   ksol= 0.32   Bsol= 41.23   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.29,-1.93,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130485                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.994126              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.527  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.276988              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.690  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1711 = 1.99 * 0.50 * 5.1316 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1645 = 1.99 * 0.50 * 5.1221 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.0375 = 5.28 * 1.00 * 5.1221 + 1.00 * 0.0082                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.0092 = 5.28 * 1.00 * 5.1165 + 1.00 * 0.0095                              |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.86   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    99.86   17.24    None  None   None       |
|    Sol.    : 438    0      5.37    82.98   40.55    None  None   None       |
|    Mac.    : 2385   0      0.00    99.86   12.95    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 -   9.986: 1028   |   5:    49.929 -  59.914:   98        |
|      1:     9.986 -  19.972: 1151   |   6:    59.914 -  69.900:   42        |
|      2:    19.972 -  29.957:  219   |   7:    69.900 -  79.886:   19        |
|      3:    29.957 -  39.943:  135   |   8:    79.886 -  89.872:    5        |
|      4:    39.943 -  49.929:  123   |   9:    89.872 -  99.857:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1068 r_free = 0.1567             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1567             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1567   ksol= 0.32   Bsol= 41.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.29,-1.93,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122473                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6579 0.99   1419  158 0.0941 0.1234      5.3467      5.5222|
|  2:  4.6579 -  3.7160 0.99   1366  147 0.0810 0.1084       5.387       5.602|
|  3:  3.7160 -  3.2519 0.99   1339  157 0.1026 0.1547      5.4394      5.8397|
|  4:  3.2519 -  2.9571 0.99   1339  145 0.1174 0.1494       5.434      5.5801|
|  5:  2.9571 -  2.7466 0.99   1313  146 0.1221 0.1712       5.274      5.4758|
|  6:  2.7466 -  2.5855 0.98   1319  145 0.1186 0.1848      5.1797        5.42|
|  7:  2.5855 -  2.4566 0.99   1326  149 0.1169 0.1642      5.1147      5.3555|
|  8:  2.4566 -  2.3501 0.99   1289  145 0.1109 0.1701      5.0309      5.2613|
|  9:  2.3501 -  2.2600 0.98   1322  149 0.1110 0.1832      4.9994      5.3076|
| 10:  2.2600 -  2.1822 0.98   1282  144 0.1082 0.1737      4.9529      5.2211|
| 11:  2.1822 -  2.1142 0.98   1285  137 0.1098 0.1799      4.9192      5.2746|
| 12:  2.1142 -  2.0539 0.99   1293  145 0.1039 0.1728      4.8484      5.0872|
| 13:  2.0539 -  2.0000 0.97   1288  144 0.1110 0.1705      4.7719      5.0213|
| 14:  2.0000 -  1.9513 0.34    450   48 0.1007 0.1668      4.6337         4.9|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6579  1419   158  0.94   8.47   0.98     0.96       6611.58|
|  2:  4.6579 -  3.7160  1366   147  0.95   7.81   1.02     1.01       8400.51|
|  3:  3.7160 -  3.2519  1339   157  0.94  10.95   1.03     1.03       9730.97|
|  4:  3.2519 -  2.9571  1339   145  0.92  13.64   1.01     1.00      10252.37|
|  5:  2.9571 -  2.7466  1313   146  0.90  15.45   0.99     0.97       7738.81|
|  6:  2.7466 -  2.5855  1319   145  0.90  15.72   0.99     0.96       6747.27|
|  7:  2.5855 -  2.4566  1326   149  0.91  14.66   0.99     0.96       5687.86|
|  8:  2.4566 -  2.3501  1289   145  0.91  15.27   0.99     0.96       5156.11|
|  9:  2.3501 -  2.2600  1322   149  0.91  15.31   1.00     0.97       4798.13|
| 10:  2.2600 -  2.1822  1282   144  0.90  15.58   1.00     0.96       4495.22|
| 11:  2.1822 -  2.1142  1285   137  0.90  16.35   1.00     0.96       4361.85|
| 12:  2.1142 -  2.0539  1293   145  0.91  15.31   1.00     0.98       3915.98|
| 13:  2.0539 -  2.0000  1288   144  0.90  16.08   1.00     0.99       3287.87|
| 14:  2.0000 -  1.9513   450    48  0.91  15.27   0.99     0.96       2502.17|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2502.17 max =        10252.37 mean =      6182.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.86|
|phase err.(test): min =        0.00 max =           88.90 mean =        13.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1567   ksol= 0.32   Bsol= 42.64   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.10,-1.78,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122472                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1567   ksol= 0.32   Bsol= 42.64   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.10,-1.78,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122472                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6579 0.99   1419  158 0.0942 0.1237      5.3483      5.5248|
|  2:  4.6579 -  3.7160 0.99   1366  147 0.0811 0.1083      5.3883      5.6021|
|  3:  3.7160 -  3.2519 0.99   1339  157 0.1027 0.1547      5.4397      5.8404|
|  4:  3.2519 -  2.9571 0.99   1339  145 0.1174 0.1494      5.4339      5.5797|
|  5:  2.9571 -  2.7466 0.99   1313  146 0.1220 0.1712      5.2735       5.475|
|  6:  2.7466 -  2.5855 0.98   1319  145 0.1186 0.1848      5.1793      5.4198|
|  7:  2.5855 -  2.4566 0.99   1326  149 0.1169 0.1641      5.1146      5.3554|
|  8:  2.4566 -  2.3501 0.99   1289  145 0.1109 0.1700      5.0305      5.2606|
|  9:  2.3501 -  2.2600 0.98   1322  149 0.1110 0.1833      4.9993      5.3081|
| 10:  2.2600 -  2.1822 0.98   1282  144 0.1081 0.1736      4.9527      5.2201|
| 11:  2.1822 -  2.1142 0.98   1285  137 0.1097 0.1799       4.919      5.2747|
| 12:  2.1142 -  2.0539 0.99   1293  145 0.1038 0.1727      4.8478      5.0866|
| 13:  2.0539 -  2.0000 0.97   1288  144 0.1110 0.1702      4.7714        5.02|
| 14:  2.0000 -  1.9513 0.34    450   48 0.1007 0.1670      4.6335      4.9015|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6579  1419   158  0.94   8.50   0.98     0.96       6639.81|
|  2:  4.6579 -  3.7160  1366   147  0.95   7.82   1.03     1.01       8420.78|
|  3:  3.7160 -  3.2519  1339   157  0.94  10.96   1.04     1.03       9737.60|
|  4:  3.2519 -  2.9571  1339   145  0.92  13.64   1.02     1.00      10248.63|
