# Date 2008-01-16 Time 04:00:51 PST -0800 (1200484851.74 s)
#phil __OFF__

Command line arguments: "../137.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5612
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 137

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 45.9914, 86.39, 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: (68.845, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7736 1.96033
Completeness in resolution range: 0.966881
Completeness with d_max=infinity: 0.963883

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7736
                             d_min =   1.9603

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7736 1.96033
Completeness in resolution range: 0.966881
Completeness with d_max=infinity: 0.963883

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7740 -  4.1942 [2139/2163]  1921   218  10.2%
  bin  2:  4.1942 -  3.3417 [2039/2059]  1841   198   9.7%
  bin  3:  3.3417 -  2.9230 [2018/2037]  1815   203  10.1%
  bin  4:  2.9230 -  2.6575 [1981/2011]  1777   204  10.3%
  bin  5:  2.6575 -  2.4679 [2004/2023]  1808   196   9.8%
  bin  6:  2.4679 -  2.3230 [1979/2004]  1779   200  10.1%
  bin  7:  2.3230 -  2.2071 [1960/1988]  1766   194   9.9%
  bin  8:  2.2071 -  2.1113 [1966/2002]  1769   197  10.0%
  bin  9:  2.1113 -  2.0302 [1945/1987]  1754   191   9.8%
  bin 10:  2.0302 -  1.9603 [1558/1986]  1400   158  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_137/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:
        1.47 -     2.16: 26
        2.16 -     2.84: 1121
        2.84 -     3.53: 4544
        3.53 -     4.21: 9513
        4.21 -     4.90: 13745
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.475 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.565 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.595 3.040 -x+1/2,-y+1,z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.738 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.744 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28944 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_137/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_137/model_refine_001.geo

CPU time processing inputs: 9.54


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 45.9914 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4374   r_free= 0.4305   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.248970                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7740 -  4.6778 0.99   1389  152 0.3575 0.3459      6.5209      6.5004|
|  2:  4.6778 -  3.7326 0.99   1320  154 0.3625 0.3368      6.7299      6.6971|
|  3:  3.7326 -  3.2666 0.99   1299  140 0.4109 0.3928      6.6593      6.6931|
|  4:  3.2666 -  2.9706 0.99   1308  142 0.4169 0.4225       6.491      6.5247|
|  5:  2.9706 -  2.7591 0.99   1278  145 0.4670 0.4159      6.3407      6.3073|
|  6:  2.7591 -  2.5974 0.99   1290  143 0.4674 0.4859      6.2548      6.1905|
|  7:  2.5974 -  2.4679 0.99   1278  143 0.4718 0.4494       6.214       6.134|
|  8:  2.4679 -  2.3610 0.98   1269  138 0.4811 0.5020      6.1653      6.2081|
|  9:  2.3610 -  2.2704 0.98   1267  143 0.4795 0.5014      6.1074      6.1547|
| 10:  2.2704 -  2.1923 1.00   1276  142 0.4845 0.4702      6.0974       6.056|
| 11:  2.1923 -  2.1240 0.97   1254  135 0.4730 0.5192      6.0079      6.0735|
| 12:  2.1240 -  2.0634 0.98   1244  141 0.4921 0.4768      5.9633      6.0097|
| 13:  2.0634 -  2.0092 1.00   1261  135 0.4812 0.4644      5.8799      5.8355|
| 14:  2.0092 -  1.9603 0.70    897  106 0.5022 0.4749      5.8699      5.7559|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7740 -  4.6778  1389   152  0.72  32.71   0.84     0.77      65840.70|
|  2:  4.6778 -  3.7326  1320   154  0.74  32.07   0.94     0.85      92893.42|
|  3:  3.7326 -  3.2666  1299   140  0.64  40.26   0.95     0.83     100194.51|
|  4:  3.2666 -  2.9706  1308   142  0.57  46.57   0.95     0.76      91757.92|
|  5:  2.9706 -  2.7591  1278   145  0.49  52.47   0.92     0.70      71030.62|
|  6:  2.7591 -  2.5974  1290   143  0.49  52.45   0.91     0.68      59924.34|
|  7:  2.5974 -  2.4679  1278   143  0.47  54.67   0.96     0.65      55978.22|
|  8:  2.4679 -  2.3610  1269   138  0.43  57.56   0.94     0.62      53845.71|
|  9:  2.3610 -  2.2704  1267   143  0.41  58.77   0.94     0.60      51635.53|
| 10:  2.2704 -  2.1923  1276   142  0.42  58.38   0.98     0.61      45006.06|
| 11:  2.1923 -  2.1240  1254   135  0.41  58.87   0.98     0.63      42514.28|
| 12:  2.1240 -  2.0634  1244   141  0.42  58.85   0.99     0.64      37583.60|
| 13:  2.0634 -  2.0092  1261   135  0.40  59.73   0.99     0.62      32840.68|
| 14:  2.0092 -  1.9603   897   106  0.43  57.46   0.99     0.59      25680.38|
|alpha:            min =        0.59 max =            0.85 mean =         0.69|
|beta:             min =    25680.38 max =       100194.51 mean =     60099.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.13|
|phase err.(test): min =        0.00 max =           89.97 mean =        51.06|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.607066              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.049   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.707520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.096   (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 |  1.475 -  1.817:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.817 -  2.160:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.160 -  2.502:       61 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.502 -  2.845:     1060 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.845 -  3.187:     2017 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.187 -  3.530:     2527 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.530 -  3.872:     4752 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.872 -  4.215:     4761 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.215 -  4.557:     6248 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.557 -  4.900:     7497 |
|-----------------------------------------------------------------------------|
|-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 |        0.197 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.475 |       0.736 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.365)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4374   r_free= 0.4305   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.248970                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4267   r_free= 0.4213   ksol= 0.34   Bsol= 20.00   scale= 0.952   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,2.50,-1.70,0.00,-0.00,-0.00); trace/3= 0.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.239670                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.918238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.809   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.920303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.802   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4267      final r-factor (work) = 0.3150          |
| start r-factor (free) = 0.4213      final r-factor (free) = 0.3515          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8940 = 7.92 * 0.50 * 6.2380 + 1.00 * 0.1970                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2525 = 7.92 * 0.50 * 6.0949 + 1.00 * 0.1220                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3150      final r-factor (work) = 0.2852          |
| start r-factor (free) = 0.3515      final r-factor (free) = 0.3647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6152 = 0.92 * 1.00 * 6.0949 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4970 = 0.92 * 1.00 * 5.9547 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.365)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.21  18.36    None  None   None       |
|    all(noH): 2823   0      0.00    106.21  18.36    None  None   None       |
|    Sol.    : 438    0      3.96    106.21  38.09    None  None   None       |
|    Mac.    : 2385   0      0.00    76.97   14.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.621: 1015   |   5:    53.106 -  63.728:   71        |
|      1:    10.621 -  21.243:  946   |   6:    63.728 -  74.349:   21        |
|      2:    21.243 -  31.864:  423   |   7:    74.349 -  84.970:    8        |
|      3:    31.864 -  42.485:  207   |   8:    84.970 -  95.591:    0        |
