# Date 2008-01-16 Time 06:10:55 PST -0800 (1200492655.19 s)
#phil __OFF__

Command line arguments: "../1037.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2898
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1037

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.1647, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.73, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98118
Completeness in resolution range: 0.94954
Completeness with d_max=infinity: 0.946694

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9812

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98118
Completeness in resolution range: 0.94954
Completeness with d_max=infinity: 0.946694

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.2399 [2167/2196]  1953   214   9.9%
  bin  2:  4.2399 -  3.3777 [2074/2090]  1864   210  10.1%
  bin  3:  3.3777 -  2.9543 [2048/2067]  1842   206  10.1%
  bin  4:  2.9543 -  2.6858 [2047/2077]  1849   198   9.7%
  bin  5:  2.6858 -  2.4943 [2034/2053]  1830   204  10.0%
  bin  6:  2.4943 -  2.3478 [2011/2047]  1803   208  10.3%
  bin  7:  2.3478 -  2.2306 [1986/2019]  1786   200  10.1%
  bin  8:  2.2306 -  2.1338 [2002/2036]  1806   196   9.8%
  bin  9:  2.1338 -  2.0518 [1984/2012]  1784   200  10.1%
  bin 10:  2.0518 -  1.9812 [1236/2033]  1113   123  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1037/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.11 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2187
        3.04 -     3.66: 4651
        3.66 -     4.28: 8986
        4.28 -     4.90: 12339
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.852 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.149 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.162 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.163 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28173 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_1037/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1037/model_refine_001.geo

CPU time processing inputs: 7.83


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.16465 85.5261 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: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3204   r_free= 0.3228   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.022927                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7292 0.99   1402  157 0.2804 0.2757      6.3341      6.2981|
|  2:  4.7292 -  3.7729 0.99   1359  145 0.2397 0.2409      6.3767      6.3481|
|  3:  3.7729 -  3.3017 0.99   1322  152 0.2744 0.2574       6.284      6.3394|
|  4:  3.3017 -  3.0024 0.99   1328  149 0.2906 0.3034      6.1852      6.1873|
|  5:  3.0024 -  2.7886 0.99   1315  143 0.3148 0.3234      6.0569      6.1247|
|  6:  2.7886 -  2.6251 0.99   1298  145 0.3478 0.3375      6.0229      6.0047|
|  7:  2.6251 -  2.4943 0.99   1314  141 0.3465 0.3132      6.0095      5.9555|
|  8:  2.4943 -  2.3861 0.98   1275  150 0.3634 0.3666      5.9385       5.994|
|  9:  2.3861 -  2.2946 0.98   1295  147 0.3593 0.3589      5.9109      5.8786|
| 10:  2.2946 -  2.2157 0.98   1279  134 0.3693 0.4419      5.8997       6.024|
| 11:  2.2157 -  2.1466 1.00   1285  143 0.3784 0.4121      5.8586      5.9022|
| 12:  2.1466 -  2.0854 0.97   1259  139 0.3930 0.3795      5.8104       5.856|
| 13:  2.0854 -  2.0306 0.98   1284  143 0.3796 0.3760      5.7163      5.6212|
| 14:  2.0306 -  1.9812 0.47    615   71 0.3727 0.3975      5.6619       5.677|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7292  1402   157  0.80  24.76   0.86     0.81      39071.74|
|  2:  4.7292 -  3.7729  1359   145  0.85  21.51   0.98     0.91      41965.12|
|  3:  3.7729 -  3.3017  1322   152  0.81  25.69   0.99     0.94      42118.33|
|  4:  3.3017 -  3.0024  1328   149  0.78  28.57   0.99     0.93      38643.34|
|  5:  3.0024 -  2.7886  1315   143  0.72  33.89   0.98     0.89      33251.67|
|  6:  2.7886 -  2.6251  1298   145  0.72  34.27   1.01     0.89      28414.66|
|  7:  2.6251 -  2.4943  1314   141  0.73  33.24   1.00     0.91      25320.87|
|  8:  2.4943 -  2.3861  1275   150  0.70  35.84   0.99     0.92      24827.74|
|  9:  2.3861 -  2.2946  1295   147  0.68  37.07   1.03     0.90      24513.06|
| 10:  2.2946 -  2.2157  1279   134  0.66  39.55   1.03     0.88      25459.08|
| 11:  2.2157 -  2.1466  1285   143  0.65  40.20   1.04     0.88      23762.36|
| 12:  2.1466 -  2.0854  1259   139  0.65  40.33   1.02     0.92      22020.66|
| 13:  2.0854 -  2.0306  1284   143  0.65  39.79   1.01     0.91      17864.99|
| 14:  2.0306 -  1.9812   615    71  0.66  39.34   1.05     0.85      14563.82|
|alpha:            min =        0.81 max =            0.94 mean =         0.90|
|beta:             min =    14563.82 max =        42118.33 mean =     29427.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.97 mean =        33.50|
|phase err.(test): min =        0.00 max =           89.27 mean =        33.24|
|-----------------------------------------------------------------------------|