|  5:  2.9571 -  2.7466  1313   146  0.90  15.44   1.00     0.97       7733.56|
|  6:  2.7466 -  2.5855  1319   145  0.90  15.71   1.00     0.97       6740.83|
|  7:  2.5855 -  2.4566  1326   149  0.91  14.65   1.00     0.97       5683.50|
|  8:  2.4566 -  2.3501  1289   145  0.91  15.27   1.00     0.97       5151.55|
|  9:  2.3501 -  2.2600  1322   149  0.91  15.30   1.01     0.98       4795.28|
| 10:  2.2600 -  2.1822  1282   144  0.90  15.57   1.01     0.97       4491.71|
| 11:  2.1822 -  2.1142  1285   137  0.90  16.35   1.01     0.97       4357.72|
| 12:  2.1142 -  2.0539  1293   145  0.91  15.30   1.01     0.99       3909.25|
| 13:  2.0539 -  2.0000  1288   144  0.90  16.07   1.01     1.00       3284.45|
| 14:  2.0000 -  1.9513   450    48  0.91  15.27   1.00     0.97       2501.85|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2501.85 max =        10248.63 mean =      6183.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.86|
|phase err.(test): min =        0.00 max =           88.94 mean =        13.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.86   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    99.86   17.24    None  None   None       |
|    Sol.    : 438    0      5.37    82.98   40.56    None  None   None       |
|    Mac.    : 2385   0      0.00    99.86   12.96    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 -   9.989: 1028   |   5:    49.932 -  59.917:   98        |
|      1:     9.989 -  19.974: 1151   |   6:    59.917 -  69.903:   42        |
|      2:    19.974 -  29.960:  219   |   7:    69.903 -  79.889:   19        |
|      3:    29.960 -  39.946:  135   |   8:    79.889 -  89.875:    5        |
|      4:    39.946 -  49.932:  123   |   9:    89.875 -  99.860:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.514 - 5.566
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 304
   mapped sites are within: 0.717 - 5.566

peak=    5.777 closest distance to " NH2 ARG A  56 " =    2.128
peak=    5.510 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.328 closest distance to " CG  PRO A  54 " =    1.162
peak=    5.291 closest distance to " CB  SER A  63 " =    1.225
peak=    5.269 closest distance to " O   HOH Z 126 " =    1.866
peak=    5.238 closest distance to " O   HOH Z 144 " =    1.722
peak=    5.147 closest distance to " NE2 GLN A  11 " =    1.081
peak=    5.067 closest distance to " O   HOH Z 232 " =    2.280
peak=    5.031 closest distance to " CG  PRO A 213 " =    1.204
peak=    5.014 closest distance to " CB  GLN A 183 " =    1.283
peak=    4.922 closest distance to " O   HOH Z 193 " =    1.780
peak=    4.917 closest distance to " CB  ARG A 275 " =    0.924
peak=    4.695 closest distance to " O   HOH Z 427 " =    2.772
peak=    4.587 closest distance to " O   HOH Z  78 " =    1.752
peak=    4.568 closest distance to " CB  ASN A 148 " =    1.561
peak=    4.556 closest distance to " CA  TYR A  30 " =    0.970
peak=    4.529 closest distance to " C   PRO A 198 " =    1.512
peak=    4.521 closest distance to " CG  PRO A  90 " =    1.074
peak=    4.485 closest distance to " CB  GLU A 128 " =    1.135
peak=    4.472 closest distance to " OD1 ASN A  69 " =    2.618
peak=    4.469 closest distance to " CB  PRO A  54 " =    0.942
peak=    4.432 closest distance to " O   HOH Z 236 " =    2.015
peak=    4.419 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.408 closest distance to " O   HOH Z  15 " =    2.047
peak=    4.366 closest distance to " O   HOH Z 298 " =    1.891
peak=    4.358 closest distance to " OD2 ASP A 286 " =    2.780
peak=    4.347 closest distance to " CB  SER A   3 " =    1.359
peak=    4.320 closest distance to " O   HOH Z 203 " =    1.821
peak=    4.310 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.306 closest distance to " CB  TYR A 169 " =    0.789
peak=    4.303 closest distance to " O   HOH Z 368 " =    2.014
peak=    4.258 closest distance to " O   HOH Z 234 " =    3.699
peak=    4.239 closest distance to " O   HOH Z 344 " =    3.001
peak=    4.228 closest distance to " O   HOH Z 316 " =    2.948
peak=    4.206 closest distance to " CB  LEU A 228 " =    1.130
peak=    4.203 closest distance to " O   HOH Z 108 " =    1.380
peak=    4.181 closest distance to " CB  TRP A 179 " =    1.293
peak=    4.173 closest distance to " CB  ARG A  79 " =    1.477
peak=    4.171 closest distance to " O   HOH Z 389 " =    1.847
peak=    4.142 closest distance to " CA  ALA A  21 " =    1.117
peak=    4.110 closest distance to " O   HOH Z  93 " =    2.401
peak=    4.099 closest distance to " O   HOH Z 144 " =    2.267
peak=    4.098 closest distance to " ND2 ASN A 187 " =    1.453
peak=    4.083 closest distance to " O   HOH Z 272 " =    1.814
peak=    4.073 closest distance to " O   HOH Z 134 " =    1.348
peak=    4.064 closest distance to " O   HOH Z   6 " =    2.263
peak=    4.063 closest distance to " O   HOH Z 371 " =    3.343
peak=    4.057 closest distance to " O   HOH Z 207 " =    1.856
peak=    4.041 closest distance to " O   HOH Z 278 " =    0.906
peak=    4.025 closest distance to " O   HOH Z  97 " =    1.940
peak=    4.021 closest distance to " O   SER A  87 " =    2.295
peak=    4.005 closest distance to " O   MET A 105 " =    1.794
peak=    3.987 closest distance to " O   HOH Z 193 " =    2.075
peak=    3.986 closest distance to " O   HOH Z 180 " =    2.239
peak=    3.983 closest distance to " O   HOH Z  10 " =    1.901
peak=    3.983 closest distance to " O   HOH Z  54 " =    1.728
peak=    3.979 closest distance to " CA  THR A 221 " =    0.945
peak=    3.950 closest distance to " CG1 ILE A  33 " =    1.271
peak=    3.934 closest distance to " NZ  LYS A 117 " =    3.276
peak=    3.927 closest distance to " OG BSER A 164 " =    2.384
peak=    3.913 closest distance to " O   HOH Z  43 " =    1.995
peak=    3.911 closest distance to " CB  VAL A 265 " =    1.244
peak=    3.906 closest distance to " O   HOH Z  59 " =    1.996
peak=    3.902 closest distance to " O   HOH Z 124 " =    1.394
peak=    3.887 closest distance to " O   HOH Z 369 " =    2.034
peak=    3.885 closest distance to " CA  ASN A 215 " =    1.219
peak=    3.884 closest distance to " CA  MET A  40 " =    1.026
peak=    3.866 closest distance to " O   HOH Z 411 " =    3.825
peak=    3.848 closest distance to " CG  ARG A  66 " =    2.507
peak=    3.836 closest distance to " O   HOH Z  88 " =    3.263