|      4:    42.485 -  53.106:  131   |   9:    95.591 - 106.212:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2852 r_free = 0.3647             target_work(ml) = 5.972         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2849 r_free = 0.3655             target_work(ml) = 5.972         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2849   r_free= 0.3655   ksol= 0.34   Bsol= 20.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,2.50,-1.70,0.00,-0.00,-0.00); trace/3= 0.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.971849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2830   r_free= 0.3622   ksol= 0.34   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,0.32,-0.75,0.00,-0.00,-0.00); trace/3= -0.69                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.964628                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.731395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.173   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.295301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.162  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2830      final r-factor (work) = 0.2251          |
| start r-factor (free) = 0.3622      final r-factor (free) = 0.2920          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2035 = 4.73 * 0.50 * 5.9524 + 1.00 * 0.1220                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9766 = 4.73 * 0.50 * 5.8763 + 1.00 * 0.0750                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2251      final r-factor (work) = 0.2138          |
| start r-factor (free) = 0.2920      final r-factor (free) = 0.2743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7518 = 0.30 * 1.00 * 5.8763 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7159 = 0.30 * 1.00 * 5.7415 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.365)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.41  17.69    None  None   None       |
|    all(noH): 2823   0      0.00    103.41  17.69    None  None   None       |
|    Sol.    : 438    0      5.27    103.41  38.04    None  None   None       |
|    Mac.    : 2385   0      0.00    89.13   13.95    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 -  10.341: 1012   |   5:    51.707 -  62.048:   72        |
|      1:    10.341 -  20.683: 1036   |   6:    62.048 -  72.389:   16        |
|      2:    20.683 -  31.024:  339   |   7:    72.389 -  82.730:    6        |
|      3:    31.024 -  41.365:  215   |   8:    82.730 -  93.072:    1        |
|      4:    41.365 -  51.707:  125   |   9:    93.072 - 103.413:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2138 r_free = 0.2743             target_work(ml) = 5.716         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2135 r_free = 0.2736             target_work(ml) = 5.714         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2135   r_free= 0.2736   ksol= 0.34   Bsol= 50.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,0.32,-0.75,0.00,-0.00,-0.00); trace/3= -0.69                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.713803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2132   r_free= 0.2726   ksol= 0.33   Bsol= 43.36   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-0.76,-0.56,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.711119                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.352993              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.984   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.415155              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.803   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2132      final r-factor (work) = 0.1592          |
| start r-factor (free) = 0.2726      final r-factor (free) = 0.2081          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5692 = 4.35 * 0.50 * 5.7407 + 1.00 * 0.0745                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2190 = 4.35 * 0.50 * 5.5845 + 1.00 * 0.0643                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1592      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.2081      final r-factor (free) = 0.1938          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3303 = 0.42 * 1.00 * 5.5845 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2442 = 0.42 * 1.00 * 5.3837 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.365)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.21   17.42    None  None   None       |
|    all(noH): 2823   0      0.00    99.21   17.42    None  None   None       |
|    Sol.    : 438    0      5.21    99.21   41.46    None  None   None       |
|    Mac.    : 2385   0      0.00    85.72   13.00    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 -   9.921: 1020   |   5:    49.603 -  59.523:  109        |
|      1:     9.921 -  19.841: 1121   |   6:    59.523 -  69.444:   57        |
|      2:    19.841 -  29.762:  232   |   7:    69.444 -  79.364:   11        |
|      3:    29.762 -  39.682:  151   |   8:    79.364 -  89.285:    4        |
|      4:    39.682 -  49.603:  117   |   9:    89.285 -  99.205:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1421 r_free = 0.1938             target_work(ml) = 5.347         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1419 r_free = 0.1933             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1933   ksol= 0.33   Bsol= 43.36   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-0.76,-0.56,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.345333                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1928   ksol= 0.32   Bsol= 43.36   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.93,-0.88,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.340684                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.088446              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.982  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.105624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.755  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1417      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1928      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3824 = 3.09 * 0.50 * 5.3866 + 1.00 * 0.0643                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2124 = 3.09 * 0.50 * 5.2798 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1710      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5668 = 0.11 * 1.00 * 5.2798 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5573 = 0.11 * 1.00 * 5.2147 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.365)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.32    88.11   16.49    None  None   None       |
|    all(noH): 2823   0      1.32    88.11   16.49    None  None   None       |
|    Sol.    : 438    0      3.65    88.11   37.73    None  None   None       |
|    Mac.    : 2385   0      1.32    83.25   12.59    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:     1.318 -   9.997: 1035   |   5:    44.713 -  53.392:  105        |
|      1:     9.997 -  18.676: 1129   |   6:    53.392 -  62.071:   47        |
|      2:    18.676 -  27.355:  222   |   7:    62.071 -  70.750:   15        |
|      3:    27.355 -  36.034:  140   |   8:    70.750 -  79.429:    5        |
|      4:    36.034 -  44.713:  121   |   9:    79.429 -  88.108:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1211 r_free = 0.1647             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1645             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1645   ksol= 0.32   Bsol= 43.36   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.93,-0.88,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.192776                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1643   ksol= 0.32   Bsol= 43.36   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.22,-0.88,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.192260                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.936672              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.955  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.396745              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.887  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7151 = 2.94 * 0.50 * 5.2140 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6426 = 2.94 * 0.50 * 5.1600 + 1.00 * 0.0659                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0537 = 0.40 * 1.00 * 5.1600 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0409 = 0.40 * 1.00 * 5.1243 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.365)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.53    88.31   16.66    None  None   None       |