============================== 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 = 3.885668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.052   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.695854              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.549   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      190 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1997 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1835 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2816 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4636 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4350 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5606 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6733 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.170 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    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: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3204   r_free= 0.3228   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.022927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3082   r_free= 0.3117   ksol= 0.31   Bsol= 44.63   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.01,-1.82,-0.56,-0.00,-0.00,-0.00); trace/3= -0.79                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.004685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.350842              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.328   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.357614              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.181   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3082      final r-factor (work) = 0.1796          |
| start r-factor (free) = 0.3117      final r-factor (free) = 0.2010          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2329 = 3.35 * 0.50 * 6.0107 + 1.00 * 0.1625                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6732 = 3.35 * 0.50 * 5.7340 + 1.00 * 0.0663                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1796      final r-factor (work) = 0.1678          |
| start r-factor (free) = 0.2010      final r-factor (free) = 0.2042          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0573 = 0.36 * 1.00 * 5.7340 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0071 = 0.36 * 1.00 * 5.4614 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.94   16.50    None  None   None       |
|    all(noH): 2823   0      0.00    77.94   16.50    None  None   None       |
|    Sol.    : 438    0      6.22    63.02   37.42    None  None   None       |
|    Mac.    : 2385   0      0.00    77.94   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.794:  446   |   5:    38.968 -  46.761:  122        |
|      1:     7.794 -  15.587: 1455   |   6:    46.761 -  54.555:   82        |
|      2:    15.587 -  23.381:  415   |   7:    54.555 -  62.348:   38        |
|      3:    23.381 -  31.174:  145   |   8:    62.348 -  70.142:    1        |
|      4:    31.174 -  38.968:  118   |   9:    70.142 -  77.936:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1678 r_free = 0.2042             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1672 r_free = 0.2042             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1672   r_free= 0.2042   ksol= 0.31   Bsol= 44.63   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.01,-1.82,-0.56,-0.00,-0.00,-0.00); trace/3= -0.79                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.465355                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1660   r_free= 0.2018   ksol= 0.33   Bsol= 57.85   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.58,-1.77,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464299                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.244863              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.927   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.502627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.539   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1660      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.2018      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6998 = 4.24 * 0.50 * 5.4812 + 1.00 * 0.0663                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3957 = 4.24 * 0.50 * 5.3358 + 1.00 * 0.0709                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6930 = 0.50 * 1.00 * 5.3358 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6278 = 0.50 * 1.00 * 5.1975 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 3      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.93   16.53    None  None   None       |
|    all(noH): 2823   0      0.00    68.93   16.53    None  None   None       |
|    Sol.    : 438    0      4.51    63.10   37.54    None  None   None       |
|    Mac.    : 2385   0      0.00    68.93   12.67    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 -   6.893:  266   |   5:    34.465 -  41.358:  105        |
|      1:     6.893 -  13.786: 1419   |   6:    41.358 -  48.251:   86        |
|      2:    13.786 -  20.679:  547   |   7:    48.251 -  55.144:   74        |
|      3:    20.679 -  27.572:  157   |   8:    55.144 -  62.037:   37        |