peak=    3.835 closest distance to " O   HOH Z  21 " =    1.656
peak=    3.834 closest distance to " O   HOH Z 128 " =    2.205
peak=    3.830 closest distance to " O   HOH Z 132 " =    2.337
peak=    3.828 closest distance to " CD BLYS A 290 " =    1.205
peak=    3.826 closest distance to " O   HOH Z 303 " =    1.913
peak=    3.825 closest distance to " CG  PRO A 243 " =    1.185
peak=    3.800 closest distance to " CB  VAL A 202 " =    1.680
peak=    3.796 closest distance to " O   HOH Z  61 " =    1.635
peak=    3.791 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.783 closest distance to " O   HOH Z 284 " =    2.894
peak=    3.764 closest distance to " O   HOH Z 426 " =    1.427
peak=    3.756 closest distance to " O   HOH Z 108 " =    1.973
peak=    3.754 closest distance to " O   HOH Z 346 " =    1.661
peak=    3.734 closest distance to " O   HOH Z 403 " =    1.678
peak=    3.726 closest distance to " NH2BARG A 145 " =    2.004
peak=    3.724 closest distance to " O   HOH Z 197 " =    2.897
peak=    3.722 closest distance to " CG2 VAL A 257 " =    0.886
peak=    3.712 closest distance to " O   HOH Z   3 " =    1.680
peak=    3.710 closest distance to " O   HOH Z 209 " =    2.412
peak=    3.702 closest distance to " CB  GLU A 277 " =    3.500
peak=    3.700 closest distance to " CG2 THR A 221 " =    1.131
peak=    3.696 closest distance to " O   HOH Z 326 " =    1.489
peak=    3.695 closest distance to " CD  LYS A 119 " =    1.173
peak=    3.684 closest distance to " O   HOH Z 172 " =    3.681
peak=    3.674 closest distance to " CB  ARG A 190 " =    1.730
peak=    3.663 closest distance to " O   HOH Z 163 " =    1.891
peak=    3.661 closest distance to " O   HOH Z   1 " =    1.821
peak=    3.656 closest distance to " O   HOH Z 407 " =    2.534
peak=    3.649 closest distance to " O   HOH Z 128 " =    2.102
peak=    3.644 closest distance to " O   HOH Z 183 " =    1.411
peak=    3.643 closest distance to " O   HOH Z 403 " =    1.313
peak=    3.631 closest distance to " O   HOH Z 279 " =    2.127
peak=    3.628 closest distance to " O   HOH Z 158 " =    2.975
peak=    3.623 closest distance to " O   HOH Z 156 " =    2.951
peak=    3.620 closest distance to " O   HOH Z 263 " =    2.265
peak=    3.615 closest distance to " CD2 LEU A 297 " =    0.937
peak=    3.613 closest distance to " CB  ARG A 139 " =    0.904
peak=    3.611 closest distance to " NZ  LYS A 119 " =    1.614
peak=    3.610 closest distance to " O   HOH Z 211 " =    2.413
peak=    3.607 closest distance to " O   HOH Z  44 " =    1.822
peak=    3.601 closest distance to " CG2 ILE A 120 " =    1.189
peak=    3.586 closest distance to " CB  SER A 141 " =    1.090
peak=    3.583 closest distance to " CD1 LEU A 300 " =    1.220
peak=    3.581 closest distance to " NH1BARG A 145 " =    1.215
peak=    3.580 closest distance to " O   HOH Z 214 " =    2.020
peak=    3.578 closest distance to " O   HOH Z 273 " =    2.819
peak=    3.572 closest distance to " O   HOH Z 189 " =    1.719
peak=    3.564 closest distance to " O   HOH Z 374 " =    2.485
peak=    3.563 closest distance to " O   HOH Z 250 " =    1.352
peak=    3.560 closest distance to " O   HOH Z 173 " =    1.869
peak=    3.560 closest distance to " O   HOH Z 313 " =    1.674
peak=    3.554 closest distance to " O   HOH Z  48 " =    1.368
peak=    3.547 closest distance to " NH1AARG A 145 " =    1.030
peak=    3.542 closest distance to " O   HOH Z  40 " =    1.634
peak=    3.539 closest distance to " CG  MET A 185 " =    1.135
peak=    3.538 closest distance to " O   HOH Z 295 " =    1.502
peak=    3.535 closest distance to " CD  ARG A 159 " =    0.760
peak=    3.534 closest distance to " CE  LYS A  76 " =    0.813
peak=    3.526 closest distance to " O   HOH Z 368 " =    3.643
peak=    3.525 closest distance to " O   HOH Z 260 " =    1.129
peak=    3.525 closest distance to " N   ASN A  39 " =    1.242
peak=    3.521 closest distance to " O   HOH Z  66 " =    2.087
peak=    3.518 closest distance to " NH2 ARG A 156 " =    1.219
peak=    3.515 closest distance to " CB  ALA A 291 " =    1.345
peak=    3.513 closest distance to " O   HOH Z 345 " =    3.307
peak=    3.511 closest distance to " O   HOH Z 261 " =    1.515
peak=    3.510 closest distance to " O   HOH Z 133 " =    1.487
peak=    3.510 closest distance to " O   HOH Z  73 " =    1.515
peak=    3.507 closest distance to " CG1BVAL A  72 " =    1.541
peak=    3.497 closest distance to " O   HOH Z 227 " =    1.613
peak=    3.496 closest distance to " O   HOH Z 423 " =    1.968
peak=    3.491 closest distance to " O   HOH Z 327 " =    1.701
peak=    3.487 closest distance to " CE1 TYR A 186 " =    1.245
peak=    3.487 closest distance to " CG2BVAL A  41 " =    0.854
peak=    3.478 closest distance to " CA  THR A 264 " =    0.846
peak=    3.477 closest distance to " NH2AARG A 190 " =    1.289
peak=    3.472 closest distance to " O   HOH Z 409 " =    3.035
peak=    3.464 closest distance to " CZ2 TRP A 179 " =    1.642
peak=    3.461 closest distance to " O   HOH Z 133 " =    2.391
peak=    3.457 closest distance to " CD2 LEU A 255 " =    1.260
peak=    3.452 closest distance to " CB  SER A  62 " =    1.297
peak=    3.442 closest distance to " CB  SER A 216 " =    0.806
peak=    3.441 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.439 closest distance to " O   HOH Z  71 " =    1.156
peak=    3.430 closest distance to " CA  VAL A 126 " =    1.217
peak=    3.430 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.427 closest distance to " N   ARG A 156 " =    1.287
peak=    3.427 closest distance to " N   ASN A 127 " =    1.237
peak=    3.422 closest distance to " O   HOH Z  49 " =    2.042
peak=    3.416 closest distance to " CD  LYS A 166 " =    1.267
peak=    3.412 closest distance to " CA  ASN A 176 " =    1.184
peak=    3.410 closest distance to " OG  SER A  62 " =    2.996
peak=    3.407 closest distance to " O   ALA A 165 " =    1.385
peak=    3.406 closest distance to " O   HOH Z 135 " =    1.611
peak=    3.397 closest distance to " O   HOH Z 353 " =    2.606
peak=    3.394 closest distance to " O   HOH Z 366 " =    3.104
peak=    3.390 closest distance to " O   HOH Z 145 " =    2.292
peak=    3.383 closest distance to " O   HOH Z 406 " =    1.703
peak=    3.383 closest distance to " O   HOH Z  63 " =    2.048
peak=    3.383 closest distance to " O   HOH Z  68 " =    1.500