|    all(noH): 2823   0      0.53    88.31   16.66    None  None   None       |
|    Sol.    : 438    0      4.39    88.31   39.21    None  None   None       |
|    Mac.    : 2385   0      0.53    87.29   12.52    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:     0.534 -   9.312:  907   |   5:    44.423 -  53.200:  103        |
|      1:     9.312 -  18.090: 1218   |   6:    53.200 -  61.978:   61        |
|      2:    18.090 -  26.867:  247   |   7:    61.978 -  70.756:   30        |
|      3:    26.867 -  35.645:  125   |   8:    70.756 -  79.534:    5        |
|      4:    35.645 -  44.423:  122   |   9:    79.534 -  88.311:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1558             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1557             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1557   ksol= 0.32   Bsol= 43.36   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.22,-0.88,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122274                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7740 -  4.6778 0.99   1389  152 0.0996 0.1243      5.3668      5.5217|
|  2:  4.6778 -  3.7326 0.99   1320  154 0.0832 0.1132      5.4223      5.6182|
|  3:  3.7326 -  3.2666 0.99   1299  140 0.1068 0.1475      5.4757      5.8353|
|  4:  3.2666 -  2.9706 0.99   1308  142 0.1208 0.1598      5.4342      5.5769|
|  5:  2.9706 -  2.7591 0.99   1278  145 0.1289 0.1720      5.3021      5.5287|
|  6:  2.7591 -  2.5974 0.99   1290  143 0.1184 0.1959      5.1865      5.4683|
|  7:  2.5974 -  2.4679 0.99   1278  143 0.1230 0.1551      5.1444      5.3049|
|  8:  2.4679 -  2.3610 0.98   1269  138 0.1155 0.1585      5.0585      5.3076|
|  9:  2.3610 -  2.2704 0.98   1267  143 0.1133 0.1696      5.0035      5.2622|
| 10:  2.2704 -  2.1923 1.00   1276  142 0.1077 0.1682      4.9278      5.1596|
| 11:  2.1923 -  2.1240 0.97   1254  135 0.1067 0.1784      4.9118      5.2658|
| 12:  2.1240 -  2.0634 0.98   1244  141 0.1100 0.1646      4.8639      5.2085|
| 13:  2.0634 -  2.0092 1.00   1261  135 0.1050 0.1794      4.7659      5.0483|
| 14:  2.0092 -  1.9603 0.70    897  106 0.0954 0.1669      4.6432      4.9035|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7740 -  4.6778  1389   152  0.94   8.76   0.99     0.96       6587.51|
|  2:  4.6778 -  3.7326  1320   154  0.95   7.67   1.03     1.02       8808.08|
|  3:  3.7326 -  3.2666  1299   140  0.93  11.08   1.04     1.03      10068.45|
|  4:  3.2666 -  2.9706  1308   142  0.92  13.18   1.01     1.00       9731.97|
|  5:  2.9706 -  2.7591  1278   145  0.91  15.11   1.01     0.98       7761.84|
|  6:  2.7591 -  2.5974  1290   143  0.90  15.60   0.99     0.96       6650.13|
|  7:  2.5974 -  2.4679  1278   143  0.91  15.37   0.99     0.96       5899.10|
|  8:  2.4679 -  2.3610  1269   138  0.91  14.72   1.00     0.99       5111.69|
|  9:  2.3610 -  2.2704  1267   143  0.92  14.60   1.01     0.98       4697.55|
| 10:  2.2704 -  2.1923  1276   142  0.90  15.34   1.01     0.98       4166.15|
| 11:  2.1923 -  2.1240  1254   135  0.90  15.78   1.01     0.97       4312.77|
| 12:  2.1240 -  2.0634  1244   141  0.91  15.71   1.03     1.02       3942.00|
| 13:  2.0634 -  2.0092  1261   135  0.91  15.63   1.02     1.00       3299.85|
| 14:  2.0092 -  1.9603   897   106  0.92  13.77   1.00     0.96       2527.54|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2527.54 max =        10068.45 mean =      6075.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.68|
|phase err.(test): min =        0.00 max =           89.53 mean =        13.29|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1558   ksol= 0.32   Bsol= 43.34   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.25,-0.80,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121833                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1558   ksol= 0.32   Bsol= 43.34   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.25,-0.80,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121833                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7740 -  4.6778 0.99   1389  152 0.0970 0.1268      5.3544      5.5123|
|  2:  4.6778 -  3.7326 0.99   1320  154 0.0839 0.1132       5.427      5.6273|
|  3:  3.7326 -  3.2666 0.99   1299  140 0.1075 0.1471      5.4797        5.83|
|  4:  3.2666 -  2.9706 0.99   1308  142 0.1206 0.1606      5.4341      5.5815|
|  5:  2.9706 -  2.7591 0.99   1278  145 0.1286 0.1705      5.3041       5.524|
|  6:  2.7591 -  2.5974 0.99   1290  143 0.1185 0.1964      5.1861      5.4689|
|  7:  2.5974 -  2.4679 0.99   1278  143 0.1231 0.1553      5.1445      5.3065|
|  8:  2.4679 -  2.3610 0.98   1269  138 0.1152 0.1581      5.0571      5.3046|
|  9:  2.3610 -  2.2704 0.98   1267  143 0.1131 0.1698       5.003      5.2655|
| 10:  2.2704 -  2.1923 1.00   1276  142 0.1074 0.1687      4.9279      5.1613|
| 11:  2.1923 -  2.1240 0.97   1254  135 0.1065 0.1778      4.9118      5.2645|
| 12:  2.1240 -  2.0634 0.98   1244  141 0.1096 0.1652      4.8634      5.2111|
| 13:  2.0634 -  2.0092 1.00   1261  135 0.1048 0.1790      4.7656      5.0483|
| 14:  2.0092 -  1.9603 0.70    897  106 0.0953 0.1665      4.6428      4.9028|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7740 -  4.6778  1389   152  0.94   8.76   0.99     0.96       6560.30|
|  2:  4.6778 -  3.7326  1320   154  0.95   7.75   1.03     1.02       8817.35|
|  3:  3.7326 -  3.2666  1299   140  0.93  11.13   1.04     1.04      10148.11|
|  4:  3.2666 -  2.9706  1308   142  0.92  13.20   1.01     1.00       9759.21|
|  5:  2.9706 -  2.7591  1278   145  0.91  15.14   1.01     0.98       7792.91|
|  6:  2.7591 -  2.5974  1290   143  0.90  15.61   0.99     0.96       6654.50|
|  7:  2.5974 -  2.4679  1278   143  0.91  15.40   0.99     0.96       5907.00|
|  8:  2.4679 -  2.3610  1269   138  0.91  14.73   1.00     0.99       5105.91|
|  9:  2.3610 -  2.2704  1267   143  0.92  14.61   1.01     0.99       4706.56|
| 10:  2.2704 -  2.1923  1276   142  0.90  15.36   1.01     0.98       4173.89|
| 11:  2.1923 -  2.1240  1254   135  0.90  15.79   1.01     0.98       4320.65|
| 12:  2.1240 -  2.0634  1244   141  0.91  15.71   1.03     1.02       3946.66|
| 13:  2.0634 -  2.0092  1261   135  0.91  15.64   1.02     1.00       3303.00|
| 14:  2.0092 -  1.9603   897   106  0.92  13.77   1.00     0.96       2525.75|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2525.75 max =        10148.11 mean =      6087.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.70|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.365)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    88.29   16.64    None  None   None       |
|    all(noH): 2823   0      0.52    88.29   16.64    None  None   None       |
|    Sol.    : 438    0      4.38    88.29   39.20    None  None   None       |
|    Mac.    : 2385   0      0.52    87.27   12.50    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:     0.517 -   9.295:  907   |   5:    44.406 -  53.183:  103        |
|      1:     9.295 -  18.073: 1218   |   6:    53.183 -  61.961:   61        |
|      2:    18.073 -  26.850:  247   |   7:    61.961 -  70.739:   30        |
|      3:    26.850 -  35.628:  125   |   8:    70.739 -  79.517:    5        |
|      4:    35.628 -  44.406:  122   |   9:    79.517 -  88.294:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.655 - 4.595
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 308
   mapped sites are within: 0.713 - 4.595

peak=    6.762 closest distance to " O   HOH Z 142 " =    1.909
peak=    6.650 closest distance to " NE2 GLN A  11 " =    1.277
peak=    6.077 closest distance to " O   HOH Z 375 " =    1.402
peak=    5.848 closest distance to " O   HOH Z 126 " =    2.076
peak=    5.533 closest distance to " O   HOH Z 112 " =    1.411
peak=    5.521 closest distance to " NH2 ARG A  56 " =    2.116
peak=    5.387 closest distance to " CB  ARG A 275 " =    0.936
peak=    5.347 closest distance to " CG  PRO A  54 " =    1.235
peak=    5.220 closest distance to " O   HOH Z 236 " =    1.472
peak=    5.194 closest distance to " O   HOH Z 417 " =    2.032
peak=    4.965 closest distance to " O   HOH Z 232 " =    2.419
peak=    4.908 closest distance to " O   HOH Z   9 " =    1.226
peak=    4.864 closest distance to " O   HOH Z 427 " =    2.461
peak=    4.822 closest distance to " CB  PRO A  54 " =    0.929