|      4:    27.572 -  34.465:  130   |   9:    62.037 -  68.930:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1199 r_free = 0.1597             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1196 r_free = 0.1597             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1597   ksol= 0.33   Bsol= 57.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.58,-1.77,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.186486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1594   ksol= 0.33   Bsol= 57.85   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.52,-1.76,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.186921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.706067              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.891  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.295387              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.633   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1021 = 2.71 * 0.50 * 5.1966 + 1.00 * 0.0709                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0599 = 2.71 * 0.50 * 5.1678 + 1.00 * 0.0677                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5437 = 0.30 * 1.00 * 5.1678 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5267 = 0.30 * 1.00 * 5.1425 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    72.19   16.75    None  None   None       |
|    all(noH): 2823   0      1.39    72.19   16.75    None  None   None       |
|    Sol.    : 438    0      5.73    66.49   38.06    None  None   None       |
|    Mac.    : 2385   0      1.39    72.19   12.84    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:     1.391 -   8.471:  598   |   5:    36.790 -  43.870:  116        |
|      1:     8.471 -  15.551: 1323   |   6:    43.870 -  50.950:   85        |
|      2:    15.551 -  22.631:  357   |   7:    50.950 -  58.030:   76        |
|      3:    22.631 -  29.710:  136   |   8:    58.030 -  65.110:   26        |
|      4:    29.710 -  36.790:  102   |   9:    65.110 -  72.190:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1554             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1554             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1554   ksol= 0.33   Bsol= 57.85   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.52,-1.76,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136995                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1554   ksol= 0.33   Bsol= 57.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.35,-1.69,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.237983              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.291  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.500639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.060  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8222 = 2.24 * 0.50 * 5.1426 + 1.00 * 0.0677                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8090 = 2.24 * 0.50 * 5.1353 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5786 = 0.50 * 1.00 * 5.1353 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5784 = 0.50 * 1.00 * 5.1330 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.67    83.05   16.88    None  None   None       |
|    all(noH): 2823   0      0.67    83.05   16.88    None  None   None       |
|    Sol.    : 438    0      6.08    72.23   38.92    None  None   None       |
|    Mac.    : 2385   0      0.67    83.05   12.84    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:     0.674 -   8.912:  772   |   5:    41.862 -  50.100:  103        |
|      1:     8.912 -  17.149: 1263   |   6:    50.100 -  58.338:   82        |
|      2:    17.149 -  25.387:  301   |   7:    58.338 -  66.575:   41        |
|      3:    25.387 -  33.625:  132   |   8:    66.575 -  74.813:   11        |
|      4:    33.625 -  41.862:  113   |   9:    74.813 -  83.051:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1569             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1569             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1569   ksol= 0.33   Bsol= 57.85   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.35,-1.69,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135307                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1569   ksol= 0.33   Bsol= 57.85   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.14,-1.50,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135408                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.960849              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 167.201  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.185433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.985  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6629 = 2.96 * 0.50 * 5.1338 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6612 = 2.96 * 0.50 * 5.1266 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9592 = 0.19 * 1.00 * 5.1266 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9589 = 0.19 * 1.00 * 5.1313 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    81.73   16.42    None  None   None       |