peak=    3.382 closest distance to " O   HOH Z 281 " =    4.428
peak=    3.382 closest distance to " O   HOH Z 185 " =    1.699
peak=    3.379 closest distance to " O   HOH Z  19 " =    2.410
peak=    3.379 closest distance to " CA  ASP A 140 " =    1.086
peak=    3.374 closest distance to " O   HOH Z 227 " =    2.209
peak=    3.372 closest distance to " CB  SER A  26 " =    1.552
peak=    3.370 closest distance to " NE2 GLN A  58 " =    4.313
peak=    3.365 closest distance to " CA  ARG A  36 " =    1.058
peak=    3.364 closest distance to " CG1 VAL A 202 " =    2.016
peak=    3.361 closest distance to " CB  MET A  47 " =    1.095
peak=    3.360 closest distance to " CA  ALA A 291 " =    0.890
peak=    3.355 closest distance to " O   HOH Z 427 " =    3.050
peak=    3.353 closest distance to " O   HOH Z 368 " =    2.603
peak=    3.343 closest distance to " C   ALA A   1 " =    1.606
peak=    3.343 closest distance to " O   HOH Z 402 " =    1.424
peak=    3.339 closest distance to " CD  ARG A 269 " =    0.960
peak=    3.338 closest distance to " CA  ALA A  51 " =    0.969
peak=    3.336 closest distance to " O   HOH Z 291 " =    1.875
peak=    3.329 closest distance to " CD2 TRP A 179 " =    1.401
peak=    3.327 closest distance to " O   HOH Z  40 " =    2.812
peak=    3.326 closest distance to " CG  MET A 185 " =    1.067
peak=    3.324 closest distance to " O   HOH Z 425 " =    1.966
peak=    3.322 closest distance to " O   HOH Z 334 " =    1.423
peak=    3.321 closest distance to " CB  SER A 212 " =    0.965
peak=    3.321 closest distance to " O   HOH Z 437 " =    1.683
peak=    3.320 closest distance to " CB  LEU A 255 " =    0.717
peak=    3.320 closest distance to " CA  ALA A 248 " =    1.150
peak=    3.319 closest distance to " O   HOH Z 247 " =    1.207
peak=    3.313 closest distance to " O   HOH Z 337 " =    3.625
peak=    3.309 closest distance to " O   HOH Z 175 " =    2.231
peak=    3.304 closest distance to " O   HOH Z 380 " =    1.821
peak=    3.304 closest distance to " O   HOH Z 189 " =    1.347
peak=    3.292 closest distance to " O   HOH Z  59 " =    2.287
peak=    3.290 closest distance to " O   HOH Z 367 " =    3.392
peak=    3.288 closest distance to " O   HOH Z 106 " =    2.271
peak=    3.286 closest distance to " OG  SER A  22 " =    2.686
peak=    3.285 closest distance to " CA  LYS A 117 " =    1.206
peak=    3.285 closest distance to " O   SER A  26 " =    1.654
peak=    3.284 closest distance to " CG  GLU A 277 " =    2.090
peak=    3.282 closest distance to " CA  ALA A 233 " =    1.256
peak=    3.281 closest distance to " O   HOH Z 411 " =    1.786
peak=    3.281 closest distance to " CA  ALA A  43 " =    1.240
peak=    3.280 closest distance to " O   HOH Z 147 " =    1.672
peak=    3.278 closest distance to " CG AARG A 275 " =    0.957
peak=    3.264 closest distance to " O   HOH Z 227 " =    1.552
peak=    3.260 closest distance to " O   HOH Z 245 " =    1.268
peak=    3.256 closest distance to " CZ  PHE A 218 " =    1.023
peak=    3.255 closest distance to " NH2 ARG A 219 " =    1.918
peak=    3.252 closest distance to " CG2 VAL A  78 " =    0.874
peak=    3.249 closest distance to " O   HOH Z 267 " =    2.116
peak=    3.248 closest distance to " O   HOH Z 286 " =    2.178
peak=    3.247 closest distance to " ND1 HIS A  81 " =    1.549
peak=    3.246 closest distance to " O   HOH Z 116 " =    1.807
peak=    3.241 closest distance to " O   HOH Z  63 " =    2.272
peak=    3.236 closest distance to " CA  ARG A 195 " =    1.224
peak=    3.235 closest distance to " CG  GLN A  77 " =    2.147
peak=    3.233 closest distance to " O   HOH Z 271 " =    2.238
peak=    3.232 closest distance to " CA  ALA A 160 " =    0.783
peak=    3.232 closest distance to " O   HOH Z 425 " =    1.223
peak=    3.229 closest distance to " O   HOH Z 209 " =    2.377
peak=    3.226 closest distance to " O   ALA A 158 " =    1.273
peak=    3.222 closest distance to " CG1 ILE A 151 " =    0.849
peak=    3.218 closest distance to " O   HOH Z 366 " =    2.838
peak=    3.214 closest distance to " C   TYR A 214 " =    1.430
peak=    3.213 closest distance to " O   ALA A   1 " =    1.442
peak=    3.209 closest distance to " CD2 HIS A  81 " =    1.172
peak=    3.209 closest distance to " O   HOH Z  88 " =    2.664
peak=    3.208 closest distance to " CE AMET A  47 " =    1.416
peak=    3.207 closest distance to " ND1 HIS A  86 " =    1.789
peak=    3.202 closest distance to " O   HOH Z 193 " =    1.550
peak=    3.200 closest distance to " O   HOH Z 329 " =    3.487
peak=    3.199 closest distance to " OE2 GLU A  53 " =    2.141
peak=    3.195 closest distance to " CB  ALA A  34 " =    1.084
peak=    3.194 closest distance to " OD1 ASP A 231 " =    1.854
peak=    3.194 closest distance to " O   HOH Z 410 " =    1.888
peak=    3.193 closest distance to " CB  ALA A  71 " =    1.369
peak=    3.192 closest distance to " O   HOH Z 266 " =    2.879
peak=    3.185 closest distance to " CB  ASP A 140 " =    0.931
peak=    3.183 closest distance to " CG  GLN A  58 " =    2.530
peak=    3.179 closest distance to " O   HOH Z 373 " =    1.515
peak=    3.175 closest distance to " O   THR A 220 " =    1.379
peak=    3.173 closest distance to " O   HOH Z 276 " =    1.237
peak=    3.169 closest distance to " CA  ILE A  33 " =    1.568
peak=    3.166 closest distance to " O   HOH Z 392 " =    1.680
peak=    3.164 closest distance to " CE BMET A  47 " =    1.500
peak=    3.161 closest distance to " CA  VAL A  41 " =    0.922
peak=    3.160 closest distance to " O   HOH Z 151 " =    1.451
peak=    3.160 closest distance to " CG  MET A  93 " =    0.981
peak=    3.155 closest distance to " O   HOH Z 357 " =    1.892
peak=    3.154 closest distance to " CG  LYS A  76 " =    1.093
peak=    3.153 closest distance to " O   HOH Z 287 " =    2.248
peak=    3.153 closest distance to " NZ  LYS A  76 " =    1.233
peak=    3.152 closest distance to " O   HOH Z 261 " =    1.951
peak=    3.152 closest distance to " CA  ALA A 158 " =    1.131
peak=    3.146 closest distance to " OE1 GLN A  11 " =    1.894
peak=    3.145 closest distance to " O   HOH Z  64 " =    2.117
peak=    3.142 closest distance to " CG2 VAL A 174 " =    1.319
peak=    3.138 closest distance to " O   HOH Z 286 " =    2.403
peak=    3.134 closest distance to " O   HOH Z 250 " =    1.631
peak=    3.132 closest distance to " O   HOH Z 341 " =    1.808