peak=    4.816 closest distance to " O   HOH Z 287 " =    1.845
peak=    4.777 closest distance to " O   HOH Z  78 " =    1.601
peak=    4.772 closest distance to " O   HOH Z 423 " =    1.588
peak=    4.738 closest distance to " O   HOH Z  63 " =    1.547
peak=    4.731 closest distance to " O   HOH Z 371 " =    2.082
peak=    4.688 closest distance to " O   HOH Z 380 " =    1.856
peak=    4.669 closest distance to " CB  SER A  63 " =    1.156
peak=    4.641 closest distance to " CB  ASN A 148 " =    1.370
peak=    4.573 closest distance to " O   HOH Z  57 " =    2.511
peak=    4.564 closest distance to " O   SER A  87 " =    2.251
peak=    4.504 closest distance to " CB  GLN A 223 " =    1.569
peak=    4.483 closest distance to " O   HOH Z 209 " =    2.212
peak=    4.443 closest distance to " O   HOH Z 298 " =    1.867
peak=    4.378 closest distance to " O   HOH Z 193 " =    1.709
peak=    4.357 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.348 closest distance to " O   HOH Z 371 " =    1.870
peak=    4.348 closest distance to " CB  ARG A  79 " =    1.388
peak=    4.322 closest distance to " CG  ARG A  66 " =    2.636
peak=    4.266 closest distance to " CB  GLU A 152 " =    1.297
peak=    4.265 closest distance to " O   HOH Z 272 " =    1.837
peak=    4.261 closest distance to " OG BSER A 164 " =    2.158
peak=    4.261 closest distance to " O   HOH Z 327 " =    1.690
peak=    4.231 closest distance to " CG2 VAL A 257 " =    0.868
peak=    4.222 closest distance to " CG  TRP A 179 " =    2.126
peak=    4.215 closest distance to " NZ  LYS A 119 " =    2.533
peak=    4.194 closest distance to " O   HOH Z 124 " =    1.342
peak=    4.191 closest distance to " CB  GLN A 183 " =    1.196
peak=    4.167 closest distance to " O   HOH Z 250 " =    1.497
peak=    4.131 closest distance to " CB  SER A   3 " =    1.265
peak=    4.127 closest distance to " O   HOH Z 289 " =    1.688
peak=    4.094 closest distance to " O   HOH Z   1 " =    1.674
peak=    4.089 closest distance to " O   HOH Z  44 " =    1.709
peak=    4.076 closest distance to " C   PRO A 198 " =    1.438
peak=    4.054 closest distance to " O   HOH Z 403 " =    1.787
peak=    4.051 closest distance to " NZ  LYS A 117 " =    2.856
peak=    4.042 closest distance to " O   HOH Z 365 " =    2.705
peak=    4.041 closest distance to " CB  ASN A 148 " =    1.898
peak=    4.028 closest distance to " O   HOH Z 203 " =    1.747
peak=    3.982 closest distance to " O   HOH Z 316 " =    2.971
peak=    3.981 closest distance to " O   HOH Z  61 " =    1.476
peak=    3.962 closest distance to " O   HOH Z 394 " =    1.716
peak=    3.959 closest distance to " O   HOH Z 368 " =    3.447
peak=    3.951 closest distance to " CG  PRO A 213 " =    1.219
peak=    3.924 closest distance to " O   HOH Z  65 " =    0.985
peak=    3.915 closest distance to " O   HOH Z  93 " =    2.096
peak=    3.915 closest distance to " O   HOH Z  30 " =    1.841
peak=    3.906 closest distance to " CB  ASN A 187 " =    1.256
peak=    3.897 closest distance to " CE  LYS A 119 " =    1.236
peak=    3.885 closest distance to " ND2 ASN A 187 " =    1.592
peak=    3.884 closest distance to " O   HOH Z 286 " =    2.313
peak=    3.877 closest distance to " CB  ARG A 190 " =    1.660
peak=    3.861 closest distance to " O   HOH Z 130 " =    1.102
peak=    3.856 closest distance to " O   HOH Z 128 " =    2.013
peak=    3.855 closest distance to " O   HOH Z 144 " =    2.074
peak=    3.854 closest distance to " O   HOH Z 425 " =    1.991
peak=    3.849 closest distance to " O   HOH Z  61 " =    1.637
peak=    3.843 closest distance to " O   HOH Z  97 " =    1.943
peak=    3.843 closest distance to " O   HOH Z   9 " =    2.052
peak=    3.838 closest distance to " O   HOH Z 234 " =    3.535
peak=    3.836 closest distance to " CB  ALA A 114 " =    1.444
peak=    3.832 closest distance to " O   HOH Z 128 " =    1.920
peak=    3.828 closest distance to " CB  ARG A 139 " =    1.113
peak=    3.809 closest distance to " CB  VAL A 265 " =    1.313
peak=    3.804 closest distance to " O   HOH Z 158 " =    2.801
peak=    3.804 closest distance to " O   HOH Z 425 " =    1.330
peak=    3.798 closest distance to " OD1 ASN A  69 " =    2.451
peak=    3.788 closest distance to " NH2AARG A 190 " =    1.780
peak=    3.781 closest distance to " O   HOH Z 405 " =    1.243
peak=    3.767 closest distance to " O   HOH Z 357 " =    1.877
peak=    3.765 closest distance to " CB  THR A  31 " =    1.608
peak=    3.756 closest distance to " N   PHE A 130 " =    1.261
peak=    3.748 closest distance to " O   HOH Z 368 " =    1.832
peak=    3.732 closest distance to " CB  GLU A 128 " =    0.968
peak=    3.725 closest distance to " CB  ILE A 120 " =    1.381
peak=    3.724 closest distance to " CB  GLU A 277 " =    3.391
peak=    3.722 closest distance to " O   HOH Z 407 " =    2.218
peak=    3.716 closest distance to " NH1BARG A 145 " =    1.376
peak=    3.715 closest distance to " NH1AARG A 145 " =    1.160
peak=    3.712 closest distance to " CA  ASN A 215 " =    1.040
peak=    3.710 closest distance to " O   HOH Z 305 " =    3.535
peak=    3.699 closest distance to " O   HOH Z 402 " =    1.454
peak=    3.697 closest distance to " O   HOH Z 130 " =    2.407
peak=    3.695 closest distance to " O   HOH Z 419 " =    1.796
peak=    3.690 closest distance to " O   HOH Z 189 " =    2.050
peak=    3.687 closest distance to " O   HOH Z   3 " =    1.982
peak=    3.674 closest distance to " O   HOH Z 213 " =    1.558
peak=    3.656 closest distance to " CD2 TRP A 179 " =    1.278
peak=    3.650 closest distance to " O   HOH Z 126 " =    1.460
peak=    3.642 closest distance to " CB  SER A  26 " =    1.639
peak=    3.636 closest distance to " CB  THR A 157 " =    1.089
peak=    3.626 closest distance to " O   HOH Z 116 " =    2.742
peak=    3.622 closest distance to " CA  ALA A  84 " =    1.260
peak=    3.622 closest distance to " O   HOH Z 166 " =    1.341
peak=    3.616 closest distance to " O   HOH Z 109 " =    2.355
peak=    3.611 closest distance to " O   HOH Z 153 " =    1.779
peak=    3.609 closest distance to " O   HOH Z  80 " =    1.950
peak=    3.606 closest distance to " O   HOH Z 435 " =    1.724
peak=    3.591 closest distance to " O   HOH Z 245 " =    1.354
peak=    3.582 closest distance to " O  BHOH Z  74 " =    1.369
peak=    3.571 closest distance to " O   HOH Z 151 " =    1.570
peak=    3.570 closest distance to " O   HOH Z 434 " =    1.260
peak=    3.564 closest distance to " CE  LYS A  76 " =    0.901
peak=    3.563 closest distance to " O   HOH Z 423 " =    1.762
peak=    3.563 closest distance to " O   HOH Z 132 " =    2.206
peak=    3.558 closest distance to " O   HOH Z  11 " =    1.591
peak=    3.552 closest distance to " O   HOH Z  10 " =    1.774
peak=    3.548 closest distance to " O   HOH Z 344 " =    3.260
peak=    3.547 closest distance to " CB  TRP A 266 " =    1.146
peak=    3.544 closest distance to " O   HOH Z 415 " =    3.544
peak=    3.541 closest distance to " N   GLU A   2 " =    1.316
peak=    3.536 closest distance to " O   HOH Z 272 " =    2.001
peak=    3.535 closest distance to " O   HOH Z 411 " =    3.709
peak=    3.534 closest distance to " O   HOH Z 336 " =    1.875
peak=    3.533 closest distance to " O   HOH Z 287 " =    1.679
peak=    3.523 closest distance to " O   HOH Z   6 " =    2.063
peak=    3.512 closest distance to " O   HOH Z 388 " =    2.026
peak=    3.510 closest distance to " CG1BVAL A  72 " =    1.303
peak=    3.509 closest distance to " O   HOH Z 362 " =    1.914
peak=    3.502 closest distance to " CE1 TYR A 186 " =    1.367
peak=    3.498 closest distance to " CD  PRO A 243 " =    1.557
peak=    3.496 closest distance to " O   HOH Z 148 " =    3.325
peak=    3.490 closest distance to " O   HOH Z 422 " =    2.469
peak=    3.482 closest distance to " CD  ARG A 159 " =    0.713
peak=    3.477 closest distance to " CA  ARG A 195 " =    1.349
peak=    3.475 closest distance to " O   HOH Z  92 " =    1.213
peak=    3.473 closest distance to " CB  GLU A 152 " =    1.466
peak=    3.469 closest distance to " NE2 GLN A  73 " =    3.687
peak=    3.467 closest distance to " O   HOH Z   1 " =    1.870
peak=    3.462 closest distance to " O   HOH Z  88 " =    2.397
peak=    3.462 closest distance to " O   HOH Z  68 " =    2.113
peak=    3.458 closest distance to " O   HOH Z 419 " =    1.509
peak=    3.453 closest distance to " CB  GLN A  88 " =    1.277
peak=    3.449 closest distance to " CG  PRO A 198 " =    1.306