|    all(noH): 2823   0      1.31    81.73   16.42    None  None   None       |
|    Sol.    : 438    0      5.96    71.78   37.24    None  None   None       |
|    Mac.    : 2385   0      1.31    81.73   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:     1.314 -   9.356:  898   |   5:    41.522 -  49.564:   95        |
|      1:     9.356 -  17.397: 1179   |   6:    49.564 -  57.606:   73        |
|      2:    17.397 -  25.439:  277   |   7:    57.606 -  65.647:   29        |
|      3:    25.439 -  33.481:  125   |   8:    65.647 -  73.689:    7        |
|      4:    33.481 -  41.522:  135   |   9:    73.689 -  81.731:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1568             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1075 r_free = 0.1568             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1568   ksol= 0.33   Bsol= 57.85   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.14,-1.50,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128304                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7292 0.99   1402  157 0.0983 0.1295       5.379      5.5428|
|  2:  4.7292 -  3.7729 0.99   1359  145 0.0836 0.1086      5.4196      5.6075|
|  3:  3.7729 -  3.3017 0.99   1322  152 0.1023 0.1536      5.4442      5.8674|
|  4:  3.3017 -  3.0024 0.99   1328  149 0.1156 0.1484      5.4325      5.5642|
|  5:  3.0024 -  2.7886 0.99   1315  143 0.1279 0.1798      5.3127      5.5424|
|  6:  2.7886 -  2.6251 0.99   1298  145 0.1185 0.1820      5.1945      5.4534|
|  7:  2.6251 -  2.4943 0.99   1314  141 0.1175 0.1644      5.1378      5.3574|
|  8:  2.4943 -  2.3861 0.98   1275  150 0.1108 0.1704      5.0295      5.3124|
|  9:  2.3861 -  2.2946 0.98   1295  147 0.1106 0.1792      5.0013      5.3039|
| 10:  2.2946 -  2.2157 0.98   1279  134 0.1080 0.1733      4.9415      5.1997|
| 11:  2.2157 -  2.1466 1.00   1285  143 0.1115 0.1785      4.9303      5.2642|
| 12:  2.1466 -  2.0854 0.97   1259  139 0.1041 0.1591      4.8549      5.0948|
| 13:  2.0854 -  2.0306 0.98   1284  143 0.1149 0.1736      4.7686      5.0364|
| 14:  2.0306 -  1.9812 0.47    615   71 0.0962 0.1659      4.6083      4.9117|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7292  1402   157  0.94   8.97   0.98     0.95       7048.97|
|  2:  4.7292 -  3.7729  1359   145  0.95   7.92   1.00     0.99       8789.13|
|  3:  3.7729 -  3.3017  1322   152  0.93  11.16   1.01     1.01      10004.41|
|  4:  3.3017 -  3.0024  1328   149  0.92  13.65   1.00     0.98      10331.80|
|  5:  3.0024 -  2.7886  1315   143  0.90  16.19   0.99     0.96       8363.66|
|  6:  2.7886 -  2.6251  1298   145  0.90  15.81   0.98     0.95       6970.44|
|  7:  2.6251 -  2.4943  1314   141  0.91  15.02   0.98     0.96       6000.99|
|  8:  2.4943 -  2.3861  1275   150  0.91  15.17   0.99     0.97       5101.88|
|  9:  2.3861 -  2.2946  1295   147  0.91  14.99   0.99     0.96       4816.40|
| 10:  2.2946 -  2.2157  1279   134  0.90  15.37   0.98     0.94       4273.94|
| 11:  2.2157 -  2.1466  1285   143  0.90  16.23   0.99     0.96       4347.22|
| 12:  2.1466 -  2.0854  1259   139  0.92  14.81   1.00     0.99       3931.32|
| 13:  2.0854 -  2.0306  1284   143  0.90  16.21   0.99     0.98       3213.21|
| 14:  2.0306 -  1.9812   615    71  0.92  14.00   0.97     0.94       2337.75|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2337.75 max =        10331.80 mean =      6296.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.90|
|phase err.(test): min =        0.00 max =           89.16 mean =        13.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1569   ksol= 0.33   Bsol= 57.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-1.97,-1.32,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128359                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1569   ksol= 0.33   Bsol= 57.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-1.97,-1.32,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128359                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7292 0.99   1402  157 0.0983 0.1296      5.3794      5.5434|
|  2:  4.7292 -  3.7729 0.99   1359  145 0.0836 0.1085      5.4197      5.6073|
|  3:  3.7729 -  3.3017 0.99   1322  152 0.1023 0.1536       5.444      5.8672|
|  4:  3.3017 -  3.0024 0.99   1328  149 0.1156 0.1484      5.4325      5.5642|
|  5:  3.0024 -  2.7886 0.99   1315  143 0.1279 0.1799      5.3128      5.5424|
|  6:  2.7886 -  2.6251 0.99   1298  145 0.1185 0.1819      5.1945      5.4532|
|  7:  2.6251 -  2.4943 0.99   1314  141 0.1175 0.1644      5.1377      5.3573|
|  8:  2.4943 -  2.3861 0.98   1275  150 0.1108 0.1705      5.0295      5.3124|
|  9:  2.3861 -  2.2946 0.98   1295  147 0.1106 0.1791      5.0013      5.3037|
| 10:  2.2946 -  2.2157 0.98   1279  134 0.1079 0.1734      4.9416      5.1998|
| 11:  2.2157 -  2.1466 1.00   1285  143 0.1115 0.1786      4.9305      5.2645|
| 12:  2.1466 -  2.0854 0.97   1259  139 0.1041 0.1592      4.8551      5.0951|
| 13:  2.0854 -  2.0306 0.98   1284  143 0.1149 0.1737      4.7686      5.0364|