peak=    3.130 closest distance to " CB  GLU A 152 " =    1.496
peak=    3.129 closest distance to " O   HOH Z 166 " =    3.690
peak=    3.126 closest distance to " O   HOH Z 125 " =    2.215
peak=    3.121 closest distance to " CB  THR A 157 " =    1.010
peak=    3.120 closest distance to " CA  GLY A 267 " =    1.213
peak=    3.120 closest distance to " C   GLY A  80 " =    1.108
peak=    3.116 closest distance to " CB  GLU A  46 " =    1.057
peak=    3.116 closest distance to " O   HOH Z  66 " =    2.156
peak=    3.116 closest distance to " CG2 VAL A 197 " =    1.114
peak=    3.102 closest distance to " CG  MET A 113 " =    1.239
peak=    3.101 closest distance to " CD1AILE A 234 " =    1.004
peak=    3.101 closest distance to " CA  PHE A 283 " =    1.452
peak=    3.098 closest distance to " CB  TYR A 116 " =    0.857
peak=    3.097 closest distance to " O   HOH Z 430 " =    5.566
peak=    3.096 closest distance to " CB  LYS A 117 " =    1.130
peak=    3.087 closest distance to " O   HOH Z 188 " =    2.001
peak=    3.086 closest distance to " O   TRP A 274 " =    1.847
peak=    3.085 closest distance to " CB  TYR A  30 " =    1.504
peak=    3.084 closest distance to " CB  ASN A  39 " =    0.874
peak=    3.083 closest distance to " CB  ALA A   9 " =    1.568
peak=    3.080 closest distance to " N   ALA A 154 " =    0.919
peak=    3.078 closest distance to " O   HOH Z 261 " =    1.638
peak=    3.076 closest distance to " O   HOH Z 112 " =    1.660
peak=    3.074 closest distance to " O   HOH Z 388 " =    1.898
peak=    3.074 closest distance to " OG BSER A  99 " =    2.192
peak=    3.064 closest distance to " OD1 ASP A 286 " =    1.576
peak=    3.048 closest distance to " O   HOH Z 216 " =    2.456
peak=    3.046 closest distance to " O   HOH Z 423 " =    3.151
peak=    3.039 closest distance to " CD1 LEU A 228 " =    1.941

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.800 - 5.249
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.800 - 5.249

peak=   -4.749 closest distance to " O   HOH Z 266 " =    4.216
peak=   -4.518 closest distance to " CD  ARG A 156 " =    1.950
peak=   -4.434 closest distance to " O   HOH Z 198 " =    2.112
peak=   -4.360 closest distance to " O   HOH Z 377 " =    2.009
peak=   -4.314 closest distance to " SG  CYS A 254 " =    3.309
peak=   -4.241 closest distance to " CB  ALA A 161 " =    2.586
peak=   -4.223 closest distance to " CB  PRO A 243 " =    2.569
peak=   -4.203 closest distance to " C   HIS A 108 " =    1.064
peak=   -4.199 closest distance to " O   HOH Z 372 " =    2.272
peak=   -4.162 closest distance to " O   HOH Z  13 " =    1.468
peak=   -4.083 closest distance to " N   GLN A  58 " =    1.757
peak=   -4.069 closest distance to " OXT GLY A 302 " =    2.737
peak=   -4.007 closest distance to " O   PRO A 198 " =    1.307
peak=   -4.001 closest distance to " O   HOH Z  11 " =    1.968
peak=   -3.994 closest distance to " OE1 GLN A 223 " =    2.172
peak=   -3.984 closest distance to " O   PRO A 163 " =    2.006
peak=   -3.976 closest distance to " N   ALA A 248 " =    1.602
peak=   -3.968 closest distance to " OG BSER A 134 " =    1.238
peak=   -3.956 closest distance to " N   MET A 188 " =    1.928
peak=   -3.952 closest distance to " O   HOH Z 231 " =    2.135
peak=   -3.952 closest distance to " ND2 ASN A  45 " =    0.933
peak=   -3.869 closest distance to " O   HOH Z 407 " =    3.092
peak=   -3.856 closest distance to " O   VAL A  67 " =    2.720
peak=   -3.854 closest distance to " O   HOH Z 102 " =    1.699
peak=   -3.845 closest distance to " CD  ARG A 139 " =    1.622
peak=   -3.843 closest distance to " CZ  PHE A  59 " =    1.597
peak=   -3.838 closest distance to " O   HOH Z 353 " =    2.199
peak=   -3.834 closest distance to " O   HOH Z 388 " =    1.909
peak=   -3.830 closest distance to " O   VAL A  67 " =    2.745
peak=   -3.818 closest distance to " CB  TYR A  15 " =    2.171
peak=   -3.796 closest distance to " O   HOH Z  52 " =    1.417
peak=   -3.794 closest distance to " CE2 TYR A  30 " =    2.796
peak=   -3.776 closest distance to " O   SER A 135 " =    1.538
peak=   -3.767 closest distance to " CB  ASN A  39 " =    2.184
peak=   -3.762 closest distance to " CZ3 TRP A 179 " =    1.292
peak=   -3.752 closest distance to " N   ALA A  43 " =    2.476
peak=   -3.748 closest distance to " CZ  TYR A 169 " =    1.730
peak=   -3.743 closest distance to " O   HOH Z 185 " =    2.110
peak=   -3.732 closest distance to " O   HOH Z 290 " =    1.112
peak=   -3.729 closest distance to " O   HOH Z  11 " =    1.798
peak=   -3.725 closest distance to " N   SER A 212 " =    1.946
peak=   -3.710 closest distance to " OD1 ASN A 187 " =    1.693
peak=   -3.700 closest distance to " O   HOH Z  43 " =    1.628
peak=   -3.691 closest distance to " O   VAL A 153 " =    2.312
peak=   -3.686 closest distance to " N   ASP A 286 " =    2.419
peak=   -3.679 closest distance to " O   HOH Z   3 " =    1.972
peak=   -3.678 closest distance to " C   ALA A 158 " =    1.190
peak=   -3.678 closest distance to " CD1 LEU A 101 " =    2.421
peak=   -3.670 closest distance to " O   HOH Z 118 " =    2.903
peak=   -3.666 closest distance to " CG  ASP A 231 " =    0.800
peak=   -3.663 closest distance to " OG  SER A  97 " =    2.091
peak=   -3.651 closest distance to " CG  PHE A 283 " =    2.618
peak=   -3.643 closest distance to " O   HOH Z  10 " =    1.416
peak=   -3.639 closest distance to " CD1 LEU A 228 " =    2.195
peak=   -3.638 closest distance to " O   HOH Z 395 " =    5.154
peak=   -3.615 closest distance to " CG1 VAL A 112 " =    2.786
peak=   -3.611 closest distance to " CE  MET A 105 " =    2.063
peak=   -3.608 closest distance to " O   HOH Z 166 " =    1.391
peak=   -3.608 closest distance to " CB  ALA A 291 " =    2.432
peak=   -3.601 closest distance to " CD2 LEU A 237 " =    2.611
peak=   -3.591 closest distance to " CD2 LEU A 300 " =    2.861
peak=   -3.572 closest distance to " OD1 ASP A 191 " =    1.732
peak=   -3.572 closest distance to " O   VAL A 174 " =    2.066
peak=   -3.564 closest distance to " O   HOH Z  93 " =    1.760
peak=   -3.561 closest distance to " CD1 PHE A  59 " =    1.838
peak=   -3.559 closest distance to " N   SER A 276 " =    1.253
peak=   -3.552 closest distance to " NH1 ARG A 195 " =    2.610
peak=   -3.546 closest distance to " CE2 PHE A 218 " =    2.494
peak=   -3.544 closest distance to " O   HOH Z 435 " =    2.665