peak=    3.449 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.442 closest distance to " O   HOH Z 173 " =    2.136
peak=    3.439 closest distance to " O   HOH Z  59 " =    1.471
peak=    3.439 closest distance to " O   HOH Z 248 " =    1.536
peak=    3.433 closest distance to " OD1BASN A 224 " =    2.218
peak=    3.411 closest distance to " O   HOH Z 392 " =    3.104
peak=    3.411 closest distance to " CB  TYR A 169 " =    0.822
peak=    3.409 closest distance to " CB  MET A 188 " =    1.616
peak=    3.409 closest distance to " O   HOH Z 175 " =    2.055
peak=    3.399 closest distance to " CA  ASN A 127 " =    1.010
peak=    3.398 closest distance to " OG BSER A  99 " =    2.373
peak=    3.396 closest distance to " CB  PHE A 130 " =    0.943
peak=    3.394 closest distance to " CG1 ILE A  33 " =    1.242
peak=    3.394 closest distance to " CG  MET A 185 " =    1.359
peak=    3.392 closest distance to " O   HOH Z 359 " =    1.360
peak=    3.391 closest distance to " O   HOH Z  47 " =    1.528
peak=    3.388 closest distance to " O   HOH Z 117 " =    1.313
peak=    3.385 closest distance to " O   HOH Z 146 " =    1.587
peak=    3.384 closest distance to " NE2 GLN A 278 " =    3.202
peak=    3.381 closest distance to " O   HOH Z 257 " =    2.055
peak=    3.380 closest distance to " OE1 GLN A  11 " =    1.998
peak=    3.378 closest distance to " CH2 TRP A  92 " =    2.080
peak=    3.377 closest distance to " CG  PRO A 243 " =    1.043
peak=    3.369 closest distance to " CD  ARG A  79 " =    2.346
peak=    3.366 closest distance to " O   HOH Z  43 " =    2.467
peak=    3.364 closest distance to " CB  ASN A  39 " =    0.830
peak=    3.360 closest distance to " O   HOH Z 183 " =    1.606
peak=    3.360 closest distance to " CG AARG A 275 " =    1.064
peak=    3.358 closest distance to " CA  VAL A 125 " =    1.023
peak=    3.357 closest distance to " CA  ALA A 299 " =    0.903
peak=    3.356 closest distance to " O   HOH Z 345 " =    3.123
peak=    3.355 closest distance to " OG  SER A  62 " =    2.840
peak=    3.353 closest distance to " O   HOH Z 255 " =    1.704
peak=    3.349 closest distance to " CD  GLN A 194 " =    1.411
peak=    3.349 closest distance to " O   HOH Z 234 " =    1.956
peak=    3.349 closest distance to " O   HOH Z 406 " =    1.559
peak=    3.347 closest distance to " O   HOH Z 214 " =    2.427
peak=    3.345 closest distance to " CB  SER A 216 " =    0.756
peak=    3.344 closest distance to " CA  LEU A 300 " =    1.034
peak=    3.342 closest distance to " O   HOH Z 145 " =    1.261
peak=    3.338 closest distance to " OG BSER A 210 " =    1.369
peak=    3.336 closest distance to " O   HOH Z 313 " =    1.609
peak=    3.333 closest distance to " NH1 ARG A  66 " =    1.573
peak=    3.331 closest distance to " O   HOH Z 423 " =    1.988
peak=    3.331 closest distance to " O   HOH Z  59 " =    2.099
peak=    3.329 closest distance to " CB  ASN A 110 " =    0.997
peak=    3.329 closest distance to " O   HOH Z 389 " =    1.260
peak=    3.328 closest distance to " O   HOH Z 128 " =    1.926
peak=    3.325 closest distance to " O   HOH Z  53 " =    1.505
peak=    3.325 closest distance to " CB  ALA A  34 " =    1.210
peak=    3.324 closest distance to " N   TYR A 116 " =    1.497
peak=    3.323 closest distance to " CA  PHE A 283 " =    1.294
peak=    3.319 closest distance to " O   HOH Z 154 " =    2.031
peak=    3.318 closest distance to " CB  LEU A 300 " =    0.971
peak=    3.316 closest distance to " O   HOH Z 163 " =    1.915
peak=    3.316 closest distance to " O   HOH Z 371 " =    3.146
peak=    3.314 closest distance to " CA  ASP A 162 " =    1.057
peak=    3.313 closest distance to " O   HOH Z 189 " =    2.170
peak=    3.312 closest distance to " OG ASER A  99 " =    1.464
peak=    3.301 closest distance to " O   HOH Z  44 " =    2.853
peak=    3.301 closest distance to " O   HOH Z 337 " =    3.368
peak=    3.299 closest distance to " O   HOH Z 227 " =    2.091
peak=    3.294 closest distance to " O   HOH Z 365 " =    1.615
peak=    3.289 closest distance to " O   HOH Z 414 " =    1.325
peak=    3.288 closest distance to " O   HOH Z 325 " =    3.536
peak=    3.287 closest distance to " CG2 THR A 294 " =    1.667
peak=    3.284 closest distance to " O   HOH Z 207 " =    1.696
peak=    3.283 closest distance to " O   HOH Z 145 " =    2.299
peak=    3.282 closest distance to " O   HOH Z 119 " =    4.315
peak=    3.278 closest distance to " CB  LYS A 117 " =    1.186
peak=    3.275 closest distance to " OD2 ASP A  65 " =    2.421
peak=    3.275 closest distance to " O   HOH Z 291 " =    1.452
peak=    3.275 closest distance to " O   HOH Z 299 " =    2.411
peak=    3.274 closest distance to " O   HOH Z 433 " =    1.767
peak=    3.271 closest distance to " O   HOH Z  40 " =    1.994
peak=    3.270 closest distance to " O   HOH Z 213 " =    1.877
peak=    3.269 closest distance to " O   HOH Z 106 " =    2.867
peak=    3.269 closest distance to " CA  ALA A 291 " =    0.877
peak=    3.269 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.267 closest distance to " O   HOH Z 435 " =    1.616
peak=    3.264 closest distance to " O   HOH Z  54 " =    1.671
peak=    3.263 closest distance to " CB  SER A 276 " =    1.276
peak=    3.260 closest distance to " CB  ALA A  21 " =    2.005
peak=    3.257 closest distance to " ND1 HIS A  81 " =    1.576
peak=    3.254 closest distance to " O   HOH Z  94 " =    1.948
peak=    3.253 closest distance to " CB  LYS A 290 " =    1.261
peak=    3.252 closest distance to " N   HIS A  86 " =    1.809
peak=    3.252 closest distance to " O   HOH Z  88 " =    2.525
peak=    3.251 closest distance to " N   ASP A 140 " =    1.666
peak=    3.250 closest distance to " CA  GLY A 302 " =    1.109
peak=    3.248 closest distance to " O   HOH Z 271 " =    2.133
peak=    3.248 closest distance to " O   HOH Z 421 " =    2.068
peak=    3.246 closest distance to " O   HOH Z  32 " =    1.690
peak=    3.240 closest distance to " N   GLN A 278 " =    1.191
peak=    3.240 closest distance to " CG  LYS A 119 " =    1.134
peak=    3.238 closest distance to " CE  LYS A 166 " =    1.806
peak=    3.233 closest distance to " N   ASN A  39 " =    1.148
peak=    3.223 closest distance to " CG  GLN A  89 " =    1.423
peak=    3.222 closest distance to " O   HOH Z 437 " =    1.845
peak=    3.221 closest distance to " CG  LYS A  76 " =    1.544
peak=    3.219 closest distance to " ND2 ASN A 110 " =    1.451
peak=    3.214 closest distance to " O   HOH Z 193 " =    1.933
peak=    3.214 closest distance to " CB  ASP A 191 " =    1.187
peak=    3.214 closest distance to " NH2 ARG A 219 " =    1.777
peak=    3.212 closest distance to " O   HOH Z 430 " =    1.645
peak=    3.211 closest distance to " CB  LEU A 228 " =    1.078
peak=    3.209 closest distance to " CD1 ILE A 263 " =    1.390
peak=    3.208 closest distance to " O   HOH Z  39 " =    1.075
peak=    3.207 closest distance to " O   HOH Z 193 " =    1.969
peak=    3.204 closest distance to " O   HOH Z  26 " =    1.306
peak=    3.204 closest distance to " CD  LYS A 166 " =    1.335
peak=    3.201 closest distance to " O   HOH Z 426 " =    1.863
peak=    3.199 closest distance to " O   HOH Z 406 " =    2.651
peak=    3.196 closest distance to " O   HOH Z 227 " =    2.064
peak=    3.193 closest distance to " CB  ALA A   1 " =    4.595
peak=    3.192 closest distance to " C   PHE A 208 " =    1.015
peak=    3.190 closest distance to " O   HOH Z 319 " =    2.241
peak=    3.187 closest distance to " CB  ASP A 140 " =    0.918
peak=    3.182 closest distance to " OG1 THR A 221 " =    1.303
peak=    3.180 closest distance to " CA  ALA A  51 " =    0.931
peak=    3.179 closest distance to " O   HOH Z 392 " =    1.355
peak=    3.176 closest distance to " O   ARG A 145 " =    1.815
peak=    3.172 closest distance to " N   SER A  97 " =    0.873
peak=    3.168 closest distance to " N   ASN A 127 " =    1.369
peak=    3.167 closest distance to " O   HOH Z  50 " =    1.647
peak=    3.167 closest distance to " NH2BARG A 190 " =    1.464
peak=    3.166 closest distance to " NE2 GLN A  58 " =    4.003
peak=    3.163 closest distance to " O   HOH Z 301 " =    1.810
peak=    3.159 closest distance to " O   HOH Z 158 " =    1.643
peak=    3.156 closest distance to " O   HOH Z 212 " =    1.606
peak=    3.155 closest distance to " O   HOH Z 176 " =    1.663
peak=    3.152 closest distance to " CA  ALA A 233 " =    0.856
peak=    3.151 closest distance to " O   GLY A 147 " =    1.498
peak=    3.143 closest distance to " CB  ASN A 142 " =    1.026
peak=    3.137 closest distance to " CG  GLN A  58 " =    0.946