| 14:  2.0306 -  1.9812 0.47    615   71 0.0962 0.1659      4.6084      4.9114|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7292  1402   157  0.94   8.98   0.98     0.95       7055.53|
|  2:  4.7292 -  3.7729  1359   145  0.95   7.92   1.01     0.99       8791.25|
|  3:  3.7729 -  3.3017  1322   152  0.93  11.16   1.02     1.01       9999.36|
|  4:  3.3017 -  3.0024  1328   149  0.92  13.65   1.00     0.98      10331.47|
|  5:  3.0024 -  2.7886  1315   143  0.90  16.19   0.99     0.96       8362.80|
|  6:  2.7886 -  2.6251  1298   145  0.90  15.81   0.98     0.96       6970.39|
|  7:  2.6251 -  2.4943  1314   141  0.91  15.01   0.99     0.96       5999.39|
|  8:  2.4943 -  2.3861  1275   150  0.91  15.17   0.99     0.97       5100.97|
|  9:  2.3861 -  2.2946  1295   147  0.91  14.99   1.00     0.97       4814.92|
| 10:  2.2946 -  2.2157  1279   134  0.90  15.37   0.99     0.95       4274.45|
| 11:  2.2157 -  2.1466  1285   143  0.90  16.23   1.00     0.96       4347.85|
| 12:  2.1466 -  2.0854  1259   139  0.92  14.82   1.00     0.99       3933.45|
| 13:  2.0854 -  2.0306  1284   143  0.90  16.21   1.00     0.99       3213.40|
| 14:  2.0306 -  1.9812   615    71  0.92  14.00   0.98     0.95       2337.24|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2337.24 max =        10331.47 mean =      6296.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.90|
|phase err.(test): min =        0.00 max =           89.16 mean =        13.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.27    81.68   16.37    None  None   None       |
|    all(noH): 2823   0      1.27    81.68   16.37    None  None   None       |
|    Sol.    : 438    0      5.92    71.73   37.20    None  None   None       |
|    Mac.    : 2385   0      1.27    81.68   12.55    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:     1.268 -   9.309:  898   |   5:    41.476 -  49.518:   95        |
|      1:     9.309 -  17.351: 1179   |   6:    49.518 -  57.559:   73        |
|      2:    17.351 -  25.393:  277   |   7:    57.559 -  65.601:   29        |
|      3:    25.393 -  33.434:  125   |   8:    65.601 -  73.643:    7        |
|      4:    33.434 -  41.476:  135   |   9:    73.643 -  81.684:    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)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.590 - 4.659
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 295
   mapped sites are within: 0.700 - 4.659

peak=    6.111 closest distance to " NH2 ARG A  56 " =    2.262
peak=    5.434 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.409 closest distance to " CG  PRO A  54 " =    1.245
peak=    5.372 closest distance to " O   HOH Z 126 " =    1.854
peak=    5.247 closest distance to " CB  SER A  63 " =    1.219
peak=    5.101 closest distance to " O   HOH Z 232 " =    2.264
peak=    4.716 closest distance to " CB  GLU A 152 " =    1.141
peak=    4.693 closest distance to " O   HOH Z 236 " =    1.921
peak=    4.680 closest distance to " CB  GLN A 183 " =    1.213
peak=    4.650 closest distance to " C   PRO A 198 " =    1.519
peak=    4.632 closest distance to " CB  ARG A 275 " =    0.903
peak=    4.605 closest distance to " O   HOH Z 298 " =    1.926
peak=    4.546 closest distance to " NE2 GLN A  11 " =    1.103
peak=    4.524 closest distance to " CB  LEU A 228 " =    1.046
peak=    4.519 closest distance to " CB  PRO A  54 " =    0.846
peak=    4.477 closest distance to " O   HOH Z 193 " =    1.918
peak=    4.412 closest distance to " OD1 ASN A  69 " =    2.582
peak=    4.408 closest distance to " CG  PRO A 213 " =    1.176
peak=    4.389 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.380 closest distance to " CB  TYR A 169 " =    0.787
peak=    4.343 closest distance to " O   HOH Z 369 " =    2.002
peak=    4.328 closest distance to " CA  TYR A  30 " =    0.943
peak=    4.325 closest distance to " ND2 ASN A 187 " =    1.534
peak=    4.317 closest distance to " O   HOH Z 142 " =    1.643
peak=    4.256 closest distance to " CB  GLU A 128 " =    1.067
peak=    4.193 closest distance to " CB  SER A   3 " =    1.390
peak=    4.192 closest distance to " CB  ASN A 187 " =    1.075
peak=    4.188 closest distance to " O   HOH Z 234 " =    3.769
peak=    4.185 closest distance to " CB  ARG A  79 " =    1.340
peak=    4.177 closest distance to " O   HOH Z  15 " =    2.129
peak=    4.138 closest distance to " NH2 ARG A 156 " =    1.211
peak=    4.133 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.131 closest distance to " O   HOH Z 250 " =    1.487
peak=    4.113 closest distance to " CA  ALA A  21 " =    1.250
peak=    4.086 closest distance to " O   HOH Z 261 " =    2.109
peak=    4.082 closest distance to " CB  ARG A 190 " =    1.620
peak=    4.073 closest distance to " O   HOH Z 303 " =    2.054
peak=    4.004 closest distance to " O   HOH Z 368 " =    2.008
peak=    4.002 closest distance to " O   HOH Z  21 " =    1.745
peak=    3.983 closest distance to " O   HOH Z 158 " =    3.009
peak=    3.970 closest distance to " O   HOH Z 403 " =    1.685
peak=    3.951 closest distance to " CB  VAL A 265 " =    1.250