peak=   -3.533 closest distance to " O   HOH Z  60 " =    2.242
peak=   -3.527 closest distance to " O   GLY A 211 " =    1.432
peak=   -3.518 closest distance to " N   HIS A 115 " =    1.867
peak=   -3.510 closest distance to " O   HOH Z 292 " =    4.487
peak=   -3.507 closest distance to " NH2 ARG A  79 " =    1.847
peak=   -3.505 closest distance to " CA  ASP A  27 " =    2.444
peak=   -3.494 closest distance to " O   HOH Z  90 " =    2.775
peak=   -3.493 closest distance to " OG  SER A  62 " =    1.629
peak=   -3.489 closest distance to " O   HOH Z  97 " =    1.656
peak=   -3.488 closest distance to " O   HOH Z 385 " =    2.006
peak=   -3.484 closest distance to " O   ALA A 161 " =    1.609
peak=   -3.479 closest distance to " CD  LYS A 289 " =    2.503
peak=   -3.472 closest distance to " CG  ASP A  50 " =    2.458
peak=   -3.466 closest distance to " O   HOH Z 198 " =    1.537
peak=   -3.451 closest distance to " CB  ALA A 131 " =    2.040
peak=   -3.449 closest distance to " CB  ALA A  51 " =    1.871
peak=   -3.448 closest distance to " O   HOH Z 148 " =    3.364
peak=   -3.448 closest distance to " O   HOH Z  98 " =    2.004
peak=   -3.446 closest distance to " OG BSER A 134 " =    1.689
peak=   -3.443 closest distance to " CA  GLY A 133 " =    1.909
peak=   -3.438 closest distance to " OG ASER A 134 " =    1.144
peak=   -3.437 closest distance to " OD1 ASN A 148 " =    1.643
peak=   -3.437 closest distance to " C   LEU A 143 " =    1.170
peak=   -3.430 closest distance to " O   HOH Z 311 " =    3.441
peak=   -3.426 closest distance to " OXT GLY A 302 " =    3.344
peak=   -3.423 closest distance to " CB  ALA A 248 " =    1.962
peak=   -3.422 closest distance to " O   HOH Z 313 " =    2.051
peak=   -3.421 closest distance to " N   THR A 157 " =    1.550
peak=   -3.413 closest distance to " ND2 ASN A 187 " =    1.472
peak=   -3.411 closest distance to " O   HOH Z  15 " =    1.570
peak=   -3.409 closest distance to " O   HOH Z  38 " =    1.609
peak=   -3.408 closest distance to " O   HOH Z 166 " =    1.873
peak=   -3.406 closest distance to " O   HOH Z  47 " =    1.502
peak=   -3.400 closest distance to " OD1 ASP A 191 " =    1.412
peak=   -3.397 closest distance to " OD1 ASP A 171 " =    1.521
peak=   -3.391 closest distance to " OE1 GLN A  88 " =    1.116
peak=   -3.387 closest distance to " CB  CYS A 201 " =    2.586
peak=   -3.384 closest distance to " CD  GLN A  88 " =    1.925
peak=   -3.383 closest distance to " CE3 TRP A 274 " =    2.422
peak=   -3.364 closest distance to " CB  ASP A 132 " =    2.239
peak=   -3.362 closest distance to " NH2AARG A 275 " =    5.249
peak=   -3.361 closest distance to " NH2 ARG A  66 " =    4.831
peak=   -3.360 closest distance to " O   PHE A 218 " =    1.558
peak=   -3.360 closest distance to " O   HOH Z 263 " =    2.893
peak=   -3.359 closest distance to " O   PRO A 243 " =    2.546
peak=   -3.355 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.351 closest distance to " CG  PRO A 163 " =    2.520
peak=   -3.347 closest distance to " OG1 THR A 178 " =    1.178
peak=   -3.346 closest distance to " CG2 VAL A 189 " =    2.062
peak=   -3.339 closest distance to " NH1AARG A 275 " =    1.783
peak=   -3.327 closest distance to " O   HOH Z 417 " =    2.481
peak=   -3.326 closest distance to " CB  PHE A 192 " =    1.873
peak=   -3.324 closest distance to " O   TRP A  92 " =    1.664
peak=   -3.312 closest distance to " O   HOH Z 250 " =    1.443
peak=   -3.310 closest distance to " CA  ASP A 298 " =    1.037
peak=   -3.308 closest distance to " O   HOH Z 361 " =    3.420
peak=   -3.306 closest distance to " O   MET A  40 " =    2.739
peak=   -3.305 closest distance to " OE1 GLN A  77 " =    1.766
peak=   -3.305 closest distance to " CG  LEU A  83 " =    1.901
peak=   -3.303 closest distance to " O   HOH Z 234 " =    4.073
peak=   -3.299 closest distance to " SG ACYS A 201 " =    2.213
peak=   -3.299 closest distance to " O   PRO A 198 " =    1.289
peak=   -3.295 closest distance to " CA  GLY A 203 " =    2.035
peak=   -3.294 closest distance to " OH  TYR A 214 " =    1.313
peak=   -3.289 closest distance to " O   HOH Z  63 " =    1.428
peak=   -3.288 closest distance to " O   ASN A 249 " =    1.566
peak=   -3.287 closest distance to " O   HOH Z 222 " =    1.195
peak=   -3.286 closest distance to " OD2 ASP A 171 " =    2.311
peak=   -3.284 closest distance to " CB  ALA A 291 " =    2.181
peak=   -3.273 closest distance to " CA  SER A 146 " =    2.273
peak=   -3.271 closest distance to " O   SER A 146 " =    1.025
peak=   -3.265 closest distance to " N   GLN A 122 " =    1.468
peak=   -3.263 closest distance to " N   ALA A 226 " =    2.015
peak=   -3.260 closest distance to " CG  GLU A  53 " =    1.429
peak=   -3.258 closest distance to " CE  MET A  93 " =    1.176
peak=   -3.255 closest distance to " OG  SER A  87 " =    1.300
peak=   -3.251 closest distance to " N   ALA A 248 " =    2.617
peak=   -3.238 closest distance to " OD2 ASP A 171 " =    1.704
peak=   -3.238 closest distance to " CG2 ILE A 263 " =    2.243
peak=   -3.237 closest distance to " NE2 GLN A  58 " =    1.234
peak=   -3.237 closest distance to " O   HOH Z 351 " =    1.559
peak=   -3.235 closest distance to " C   MET A 188 " =    1.574
peak=   -3.234 closest distance to " O   HOH Z 244 " =    1.976
peak=   -3.227 closest distance to " O   GLY A 196 " =    0.987
peak=   -3.225 closest distance to " CB  SER A 245 " =    2.474
peak=   -3.223 closest distance to " OD1 ASN A 176 " =    1.145
peak=   -3.222 closest distance to " CD2 TYR A 293 " =    2.053
peak=   -3.219 closest distance to " O   HOH Z 165 " =    2.042
peak=   -3.218 closest distance to " O   HOH Z  88 " =    1.889
peak=   -3.218 closest distance to " CA  TYR A  30 " =    2.858
peak=   -3.213 closest distance to " O   HOH Z 132 " =    1.139
peak=   -3.212 closest distance to " CA  TRP A 274 " =    1.576
peak=   -3.208 closest distance to " O   HOH Z 389 " =    1.736
peak=   -3.203 closest distance to " CD  GLN A 223 " =    1.500
peak=   -3.200 closest distance to " O   HOH Z 298 " =    1.279
peak=   -3.194 closest distance to " O   HOH Z  24 " =    1.566
peak=   -3.193 closest distance to " OD1 ASP A 200 " =    1.281
peak=   -3.189 closest distance to " O   ALA A  34 " =    2.615
peak=   -3.185 closest distance to " O   HOH Z 348 " =    1.824
peak=   -3.184 closest distance to " O   HOH Z 405 " =    2.716