peak=    3.133 closest distance to " CB  ARG A 219 " =    0.845
peak=    3.131 closest distance to " CG  MET A 113 " =    0.887
peak=    3.131 closest distance to " NH1 ARG A  66 " =    1.354
peak=    3.130 closest distance to " CG  LEU A 167 " =    1.243
peak=    3.130 closest distance to " ND2 ASN A 249 " =    0.850
peak=    3.129 closest distance to " OG1 THR A 264 " =    0.863
peak=    3.118 closest distance to " CB  TRP A 179 " =    1.248
peak=    3.118 closest distance to " O   HOH Z 207 " =    2.063
peak=    3.112 closest distance to " O   HOH Z 128 " =    2.990
peak=    3.109 closest distance to " O   HOH Z 251 " =    1.691
peak=    3.089 closest distance to " O   HOH Z 119 " =    1.750
peak=    3.087 closest distance to " O   HOH Z 152 " =    1.951
peak=    3.086 closest distance to " CE AMET A  47 " =    1.218
peak=    3.084 closest distance to " O   HOH Z 180 " =    2.245
peak=    3.083 closest distance to " CA  SER A  87 " =    1.003
peak=    3.080 closest distance to " CA  SER A  95 " =    1.122
peak=    3.078 closest distance to " CB  ARG A 138 " =    0.793
peak=    3.077 closest distance to " CG2 VAL A 197 " =    1.080
peak=    3.077 closest distance to " CE ALYS A 290 " =    1.204
peak=    3.062 closest distance to " CB  VAL A 126 " =    1.195
peak=    3.061 closest distance to " CD2 LEU A 255 " =    1.457
peak=    3.055 closest distance to " O   HOH Z 188 " =    2.348
peak=    3.047 closest distance to " O   HOH Z 302 " =    1.429
peak=    3.017 closest distance to " O   PRO A  90 " =    1.645
peak=    3.008 closest distance to " O   HOH Z  43 " =    2.349

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.527 - 5.584
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 208
   mapped sites are within: 0.731 - 5.584

peak=   -4.388 closest distance to " CD  ARG A 156 " =    2.086
peak=   -4.359 closest distance to " C   ILE A 239 " =    2.126
peak=   -4.355 closest distance to " OG BSER A 134 " =    1.410
peak=   -4.340 closest distance to " OD2 ASP A 191 " =    1.334
peak=   -4.295 closest distance to " CB  PRO A 243 " =    2.619
peak=   -4.289 closest distance to " O   HOH Z 385 " =    1.520
peak=   -4.254 closest distance to " N   GLN A  58 " =    1.685
peak=   -4.244 closest distance to " O   PRO A 198 " =    1.242
peak=   -4.210 closest distance to " C   HIS A 108 " =    1.216
peak=   -4.116 closest distance to " CG1 VAL A 112 " =    2.749
peak=   -4.104 closest distance to " CG  GLN A  58 " =    0.989
peak=   -4.101 closest distance to " OG  SER A   3 " =    1.548
peak=   -4.093 closest distance to " CB  ALA A 248 " =    2.124
peak=   -4.082 closest distance to " CA  VAL A  67 " =    2.912
peak=   -4.070 closest distance to " O   HOH Z 351 " =    1.563
peak=   -4.048 closest distance to " CB  PHE A 192 " =    1.897
peak=   -4.030 closest distance to " CD1 LEU A 255 " =    2.802
peak=   -4.026 closest distance to " O   VAL A  67 " =    2.677
peak=   -4.014 closest distance to " O   HOH Z 185 " =    2.140
peak=   -3.990 closest distance to " O   HOH Z 266 " =    4.692
peak=   -3.982 closest distance to " O   HOH Z 290 " =    1.184
peak=   -3.975 closest distance to " CG  PHE A 283 " =    2.543
peak=   -3.972 closest distance to " O   HOH Z 372 " =    2.425
peak=   -3.934 closest distance to " SG  CYS A 254 " =    3.316
peak=   -3.846 closest distance to " O   HOH Z 131 " =    4.106
peak=   -3.846 closest distance to " O   HOH Z  65 " =    1.067
peak=   -3.844 closest distance to " CE  MET A 105 " =    2.442
peak=   -3.840 closest distance to " O   HOH Z 313 " =    1.735
peak=   -3.839 closest distance to " CG  GLN A 223 " =    1.649
peak=   -3.802 closest distance to " O   SER A  22 " =    2.441
peak=   -3.799 closest distance to " O   ALA A 161 " =    1.657
peak=   -3.797 closest distance to " O   SER A 135 " =    1.463
peak=   -3.789 closest distance to " O   SER A  95 " =    1.398
peak=   -3.788 closest distance to " O   HOH Z 339 " =    1.724
peak=   -3.749 closest distance to " CA  GLY A  98 " =    1.662
peak=   -3.736 closest distance to " CZ2 TRP A 274 " =    0.928
peak=   -3.731 closest distance to " O   HOH Z  13 " =    1.712
peak=   -3.725 closest distance to " O   HOH Z  15 " =    1.436
peak=   -3.712 closest distance to " CB  ASN A  39 " =    2.333
peak=   -3.699 closest distance to " O   HOH Z 407 " =    2.718
peak=   -3.685 closest distance to " OD1 ASN A 148 " =    1.544
peak=   -3.684 closest distance to " O   HOH Z 231 " =    2.090
peak=   -3.672 closest distance to " CG  GLU A 152 " =    1.164
peak=   -3.658 closest distance to " OG  SER A  87 " =    1.285
peak=   -3.654 closest distance to " CB  ALA A 291 " =    2.150
peak=   -3.653 closest distance to " CA  GLY A 133 " =    1.971
peak=   -3.650 closest distance to " CB  ASP A 132 " =    2.375
peak=   -3.647 closest distance to " O   HOH Z  37 " =    1.470
peak=   -3.647 closest distance to " CB  ALA A  43 " =    2.235
peak=   -3.646 closest distance to " CZ  PHE A  59 " =    1.357
peak=   -3.638 closest distance to " CD1 ILE A 239 " =    2.554
peak=   -3.635 closest distance to " CG  GLN A  88 " =    0.731
peak=   -3.619 closest distance to " O   HOH Z  60 " =    1.712
peak=   -3.616 closest distance to " CD1 LEU A 101 " =    2.222
peak=   -3.615 closest distance to " OD1 ASP A 191 " =    1.493
peak=   -3.607 closest distance to " O   HOH Z 211 " =    1.575
peak=   -3.606 closest distance to " OXT GLY A 302 " =    2.922
peak=   -3.591 closest distance to " CZ3 TRP A 179 " =    1.217
peak=   -3.590 closest distance to " CD2 LEU A 237 " =    2.683
peak=   -3.588 closest distance to " O   HOH Z 102 " =    1.528
peak=   -3.588 closest distance to " CD1 ILE A 263 " =    2.990
peak=   -3.578 closest distance to " N   THR A 157 " =    1.447
peak=   -3.567 closest distance to " O   PRO A 198 " =    1.279
peak=   -3.560 closest distance to " O   HOH Z  24 " =    1.191
peak=   -3.558 closest distance to " O   HOH Z 213 " =    1.335
peak=   -3.547 closest distance to " O   HOH Z 298 " =    1.263
peak=   -3.544 closest distance to " O   HOH Z 385 " =    0.850
peak=   -3.533 closest distance to " CB  PRO A 163 " =    2.451
peak=   -3.532 closest distance to " O   HOH Z 427 " =    1.708
peak=   -3.529 closest distance to " ND2 ASN A  45 " =    1.156
peak=   -3.522 closest distance to " O   HOH Z 198 " =    1.633
peak=   -3.519 closest distance to " OG BSER A 134 " =    1.544
peak=   -3.508 closest distance to " OD2 ASP A 171 " =    2.205
peak=   -3.504 closest distance to " O   PHE A 218 " =    1.381
peak=   -3.498 closest distance to " O   HOH Z 139 " =    5.016
peak=   -3.497 closest distance to " CB  ALA A 114 " =    2.541
peak=   -3.492 closest distance to " O   HOH Z 250 " =    1.377
peak=   -3.486 closest distance to " CD1 PHE A  59 " =    2.065
peak=   -3.484 closest distance to " O   HOH Z  11 " =    1.827
peak=   -3.484 closest distance to " O   VAL A 189 " =    2.526
peak=   -3.466 closest distance to " OD1 ASP A 171 " =    1.613
peak=   -3.463 closest distance to " O   HOH Z 412 " =    5.584
peak=   -3.462 closest distance to " O   GLU A 152 " =    1.434
peak=   -3.462 closest distance to " NE2 GLN A 278 " =    1.573
peak=   -3.460 closest distance to " CE  LYS A  76 " =    2.824
peak=   -3.453 closest distance to " O   HOH Z  43 " =    1.873
peak=   -3.448 closest distance to " N   ALA A 248 " =    1.616
peak=   -3.441 closest distance to " O   LEU A 101 " =    2.189
peak=   -3.439 closest distance to " O   HOH Z 359 " =    3.349
peak=   -3.430 closest distance to " OG  SER A  87 " =    1.771
peak=   -3.422 closest distance to " CB  ALA A 291 " =    2.420
peak=   -3.421 closest distance to " CG1 VAL A 230 " =    1.938
peak=   -3.421 closest distance to " ND2 ASN A  45 " =    1.727
peak=   -3.394 closest distance to " CZ  TYR A 169 " =    1.762
peak=   -3.389 closest distance to " O   HOH Z 298 " =    2.448
peak=   -3.385 closest distance to " CB  PHE A 208 " =    2.241
peak=   -3.378 closest distance to " N   GLN A 122 " =    1.362
peak=   -3.371 closest distance to " O   HOH Z 198 " =    1.522
peak=   -3.366 closest distance to " O   HOH Z 191 " =    5.520
peak=   -3.356 closest distance to " O   HOH Z  90 " =    2.404
peak=   -3.356 closest distance to " NH2 ARG A  79 " =    2.095
peak=   -3.355 closest distance to " C   ALA A 114 " =    2.210
peak=   -3.354 closest distance to " O   HOH Z 137 " =    1.430
peak=   -3.353 closest distance to " CD2 TYR A 293 " =    1.954
peak=   -3.351 closest distance to " CG1 VAL A 268 " =    2.853