peak=    3.945 closest distance to " CG  PRO A 243 " =    1.108
peak=    3.936 closest distance to " CB  GLU A 277 " =    3.601
peak=    3.935 closest distance to " CA  THR A 264 " =    0.862
peak=    3.934 closest distance to " OD2 ASP A 286 " =    2.899
peak=    3.915 closest distance to " O   HOH Z 213 " =    1.788
peak=    3.906 closest distance to " CB  TRP A 266 " =    0.902
peak=    3.900 closest distance to " O   HOH Z 132 " =    2.573
peak=    3.898 closest distance to " O   HOH Z 197 " =    2.883
peak=    3.882 closest distance to " CD1 LEU A 300 " =    1.225
peak=    3.882 closest distance to " CG2 THR A 221 " =    1.020
peak=    3.878 closest distance to " CA  PRO A  54 " =    1.333
peak=    3.871 closest distance to " CB  VAL A 202 " =    1.521
peak=    3.870 closest distance to " O   HOH Z 214 " =    2.020
peak=    3.868 closest distance to " O   HOH Z 427 " =    2.997
peak=    3.848 closest distance to " CA  THR A 221 " =    0.986
peak=    3.836 closest distance to " CA  ALA A  51 " =    0.915
peak=    3.832 closest distance to " O   HOH Z 344 " =    3.175
peak=    3.828 closest distance to " O   HOH Z 108 " =    2.526
peak=    3.814 closest distance to " O   HOH Z  40 " =    1.670
peak=    3.806 closest distance to " O   HOH Z 203 " =    1.899
peak=    3.793 closest distance to " NH1AARG A 145 " =    1.201
peak=    3.783 closest distance to " ND2 ASN A 110 " =    1.745
peak=    3.773 closest distance to " O   HOH Z  10 " =    1.865
peak=    3.768 closest distance to " O   HOH Z 189 " =    2.302
peak=    3.764 closest distance to " CG  PRO A  90 " =    1.136
peak=    3.761 closest distance to " O   HOH Z  66 " =    2.179
peak=    3.753 closest distance to " CZ  PHE A 218 " =    1.082
peak=    3.752 closest distance to " CG1 ILE A  33 " =    1.240
peak=    3.744 closest distance to " O   HOH Z 193 " =    1.696
peak=    3.740 closest distance to " O   HOH Z 147 " =    1.786
peak=    3.737 closest distance to " O   HOH Z 316 " =    3.109
peak=    3.733 closest distance to " CB  TRP A 179 " =    1.390
peak=    3.733 closest distance to " O   HOH Z  61 " =    1.593
peak=    3.732 closest distance to " O   HOH Z 133 " =    2.351
peak=    3.731 closest distance to " CB  ASP A 140 " =    0.887
peak=    3.730 closest distance to " O   HOH Z  20 " =    1.726
peak=    3.721 closest distance to " O   HOH Z 135 " =    1.682
peak=    3.708 closest distance to " O   HOH Z 280 " =    2.994
peak=    3.707 closest distance to " CA  ASN A 215 " =    1.197
peak=    3.707 closest distance to " O   HOH Z  54 " =    1.716
peak=    3.704 closest distance to " CG  PRO A 198 " =    1.278
peak=    3.703 closest distance to " O   HOH Z   1 " =    2.026
peak=    3.701 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.698 closest distance to " O   HOH Z 346 " =    1.611
peak=    3.691 closest distance to " O   MET A 105 " =    1.796
peak=    3.689 closest distance to " NH2BARG A 145 " =    2.140
peak=    3.680 closest distance to " O   TRP A 274 " =    1.851
peak=    3.679 closest distance to " NZ  LYS A 117 " =    3.269
peak=    3.678 closest distance to " O   HOH Z 133 " =    1.648
peak=    3.672 closest distance to " O   HOH Z 423 " =    1.918
peak=    3.646 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.640 closest distance to " CB  SER A 212 " =    1.150
peak=    3.639 closest distance to " O   HOH Z 180 " =    2.121
peak=    3.637 closest distance to " CD  ARG A 269 " =    0.923
peak=    3.635 closest distance to " ND1 HIS A  81 " =    1.647
peak=    3.628 closest distance to " CG1BVAL A  72 " =    1.661
peak=    3.627 closest distance to " O   HOH Z 425 " =    2.014
peak=    3.626 closest distance to " ND2 ASN A 249 " =    1.963
peak=    3.623 closest distance to " O   HOH Z 426 " =    1.533
peak=    3.622 closest distance to " CB  TYR A 169 " =    0.810
peak=    3.618 closest distance to " O   HOH Z 245 " =    1.373
peak=    3.615 closest distance to " CD  ARG A  66 " =    2.356
peak=    3.610 closest distance to " O   HOH Z 193 " =    2.086
peak=    3.606 closest distance to " CD1 ILE A 106 " =    0.848
peak=    3.603 closest distance to " CE  LYS A  76 " =    0.858
peak=    3.599 closest distance to " CD  ARG A 159 " =    0.780
peak=    3.589 closest distance to " CA  MET A  40 " =    1.131
peak=    3.584 closest distance to " O   HOH Z  88 " =    3.500
peak=    3.577 closest distance to " CB  ASN A 142 " =    0.981
peak=    3.576 closest distance to " O   HOH Z 272 " =    1.842
peak=    3.573 closest distance to " ND1 HIS A  86 " =    1.634
peak=    3.572 closest distance to " CD2 LEU A 255 " =    1.415
peak=    3.560 closest distance to " CD  LYS A 166 " =    1.260
peak=    3.554 closest distance to " O   HOH Z 368 " =    3.627
peak=    3.545 closest distance to " CA  ASP A 140 " =    1.182
peak=    3.545 closest distance to " CB  ASN A  39 " =    0.886
peak=    3.542 closest distance to " CA  ASP A 191 " =    0.727
peak=    3.528 closest distance to " CB  LEU A 143 " =    1.100
peak=    3.523 closest distance to " OD1 ASN A 217 " =    1.647
peak=    3.523 closest distance to " CG2 VAL A 257 " =    0.945
peak=    3.522 closest distance to " O   HOH Z 305 " =    3.704