peak=   -3.184 closest distance to " CB  CYS A 254 " =    2.322
peak=   -3.183 closest distance to " O   HOH Z 317 " =    2.576
peak=   -3.179 closest distance to " O   HOH Z 310 " =    3.471
peak=   -3.165 closest distance to " CE  LYS A  76 " =    2.793
peak=   -3.156 closest distance to " CG  ARG A  66 " =    2.380
peak=   -3.154 closest distance to " O   LYS A 117 " =    1.633
peak=   -3.147 closest distance to " O   HOH Z  88 " =    2.443
peak=   -3.147 closest distance to " O   HOH Z  71 " =    1.510
peak=   -3.140 closest distance to " O   HOH Z 397 " =    1.136
peak=   -3.139 closest distance to " ND2 ASN A  39 " =    1.422
peak=   -3.137 closest distance to " NE2 GLN A 194 " =    2.866
peak=   -3.135 closest distance to " NH2 ARG A 159 " =    2.417
peak=   -3.135 closest distance to " NH2 ARG A  66 " =    2.128
peak=   -3.134 closest distance to " CZ  PHE A  38 " =    2.395
peak=   -3.131 closest distance to " O   HOH Z 378 " =    1.664
peak=   -3.130 closest distance to " OE1 GLN A 223 " =    1.888
peak=   -3.127 closest distance to " CB  ASP A 149 " =    2.011
peak=   -3.123 closest distance to " CA  TRP A  70 " =    2.476
peak=   -3.123 closest distance to " N   SER A 206 " =    1.913
peak=   -3.107 closest distance to " N   ALA A   9 " =    1.511
peak=   -3.106 closest distance to " O   GLY A  80 " =    2.441
peak=   -3.103 closest distance to " CD1 ILE A 239 " =    1.945
peak=   -3.089 closest distance to " CG1AVAL A  41 " =    2.900
peak=   -3.084 closest distance to " O   ALA A  51 " =    1.363
peak=   -3.082 closest distance to " CB  TRP A  85 " =    2.583
peak=   -3.069 closest distance to " O   HOH Z 423 " =    2.240
peak=   -3.066 closest distance to " SD  MET A 188 " =    2.208
peak=   -3.063 closest distance to " ND2 ASN A  60 " =    1.488
peak=   -3.063 closest distance to " O   HOH Z 210 " =    1.106
peak=   -3.052 closest distance to " O   HOH Z 427 " =    1.462
peak=   -3.031 closest distance to " O   HOH Z 193 " =    1.988
peak=   -3.019 closest distance to " O   HOH Z 108 " =    2.174
peak=   -3.005 closest distance to " O   HOH Z 148 " =    2.716
peak=   -3.001 closest distance to " O   HOH Z 283 " =    2.045

================= 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    :  0.3566 0.3572   6.141526e+00   6.153807e+00
   1_bss:  0.3377 0.3382   6.124761e+00   6.119244e+00
   1_xyz:  0.2510 0.2809   5.836327e+00   5.924938e+00
   1_adp:  0.2306 0.2874   5.787939e+00   5.943098e+00
   1_occ:  0.2303 0.2879   5.787365e+00   5.942918e+00
   2_bss:  0.2276 0.2832   5.777849e+00   5.933400e+00
   2_xyz:  0.1603 0.2096   5.454593e+00   5.648983e+00
   2_adp:  0.1461 0.1918   5.368462e+00   5.571287e+00
   2_occ:  0.1458 0.1917   5.367236e+00   5.570481e+00
   3_bss:  0.1450 0.1896   5.358570e+00   5.561203e+00
   3_xyz:  0.1191 0.1615   5.185701e+00   5.410425e+00
   3_adp:  0.1130 0.1590   5.148427e+00   5.383892e+00
   3_occ:  0.1130 0.1588   5.147791e+00   5.383458e+00
   4_bss:  0.1131 0.1591   5.148541e+00   5.384635e+00
   4_xyz:  0.1105 0.1566   5.134511e+00   5.372220e+00
   4_adp:  0.1097 0.1565   5.130809e+00   5.370372e+00
   4_occ:  0.1096 0.1565   5.130521e+00   5.370327e+00
   5_bss:  0.1095 0.1565   5.130485e+00   5.370314e+00
   5_xyz:  0.1075 0.1556   5.119832e+00   5.366464e+00
   5_adp:  0.1068 0.1567   5.122621e+00   5.374886e+00
   5_occ:  0.1068 0.1567   5.122473e+00   5.374879e+00
   5_bss:  0.1067 0.1567   5.122472e+00   5.374866e+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:  0.314  24.965  -3.174  -2.909   3.761  -0.000   0.000   0.000
   1_xyz:  0.314  24.965  -3.174  -2.909   3.761  -0.000   0.000   0.000
   1_adp:  0.314  24.965  -3.174  -2.909   3.761  -0.000   0.000   0.000
   1_occ:  0.314  24.965  -3.174  -2.909   3.761  -0.000   0.000   0.000
   2_bss:  0.324  38.887  -2.580  -2.271   0.489  -0.000   0.000   0.000
   2_xyz:  0.324  38.887  -2.580  -2.271   0.489  -0.000   0.000   0.000
   2_adp:  0.324  38.887  -2.580  -2.271   0.489  -0.000   0.000   0.000
   2_occ:  0.324  38.887  -2.580  -2.271   0.489  -0.000   0.000   0.000
   3_bss:  0.319  38.887  -2.695  -2.448  -1.419  -0.000  -0.000  -0.000
   3_xyz:  0.319  38.887  -2.695  -2.448  -1.419  -0.000  -0.000  -0.000
   3_adp:  0.319  38.887  -2.695  -2.448  -1.419  -0.000  -0.000  -0.000
   3_occ:  0.319  38.887  -2.695  -2.448  -1.419  -0.000  -0.000  -0.000
   4_bss:  0.318  41.162  -2.698  -2.449  -1.905  -0.000  -0.000  -0.000
   4_xyz:  0.318  41.162  -2.698  -2.449  -1.905  -0.000  -0.000  -0.000
   4_adp:  0.318  41.162  -2.698  -2.449  -1.905  -0.000  -0.000  -0.000
   4_occ:  0.318  41.162  -2.698  -2.449  -1.905  -0.000  -0.000  -0.000
   5_bss:  0.318  41.226  -2.568  -2.285  -1.928  -0.000  -0.000  -0.000
   5_xyz:  0.318  41.226  -2.568  -2.285  -1.928  -0.000  -0.000  -0.000
   5_adp:  0.318  41.226  -2.568  -2.285  -1.928  -0.000  -0.000  -0.000
   5_occ:  0.318  41.226  -2.568  -2.285  -1.928  -0.000  -0.000  -0.000
   5_bss:  0.320  42.635  -2.373  -2.099  -1.785  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.223 0.6302  0.8244    42520.186
   1_bss:  39.291 0.6509  0.8283    37490.883
   1_xyz:  29.173 0.7672  0.9420    21651.618
   1_adp:  30.278 0.7539  0.9309    22667.648
   1_occ:  30.294 0.7537  0.9307    22689.209
   2_bss:  29.617 0.7614  0.9192    22021.630
   2_xyz:  20.384 0.8575  0.9941    11199.307
   2_adp:  18.252 0.8784  1.0058     9572.448
   2_occ:  18.225 0.8786  1.0055     9546.119
   3_bss:  17.946 0.8811  0.9802     9319.915
   3_xyz:  14.730 0.9083  0.9918     6665.634
   3_adp:  14.162 0.9133  0.9900     6346.994
   3_occ:  14.145 0.9134  0.9899     6339.242
   4_bss:  14.161 0.9133  0.9838     6383.833
   4_xyz:  13.793 0.9167  0.9839     6167.112
   4_adp:  13.720 0.9174  0.9804     6154.157
   4_occ:  13.715 0.9175  0.9803     6153.611
   5_bss:  13.715 0.9175  0.9834     6155.886
   5_xyz:  13.667 0.9178  0.9835     6114.190
   5_adp:  13.828 0.9165  0.9778     6183.235
   5_occ:  13.824 0.9165  0.9777     6182.917
   5_bss:  13.825 0.9165  0.9841     6183.922
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7741e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7741e-01
   1_xyz:   1.203  0.010  0.074 15.481  0.005  4.109   8.3928e-02
   1_adp:   1.203  0.010  0.074 15.481  0.005  4.109   8.3928e-02
   1_occ:   1.203  0.010  0.074 15.481  0.005  4.109   8.3928e-02
   2_bss:   1.203  0.010  0.074 15.481  0.005  4.109   8.3928e-02