peak=   -3.347 closest distance to " OG1 THR A  82 " =    1.839
peak=   -3.340 closest distance to " OE2 GLU A 152 " =    1.045
peak=   -3.340 closest distance to " O   HOH Z 165 " =    2.362
peak=   -3.332 closest distance to " O   HOH Z 158 " =    2.024
peak=   -3.331 closest distance to " O   HOH Z 288 " =    1.269
peak=   -3.331 closest distance to " CE BMET A  47 " =    1.263
peak=   -3.329 closest distance to " O   HOH Z 263 " =    3.149
peak=   -3.327 closest distance to " O   PRO A 163 " =    1.224
peak=   -3.325 closest distance to " O   HOH Z 282 " =    1.111
peak=   -3.324 closest distance to " CA  GLY A  57 " =    2.133
peak=   -3.315 closest distance to " O   HOH Z 389 " =    2.015
peak=   -3.310 closest distance to " O   HOH Z 383 " =    0.993
peak=   -3.307 closest distance to " CD2 PHE A 225 " =    1.148
peak=   -3.307 closest distance to " ND2 ASN A  39 " =    1.359
peak=   -3.304 closest distance to " CD  GLN A 223 " =    0.900
peak=   -3.300 closest distance to " CE2 PHE A 218 " =    2.333
peak=   -3.299 closest distance to " O   ASP A 191 " =    1.745
peak=   -3.296 closest distance to " O   HOH Z 345 " =    2.004
peak=   -3.293 closest distance to " CB  TRP A  85 " =    2.382
peak=   -3.293 closest distance to " OG  SER A  97 " =    2.163
peak=   -3.293 closest distance to " O   MET A  40 " =    2.722
peak=   -3.291 closest distance to " CB  ASP A 286 " =    2.177
peak=   -3.290 closest distance to " CA  GLY A 203 " =    2.232
peak=   -3.290 closest distance to " OD2 ASP A 270 " =    1.076
peak=   -3.287 closest distance to " OG  SER A  63 " =    1.270
peak=   -3.285 closest distance to " O   VAL A 174 " =    2.203
peak=   -3.282 closest distance to " OG1 THR A 178 " =    1.176
peak=   -3.280 closest distance to " CB  ALA A 248 " =    2.297
peak=   -3.279 closest distance to " O   HOH Z 423 " =    2.423
peak=   -3.278 closest distance to " O   HOH Z 256 " =    1.369
peak=   -3.270 closest distance to " ND2 ASN A 187 " =    1.581
peak=   -3.270 closest distance to " O   HOH Z   1 " =    1.460
peak=   -3.264 closest distance to " N   VAL A 189 " =    1.622
peak=   -3.263 closest distance to " N   PHE A  59 " =    1.881
peak=   -3.262 closest distance to " O   PRO A 163 " =    1.846
peak=   -3.259 closest distance to " CE3 TRP A 274 " =    2.283
peak=   -3.252 closest distance to " OE1 GLN A 183 " =    1.366
peak=   -3.252 closest distance to " CA  GLY A 241 " =    2.205
peak=   -3.249 closest distance to " O   ALA A   1 " =    1.607
peak=   -3.248 closest distance to " C   ALA A 158 " =    1.551
peak=   -3.248 closest distance to " OG  SER A  97 " =    1.469
peak=   -3.245 closest distance to " N   ASN A 127 " =    1.470
peak=   -3.244 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.244 closest distance to " CB  ALA A 244 " =    2.135
peak=   -3.234 closest distance to " N   VAL A  72 " =    1.573
peak=   -3.229 closest distance to " NE  ARG A  36 " =    1.894
peak=   -3.228 closest distance to " O   ALA A  51 " =    1.200
peak=   -3.225 closest distance to " N   ALA A  43 " =    2.402
peak=   -3.223 closest distance to " CB  ASP A  27 " =    2.337
peak=   -3.218 closest distance to " O   ARG A 145 " =    1.499
peak=   -3.217 closest distance to " C   LEU A   5 " =    1.017
peak=   -3.216 closest distance to " O   HOH Z 236 " =    2.017
peak=   -3.213 closest distance to " CB  TYR A  15 " =    2.121
peak=   -3.212 closest distance to " O   HOH Z 187 " =    1.725
peak=   -3.210 closest distance to " O   HOH Z 134 " =    3.777
peak=   -3.209 closest distance to " CG2 VAL A 296 " =    1.815
peak=   -3.206 closest distance to " O   HOH Z 337 " =    1.605
peak=   -3.203 closest distance to " O   GLN A 240 " =    1.767
peak=   -3.202 closest distance to " O   LEU A 261 " =    1.574
peak=   -3.195 closest distance to " O   HOH Z 256 " =    1.503
peak=   -3.193 closest distance to " CG2 THR A 264 " =    2.047
peak=   -3.188 closest distance to " O   ALA A 180 " =    1.108
peak=   -3.187 closest distance to " CG2 ILE A 263 " =    2.237
peak=   -3.187 closest distance to " CB  GLN A  55 " =    1.349
peak=   -3.186 closest distance to " NH1AARG A 275 " =    1.901
peak=   -3.186 closest distance to " O   HOH Z 369 " =    2.159
peak=   -3.185 closest distance to " CE3 TRP A 123 " =    1.336
peak=   -3.182 closest distance to " O   HOH Z  49 " =    1.113
peak=   -3.179 closest distance to " CB  ALA A   7 " =    1.975
peak=   -3.176 closest distance to " ND2 ASN A  60 " =    4.242
peak=   -3.176 closest distance to " O   HOH Z  88 " =    1.775
peak=   -3.174 closest distance to " CG2 THR A 157 " =    2.002
peak=   -3.172 closest distance to " N   ALA A 226 " =    1.918
peak=   -3.169 closest distance to " CE2 TYR A  30 " =    2.632
peak=   -3.160 closest distance to " O   HOH Z  28 " =    2.173
peak=   -3.160 closest distance to " O   HOH Z 140 " =    1.547
peak=   -3.159 closest distance to " O   HOH Z 281 " =    2.992
peak=   -3.154 closest distance to " O   ALA A  10 " =    1.672
peak=   -3.141 closest distance to " CG1 VAL A 197 " =    2.065
peak=   -3.135 closest distance to " OD1 ASN A 301 " =    1.767
peak=   -3.134 closest distance to " N   ARG A 159 " =    1.924
peak=   -3.131 closest distance to " O   HOH Z 388 " =    2.179
peak=   -3.130 closest distance to " O   HOH Z 234 " =    3.707
peak=   -3.127 closest distance to " CE  LYS A  76 " =    2.813
peak=   -3.125 closest distance to " O   TRP A  70 " =    1.380
peak=   -3.108 closest distance to " O   HOH Z 389 " =    1.373
peak=   -3.108 closest distance to " C   ASP A 231 " =    2.411
peak=   -3.107 closest distance to " CD1 LEU A 228 " =    1.930
peak=   -3.105 closest distance to " OE2 GLU A 236 " =    1.566
peak=   -3.087 closest distance to " O   HOH Z  89 " =    2.751
peak=   -3.084 closest distance to " CD  ARG A 139 " =    1.510
peak=   -3.080 closest distance to " CG2 THR A 178 " =    2.033
peak=   -3.072 closest distance to " O   SER A 210 " =    1.978
peak=   -3.067 closest distance to " CB  SER A 210 " =    1.246
peak=   -3.048 closest distance to " O   ALA A 160 " =    1.726
peak=   -3.043 closest distance to " CE  MET A 105 " =    2.271
peak=   -3.042 closest distance to " ND2 ASN A 142 " =    2.167
peak=   -3.023 closest distance to " CG1 VAL A  78 " =    2.789
peak=   -3.022 closest distance to " O   HOH Z 166 " =    1.256
peak=   -3.017 closest distance to " O   LYS A  76 " =    1.908
peak=   -3.000 closest distance to " CA  GLY A  57 " =    2.131

================= 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    :  0.4374 0.4305   6.248970e+00   6.238864e+00
   1_bss:  0.4267 0.4213   6.239670e+00   6.221239e+00
   1_xyz:  0.3150 0.3515   6.018278e+00   6.079323e+00
   1_adp:  0.2852 0.3647   5.971666e+00   6.107320e+00
   1_occ:  0.2849 0.3655   5.971849e+00   6.108310e+00
   2_bss:  0.2830 0.3622   5.964628e+00   6.102848e+00
   2_xyz:  0.2251 0.2920   5.762766e+00   5.940854e+00
   2_adp:  0.2138 0.2743   5.715717e+00   5.892900e+00
   2_occ:  0.2135 0.2736   5.713803e+00   5.891052e+00
   3_bss:  0.2132 0.2726   5.711119e+00   5.888192e+00
   3_xyz:  0.1592 0.2081   5.439846e+00   5.646599e+00
   3_adp:  0.1421 0.1938   5.346663e+00   5.575673e+00
   3_occ:  0.1419 0.1933   5.345333e+00   5.573854e+00
   4_bss:  0.1417 0.1928   5.340684e+00   5.568172e+00
   4_xyz:  0.1218 0.1710   5.213594e+00   5.455080e+00
   4_adp:  0.1211 0.1647   5.193836e+00   5.419521e+00
   4_occ:  0.1209 0.1645   5.192776e+00   5.418389e+00
   5_bss:  0.1209 0.1643   5.192260e+00   5.417728e+00
   5_xyz:  0.1125 0.1568   5.136803e+00   5.375033e+00
   5_adp:  0.1097 0.1558   5.122793e+00   5.370641e+00
   5_occ:  0.1096 0.1557   5.122274e+00   5.369977e+00
   5_bss:  0.1093 0.1558   5.121833e+00   5.369937e+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:  0.341  20.001  -0.587   2.502  -1.703   0.000  -0.000  -0.000
   1_xyz:  0.341  20.001  -0.587   2.502  -1.703   0.000  -0.000  -0.000
   1_adp:  0.341  20.001  -0.587   2.502  -1.703   0.000  -0.000  -0.000
   1_occ:  0.341  20.001  -0.587   2.502  -1.703   0.000  -0.000  -0.000
   2_bss:  0.343  50.000  -1.630   0.318  -0.746   0.000  -0.000  -0.000
   2_xyz:  0.343  50.000  -1.630   0.318  -0.746   0.000  -0.000  -0.000
   2_adp:  0.343  50.000  -1.630   0.318  -0.746   0.000  -0.000  -0.000
   2_occ:  0.343  50.000  -1.630   0.318  -0.746   0.000  -0.000  -0.000
   3_bss:  0.329  43.358  -2.378  -0.760  -0.558  -0.000  -0.000  -0.000
   3_xyz:  0.329  43.358  -2.378  -0.760  -0.558  -0.000  -0.000  -0.000
   3_adp:  0.329  43.358  -2.378  -0.760  -0.558  -0.000  -0.000  -0.000