peak=    3.520 closest distance to " CB  SER A 216 " =    0.780
peak=    3.505 closest distance to " CA  ILE A  33 " =    1.552
peak=    3.503 closest distance to " O   HOH Z 334 " =    1.503
peak=    3.502 closest distance to " O   HOH Z 172 " =    3.512
peak=    3.497 closest distance to " O   HOH Z 291 " =    1.535
peak=    3.496 closest distance to " O   HOH Z 402 " =    1.485
peak=    3.496 closest distance to " O   SER A  87 " =    2.187
peak=    3.496 closest distance to " O   HOH Z 371 " =    3.203
peak=    3.493 closest distance to " O   HOH Z 281 " =    4.659
peak=    3.492 closest distance to " CG2 ILE A 120 " =    1.092
peak=    3.492 closest distance to " O   HOH Z  92 " =    2.571
peak=    3.491 closest distance to " CB  ARG A 139 " =    0.989
peak=    3.491 closest distance to " O   HOH Z 411 " =    3.801
peak=    3.489 closest distance to " OE1 GLU A   2 " =    2.241
peak=    3.481 closest distance to " CG  LYS A  76 " =    0.957
peak=    3.481 closest distance to " O   HOH Z  97 " =    1.937
peak=    3.476 closest distance to " O   HOH Z 265 " =    2.427
peak=    3.474 closest distance to " O   HOH Z 295 " =    1.474
peak=    3.471 closest distance to " CD2 LEU A 297 " =    0.848
peak=    3.461 closest distance to " CA  ALA A 291 " =    0.939
peak=    3.450 closest distance to " CD2 TRP A 179 " =    1.336
peak=    3.450 closest distance to " N   ARG A 156 " =    1.340
peak=    3.446 closest distance to " O   HOH Z 406 " =    1.630
peak=    3.443 closest distance to " O   HOH Z 273 " =    2.699
peak=    3.442 closest distance to " CB  SER A 141 " =    0.963
peak=    3.438 closest distance to " CB  GLU A  46 " =    0.981
peak=    3.436 closest distance to " CA  ARG A  36 " =    1.157
peak=    3.428 closest distance to " CB  MET A  40 " =    0.846
peak=    3.427 closest distance to " O   HOH Z 209 " =    2.438
peak=    3.423 closest distance to " CA  ARG A 195 " =    1.192
peak=    3.412 closest distance to " CB  ILE A 120 " =    1.220
peak=    3.402 closest distance to " CA  SER A  87 " =    0.988
peak=    3.400 closest distance to " O   HOH Z 411 " =    1.830
peak=    3.398 closest distance to " O   HOH Z 134 " =    1.402
peak=    3.390 closest distance to " OG BSER A 164 " =    2.425
peak=    3.387 closest distance to " N   ASN A 127 " =    1.246
peak=    3.384 closest distance to " O   HOH Z  44 " =    2.335
peak=    3.381 closest distance to " O  BHOH Z 338 " =    2.292
peak=    3.378 closest distance to " O   HOH Z 329 " =    3.726
peak=    3.375 closest distance to " N   VAL A 126 " =    1.362
peak=    3.373 closest distance to " CB  ASN A 224 " =    1.132
peak=    3.371 closest distance to " O   HOH Z 234 " =    1.748
peak=    3.369 closest distance to " O   HOH Z 171 " =    3.922
peak=    3.357 closest distance to " O   HOH Z 128 " =    2.125
peak=    3.357 closest distance to " O   HOH Z 383 " =    1.871
peak=    3.356 closest distance to " O   HOH Z 188 " =    2.253
peak=    3.354 closest distance to " O   HOH Z 199 " =    1.570
peak=    3.352 closest distance to " CG BARG A 275 " =    1.441
peak=    3.351 closest distance to " O   HOH Z 148 " =    3.226
peak=    3.346 closest distance to " CA  GLY A 267 " =    1.048
peak=    3.344 closest distance to " O   HOH Z 263 " =    1.756
peak=    3.342 closest distance to " CG  GLU A 277 " =    2.226
peak=    3.341 closest distance to " CA  ASP A 162 " =    1.117
peak=    3.339 closest distance to " O   HOH Z  44 " =    1.730
peak=    3.330 closest distance to " CD  ARG A 219 " =    1.026
peak=    3.323 closest distance to " CA  ALA A  84 " =    1.411
peak=    3.322 closest distance to " CB  ALA A 291 " =    1.346
peak=    3.319 closest distance to " O   HOH Z 128 " =    2.314
peak=    3.314 closest distance to " NZ  LYS A 166 " =    3.070
peak=    3.311 closest distance to " CA  ALA A 154 " =    0.908
peak=    3.309 closest distance to " NH2AARG A 275 " =    3.665
peak=    3.308 closest distance to " CZ2 TRP A 179 " =    1.707
peak=    3.303 closest distance to " CG  LEU A 167 " =    1.239
peak=    3.302 closest distance to " O   HOH Z  68 " =    1.620
peak=    3.301 closest distance to " N   SER A 135 " =    1.322
peak=    3.301 closest distance to " O   HOH Z  49 " =    2.708
peak=    3.300 closest distance to " O   HOH Z  49 " =    2.299
peak=    3.299 closest distance to " CG2BVAL A  41 " =    0.830
peak=    3.298 closest distance to " O   HOH Z 345 " =    1.753
peak=    3.296 closest distance to " O   ALA A 158 " =    1.270
peak=    3.293 closest distance to " CG  GLN A  58 " =    2.761
peak=    3.291 closest distance to " OD1BASN A 224 " =    2.328
peak=    3.288 closest distance to " O   HOH Z 173 " =    1.923
peak=    3.287 closest distance to " O   HOH Z 313 " =    1.855
peak=    3.286 closest distance to " O   HOH Z 175 " =    2.180
peak=    3.285 closest distance to " O   HOH Z 327 " =    1.889
peak=    3.277 closest distance to " CA  ALA A 233 " =    1.339
peak=    3.275 closest distance to " CB  ALA A 248 " =    0.911
peak=    3.269 closest distance to " O   HOH Z 171 " =    2.220
peak=    3.265 closest distance to " CB  TYR A 116 " =    0.899