   2_xyz:   1.078  0.007  0.074 14.206  0.004  4.118   6.2652e-02
   2_adp:   1.078  0.007  0.074 14.206  0.004  4.118   6.2652e-02
   2_occ:   1.078  0.007  0.074 14.206  0.004  4.118   6.2652e-02
   3_bss:   1.078  0.007  0.074 14.206  0.004  4.118   6.2652e-02
   3_xyz:   1.090  0.008  0.076 14.822  0.004  4.111   6.7638e-02
   3_adp:   1.090  0.008  0.076 14.822  0.004  4.111   6.7638e-02
   3_occ:   1.090  0.008  0.076 14.822  0.004  4.111   6.7638e-02
   4_bss:   1.090  0.008  0.076 14.822  0.004  4.111   6.7638e-02
   4_xyz:   0.962  0.006  0.069 14.432  0.004  4.111   5.4595e-02
   4_adp:   0.962  0.006  0.069 14.432  0.004  4.111   5.4595e-02
   4_occ:   0.962  0.006  0.069 14.432  0.004  4.111   5.4595e-02
   5_bss:   0.962  0.006  0.069 14.432  0.004  4.111   5.4595e-02
   5_xyz:   0.999  0.006  0.072 14.497  0.004  4.112   5.7485e-02
   5_adp:   0.999  0.006  0.072 14.497  0.004  4.112   5.7485e-02
   5_occ:   0.999  0.006  0.072 14.497  0.004  4.112   5.7485e-02
   5_bss:   0.999  0.006  0.072 14.497  0.004  4.112   5.7485e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.563   2.3905e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.563   2.3905e-01
   1_xyz:   8.462  0.049  0.306 85.777  0.026  2.088   8.4756e-02
   1_adp:   8.462  0.049  0.306 85.777  0.026  2.088   8.4756e-02
   1_occ:   8.462  0.049  0.306 85.777  0.026  2.088   8.4756e-02
   2_bss:   8.462  0.049  0.306 85.777  0.026  2.088   8.4756e-02
   2_xyz:   6.533  0.050  0.272 80.523  0.035  2.277   5.2876e-02
   2_adp:   6.533  0.050  0.272 80.523  0.035  2.277   5.2876e-02
   2_occ:   6.533  0.050  0.272 80.523  0.035  2.277   5.2876e-02
   3_bss:   6.533  0.050  0.272 80.523  0.035  2.277   5.2876e-02
   3_xyz:   6.618  0.044  0.276 84.212  0.038  2.294   7.9196e-02
   3_adp:   6.618  0.044  0.276 84.212  0.038  2.294   7.9196e-02
   3_occ:   6.618  0.044  0.276 84.212  0.038  2.294   7.9196e-02
   4_bss:   6.618  0.044  0.276 84.212  0.038  2.294   7.9196e-02
   4_xyz:   6.097  0.039  0.226 83.280  0.038  2.357   4.8739e-02
   4_adp:   6.097  0.039  0.226 83.280  0.038  2.357   4.8739e-02
   4_occ:   6.097  0.039  0.226 83.280  0.038  2.357   4.8739e-02
   5_bss:   6.097  0.039  0.226 83.280  0.038  2.357   4.8739e-02
   5_xyz:   6.543  0.034  0.228 83.754  0.035  2.312   4.3464e-02
   5_adp:   6.543  0.034  0.228 83.754  0.035  2.312   4.3464e-02
   5_occ:   6.543  0.034  0.228 83.754  0.035  2.312   4.3464e-02
   5_bss:   6.543  0.034  0.228 83.754  0.035  2.312   4.3464e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  75.92   0.00  17.49  75.92   0.00  13.63  73.08   3.17  38.51
   1_occ:  75.92   0.00  17.49  75.92   0.00  13.63  73.08   3.17  38.51
   2_bss:  75.92   0.00  17.49  75.92   0.00  13.63  73.08   3.17  38.51
   2_xyz:  75.92   0.00  17.49  75.92   0.00  13.63  73.08   3.17  38.51
   2_adp:  75.74   1.68  17.18  75.74   1.68  13.21  71.29   5.22  38.80
   2_occ:  75.74   1.68  17.18  75.74   1.68  13.21  71.29   5.22  38.80
   3_bss:  75.74   1.68  17.18  75.74   1.68  13.21  71.29   5.22  38.80
   3_xyz:  75.74   1.68  17.18  75.74   1.68  13.21  71.29   5.22  38.80
   3_adp:  87.97   0.00  17.28  87.97   0.00  13.08  75.35   2.38  40.18
   3_occ:  87.97   0.00  17.28  87.97   0.00  13.08  75.35   2.38  40.18
   4_bss:  87.97   0.00  17.28  87.97   0.00  13.08  75.35   2.38  40.18
   4_xyz:  87.97   0.00  17.28  87.97   0.00  13.08  75.35   2.38  40.18
   4_adp:  88.58   2.09  17.15  88.58   2.09  12.99  75.43   3.67  39.83
   4_occ:  88.58   2.09  17.15  88.58   2.09  12.99  75.43   3.67  39.83
   5_bss:  88.58   2.09  17.15  88.58   2.09  12.99  75.43   3.67  39.83
   5_xyz:  88.58   2.09  17.15  88.58   2.09  12.99  75.43   3.67  39.83
   5_adp:  99.86   0.00  17.24  99.86   0.00  12.95  82.98   5.37  40.55
   5_occ:  99.86   0.00  17.24  99.86   0.00  12.95  82.98   5.37  40.55
   5_bss:  99.86   0.00  17.24  99.86   0.00  12.96  82.98   5.37  40.56
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.837    0.015    0.277
   1_adp:    1.837    0.015    0.277
   1_occ:    1.837    0.015    0.277
   2_bss:    1.837    0.015    0.277
   2_xyz:    1.308    0.022    0.421
   2_adp:    1.308    0.022    0.421
   2_occ:    1.308    0.022    0.421
   3_bss:    1.308    0.022    0.421
   3_xyz:    1.391    0.013    0.470
   3_adp:    1.391    0.013    0.470
   3_occ:    1.391    0.013    0.470
   4_bss:    1.391    0.013    0.470
   4_xyz:    1.464    0.011    0.481
   4_adp:    1.464    0.011    0.481
   4_occ:    1.464    0.011    0.481
   5_bss:    1.464    0.011    0.481
   5_xyz:    1.527    0.023    0.491
   5_adp:    1.527    0.023    0.491
   5_occ:    1.527    0.023    0.491
   5_bss:    1.527    0.023    0.491
------------------------------------------------------------------------

CPU time actual refinement: 369.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_660/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_660/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_660/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_660/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_660/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 369.52 
  Macro-tasks:
    bulk solvent and scale       = 42.54  
    individual site refinement   = 159.17 
    weights calculation          = 30.25  
    collect and process          = 6.11   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 238.18 
  Micro-tasks:
    mask                            = 1.99   
    f_calc                          = 123.15 
    alpha_beta                      = 8.10   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 132.22 
    fmodel                         = 7.74   
    r_factors                      = 0.30   
    phase_errors                   = 10.81  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 285.71 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.144 micro seconds
Total CPU time: 6.39 minutes
from_scatterers_fft:    659 calls, 122.75 s
gradients_fft:          604 calls, 118.10 s

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

# Date 2008-01-16 Time 05:22:34 PST -0800 (1200489754.34 s)
Start R-work = 0.3566, R-free = 0.3572 (no bulk solvent and anisotropic scale)
Final R-work = 0.1322, R-free = 0.1769 (no bulk solvent and anisotropic scale)

Start R-work = 0.3377, R-free = 0.3382
Final R-work = 0.1067, R-free = 0.1567