   3_occ:  0.329  43.358  -2.378  -0.760  -0.558  -0.000  -0.000  -0.000
   4_bss:  0.319  43.358  -2.697  -1.927  -0.878  -0.000  -0.000  -0.000
   4_xyz:  0.319  43.358  -2.697  -1.927  -0.878  -0.000  -0.000  -0.000
   4_adp:  0.319  43.358  -2.697  -1.927  -0.878  -0.000  -0.000  -0.000
   4_occ:  0.319  43.358  -2.697  -1.927  -0.878  -0.000  -0.000  -0.000
   5_bss:  0.325  43.358  -2.757  -2.224  -0.875  -0.000  -0.000  -0.000
   5_xyz:  0.325  43.358  -2.757  -2.224  -0.875  -0.000  -0.000  -0.000
   5_adp:  0.325  43.358  -2.757  -2.224  -0.875  -0.000  -0.000  -0.000
   5_occ:  0.325  43.358  -2.757  -2.224  -0.875  -0.000  -0.000  -0.000
   5_bss:  0.325  43.341  -2.694  -2.252  -0.801  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.125 0.5078  0.6859    60095.039
   1_bss:  50.081 0.5192  0.7039    56557.954
   1_xyz:  36.764 0.6816  0.8919    33871.655
   1_adp:  39.031 0.6539  0.8611    37373.492
   1_occ:  39.118 0.6529  0.8591    37505.579
   2_bss:  38.436 0.6606  0.8486    36344.724
   2_xyz:  29.605 0.7616  0.9549    22407.499
   2_adp:  27.270 0.7879  0.9731    19773.601
   2_occ:  27.179 0.7888  0.9732    19629.047
   3_bss:  27.004 0.7904  0.9546    19360.984
   3_xyz:  20.014 0.8611  1.0030    11016.525
   3_adp:  18.223 0.8783  1.0019     9515.080
   3_occ:  18.184 0.8787  1.0019     9456.690
   4_bss:  18.016 0.8800  0.9813     9294.953
   4_xyz:  15.529 0.9018  0.9924     7275.295
   4_adp:  14.639 0.9096  0.9930     6830.538
   4_occ:  14.624 0.9097  0.9930     6805.373
   5_bss:  14.607 0.9098  0.9889     6798.430
   5_xyz:  13.752 0.9168  0.9914     6170.252
   5_adp:  13.648 0.9177  0.9876     6085.945
   5_occ:  13.640 0.9177  0.9876     6075.184
   5_bss:  13.664 0.9175  0.9883     6086.574
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   1.9700e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   1.9700e-01
   1_xyz:   1.487  0.011  0.099 15.164  0.006  4.105   1.2197e-01
   1_adp:   1.487  0.011  0.099 15.164  0.006  4.105   1.2197e-01
   1_occ:   1.487  0.011  0.099 15.164  0.006  4.105   1.2197e-01
   2_bss:   1.487  0.011  0.099 15.164  0.006  4.105   1.2197e-01
   2_xyz:   1.149  0.008  0.083 14.576  0.005  4.116   7.4959e-02
   2_adp:   1.149  0.008  0.083 14.576  0.005  4.116   7.4959e-02
   2_occ:   1.149  0.008  0.083 14.576  0.005  4.116   7.4959e-02
   3_bss:   1.149  0.008  0.083 14.576  0.005  4.116   7.4959e-02
   3_xyz:   1.057  0.007  0.072 14.704  0.004  4.109   6.4314e-02
   3_adp:   1.057  0.007  0.072 14.704  0.004  4.109   6.4314e-02
   3_occ:   1.057  0.007  0.072 14.704  0.004  4.109   6.4314e-02
   4_bss:   1.057  0.007  0.072 14.704  0.004  4.109   6.4314e-02
   4_xyz:   1.000  0.006  0.072 14.700  0.004  4.112   5.9190e-02
   4_adp:   1.000  0.006  0.072 14.700  0.004  4.112   5.9190e-02
   4_occ:   1.000  0.006  0.072 14.700  0.004  4.112   5.9190e-02
   5_bss:   1.000  0.006  0.072 14.700  0.004  4.112   5.9190e-02
   5_xyz:   1.059  0.007  0.077 14.934  0.005  4.106   6.5932e-02
   5_adp:   1.059  0.007  0.077 14.934  0.005  4.106   6.5932e-02
   5_occ:   1.059  0.007  0.077 14.934  0.005  4.106   6.5932e-02
   5_bss:   1.059  0.007  0.077 14.934  0.005  4.106   6.5932e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.475   2.3823e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.475   2.3823e-01
   1_xyz:   9.887  0.062  0.339 78.911  0.053  2.017   1.0307e-01
   1_adp:   9.887  0.062  0.339 78.911  0.053  2.017   1.0307e-01
   1_occ:   9.887  0.062  0.339 78.911  0.053  2.017   1.0307e-01
   2_bss:   9.887  0.062  0.339 78.911  0.053  2.017   1.0307e-01
   2_xyz:   8.611  0.039  0.315 77.739  0.035  2.197   1.2629e-01
   2_adp:   8.611  0.039  0.315 77.739  0.035  2.197   1.2629e-01
   2_occ:   8.611  0.039  0.315 77.739  0.035  2.197   1.2629e-01
   3_bss:   8.611  0.039  0.315 77.739  0.035  2.197   1.2629e-01
   3_xyz:   7.835  0.060  0.233 83.593  0.031  2.264   8.0580e-02
   3_adp:   7.835  0.060  0.233 83.593  0.031  2.264   8.0580e-02
   3_occ:   7.835  0.060  0.233 83.593  0.031  2.264   8.0580e-02
   4_bss:   7.835  0.060  0.233 83.593  0.031  2.264   8.0580e-02
   4_xyz:   7.609  0.050  0.221 82.415  0.037  2.318   4.8405e-02
   4_adp:   7.609  0.050  0.221 82.415  0.037  2.318   4.8405e-02
   4_occ:   7.609  0.050  0.221 82.415  0.037  2.318   4.8405e-02
   5_bss:   7.609  0.050  0.221 82.415  0.037  2.318   4.8405e-02
   5_xyz:   7.078  0.051  0.255 85.434  0.035  2.233   5.9458e-02
   5_adp:   7.078  0.051  0.255 85.434  0.035  2.233   5.9458e-02
   5_occ:   7.078  0.051  0.255 85.434  0.035  2.233   5.9458e-02
   5_bss:   7.078  0.051  0.255 85.434  0.035  2.233   5.9458e-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: 106.21   0.00  18.36  76.97   0.00  14.73 106.21   3.96  38.09
   1_occ: 106.21   0.00  18.36  76.97   0.00  14.73 106.21   3.96  38.09
   2_bss: 106.21   0.00  18.36  76.97   0.00  14.73 106.21   3.96  38.09
   2_xyz: 106.21   0.00  18.36  76.97   0.00  14.73 106.21   3.96  38.09
   2_adp: 103.41   0.00  17.69  89.13   0.00  13.95 103.41   5.27  38.04
   2_occ: 103.41   0.00  17.69  89.13   0.00  13.95 103.41   5.27  38.04
   3_bss: 103.41   0.00  17.69  89.13   0.00  13.95 103.41   5.27  38.04
   3_xyz: 103.41   0.00  17.69  89.13   0.00  13.95 103.41   5.27  38.04
   3_adp:  99.21   0.00  17.42  85.72   0.00  13.00  99.21   5.21  41.46
   3_occ:  99.21   0.00  17.42  85.72   0.00  13.00  99.21   5.21  41.46
   4_bss:  99.21   0.00  17.42  85.72   0.00  13.00  99.21   5.21  41.46
   4_xyz:  99.21   0.00  17.42  85.72   0.00  13.00  99.21   5.21  41.46
   4_adp:  88.11   1.32  16.49  83.25   1.32  12.59  88.11   3.65  37.73
   4_occ:  88.11   1.32  16.49  83.25   1.32  12.59  88.11   3.65  37.73
   5_bss:  88.11   1.32  16.49  83.25   1.32  12.59  88.11   3.65  37.73
   5_xyz:  88.11   1.32  16.49  83.25   1.32  12.59  88.11   3.65  37.73
   5_adp:  88.31   0.53  16.66  87.29   0.53  12.52  88.31   4.39  39.21
   5_occ:  88.31   0.53  16.66  87.29   0.53  12.52  88.31   4.39  39.21
   5_bss:  88.29   0.52  16.64  87.27   0.52  12.50  88.29   4.38  39.20
------------------------------------------------------------------------
 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:    1.824    0.017    0.374
   1_adp:    1.824    0.017    0.374
   1_occ:    1.824    0.017    0.374
   2_bss:    1.824    0.017    0.374
   2_xyz:    1.356    0.033    0.502
   2_adp:    1.356    0.033    0.502
   2_occ:    1.356    0.033    0.502
   3_bss:    1.356    0.033    0.502
   3_xyz:    1.386    0.054    0.655
   3_adp:    1.386    0.054    0.655
   3_occ:    1.386    0.054    0.655
   4_bss:    1.386    0.054    0.655
   4_xyz:    1.559    0.076    0.691
   4_adp:    1.559    0.076    0.691
   4_occ:    1.559    0.076    0.691
   5_bss:    1.559    0.076    0.691
   5_xyz:    1.664    0.086    0.717
   5_adp:    1.664    0.086    0.717
   5_occ:    1.664    0.086    0.717
   5_bss:    1.664    0.086    0.717
------------------------------------------------------------------------

CPU time actual refinement: 358.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_137/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_137/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_137/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_137/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_137/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 358.38 
  Macro-tasks:
    bulk solvent and scale       = 44.91  
    individual site refinement   = 147.78 
    weights calculation          = 29.94  
    collect and process          = 6.59   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 229.35 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 115.35 
    alpha_beta                      = 8.33   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 124.65 
    fmodel                         = 7.21   
    r_factors                      = 0.19   
    phase_errors                   = 10.37  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 269.98 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.979 micro seconds
Total CPU time: 6.20 minutes
from_scatterers_fft:    683 calls, 114.86 s
gradients_fft:          628 calls, 110.53 s

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

# Date 2008-01-16 Time 04:07:03 PST -0800 (1200485223.04 s)
Start R-work = 0.4374, R-free = 0.4305 (no bulk solvent and anisotropic scale)
Final R-work = 0.1342, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.4267, R-free = 0.4213
Final R-work = 0.1093, R-free = 0.1558