peak=    3.265 closest distance to " O   HOH Z 248 " =    1.741
peak=    3.264 closest distance to " O   HOH Z  93 " =    2.722
peak=    3.263 closest distance to " O   HOH Z 281 " =    3.989
peak=    3.261 closest distance to " O   HOH Z 219 " =    1.874
peak=    3.260 closest distance to " O   THR A 251 " =    1.221
peak=    3.255 closest distance to " OG  SER A  22 " =    2.766
peak=    3.254 closest distance to " CA  ALA A 248 " =    1.220
peak=    3.254 closest distance to " O   HOH Z 227 " =    1.648
peak=    3.253 closest distance to " CB  ALA A   9 " =    1.545
peak=    3.248 closest distance to " CG  MET A 185 " =    1.151
peak=    3.244 closest distance to " CB  ALA A  34 " =    1.016
peak=    3.239 closest distance to " CG1 VAL A 153 " =    0.918
peak=    3.239 closest distance to " O   HOH Z 286 " =    2.230
peak=    3.235 closest distance to " CB  HIS A 108 " =    0.835
peak=    3.234 closest distance to " CB  TRP A 150 " =    1.387
peak=    3.231 closest distance to " CB  GLN A 103 " =    0.815
peak=    3.230 closest distance to " OD1 ASP A 231 " =    1.874
peak=    3.227 closest distance to " CB  PHE A  16 " =    1.075
peak=    3.226 closest distance to " NH1 ARG A 138 " =    1.164
peak=    3.225 closest distance to " O   HOH Z  85 " =    2.336
peak=    3.225 closest distance to " CA  GLY A 241 " =    0.700
peak=    3.223 closest distance to " CA  ASN A 217 " =    1.301
peak=    3.221 closest distance to " O   HOH Z 345 " =    3.417
peak=    3.218 closest distance to " O   HOH Z 391 " =    2.923
peak=    3.217 closest distance to " O   HOH Z 116 " =    1.766
peak=    3.216 closest distance to " O   HOH Z 374 " =    2.730
peak=    3.214 closest distance to " CZ  PHE A 192 " =    0.954
peak=    3.214 closest distance to " CA  GLN A 223 " =    0.884
peak=    3.213 closest distance to " CD  LYS A 119 " =    1.439
peak=    3.213 closest distance to " CB  ALA A  71 " =    1.351
peak=    3.210 closest distance to " CG1 ILE A 151 " =    0.970
peak=    3.208 closest distance to " CB  GLN A 278 " =    0.869
peak=    3.208 closest distance to " O   HOH Z  59 " =    2.215
peak=    3.205 closest distance to " O   HOH Z 353 " =    2.740
peak=    3.204 closest distance to " CD BLYS A 290 " =    1.115
peak=    3.203 closest distance to " CB  ALA A 248 " =    1.343
peak=    3.202 closest distance to " O   HOH Z 255 " =    1.641
peak=    3.199 closest distance to " CA  ALA A 158 " =    1.096
peak=    3.198 closest distance to " CB  ALA A 100 " =    1.208
peak=    3.198 closest distance to " O   HOH Z 359 " =    1.477
peak=    3.194 closest distance to " OG1 THR A 294 " =    2.455
peak=    3.194 closest distance to " OG  SER A  97 " =    3.632
peak=    3.192 closest distance to " CG BARG A 102 " =    1.849
peak=    3.191 closest distance to " CB  THR A 294 " =    1.665
peak=    3.180 closest distance to " O   HOH Z 358 " =    3.764
peak=    3.179 closest distance to " CB  THR A 157 " =    1.115
peak=    3.177 closest distance to " O   ALA A   1 " =    1.509
peak=    3.176 closest distance to " CG  MET A 185 " =    1.067
peak=    3.175 closest distance to " CB  LEU A 255 " =    0.787
peak=    3.173 closest distance to " O   HOH Z 250 " =    1.489
peak=    3.169 closest distance to " N   SER A  12 " =    1.653
peak=    3.169 closest distance to " O   HOH Z 299 " =    4.529
peak=    3.167 closest distance to " O   HOH Z 261 " =    2.154
peak=    3.167 closest distance to " O   HOH Z 387 " =    3.047
peak=    3.167 closest distance to " O   HOH Z 421 " =    1.701
peak=    3.163 closest distance to " OG  SER A 206 " =    1.305
peak=    3.163 closest distance to " CD2 HIS A  81 " =    1.180
peak=    3.157 closest distance to " O   HOH Z 166 " =    3.611
peak=    3.157 closest distance to " CZ3 TRP A 123 " =    1.275
peak=    3.153 closest distance to " O   HOH Z 425 " =    1.285
peak=    3.151 closest distance to " CD1 LEU A  96 " =    0.716
peak=    3.151 closest distance to " CB  ASN A 110 " =    1.158
peak=    3.150 closest distance to " NH2AARG A 190 " =    1.295
peak=    3.149 closest distance to " O   HOH Z 163 " =    1.581
peak=    3.149 closest distance to " O   HOH Z   9 " =    2.139
peak=    3.149 closest distance to " O   HOH Z 258 " =    1.948
peak=    3.148 closest distance to " CB  LYS A 193 " =    0.956
peak=    3.144 closest distance to " O   HOH Z 417 " =    3.256
peak=    3.142 closest distance to " CA  MET A 105 " =    0.975
peak=    3.141 closest distance to " O   HOH Z 384 " =    3.034
peak=    3.138 closest distance to " NE2 GLN A  77 " =    3.326
peak=    3.136 closest distance to " O   HOH Z 144 " =    1.807
peak=    3.126 closest distance to " CG  MET A 113 " =    1.545
peak=    3.122 closest distance to " CA  TYR A 116 " =    1.410
peak=    3.113 closest distance to " OE1 GLU A 277 " =    1.939
peak=    3.112 closest distance to " CB  ASN A 215 " =    1.123
peak=    3.107 closest distance to " CA  VAL A  41 " =    0.865
peak=    3.106 closest distance to " CG ALYS A 290 " =    1.154
peak=    3.079 closest distance to " O   HOH Z 302 " =    1.981
peak=    3.078 closest distance to " O   HOH Z 423 " =    3.073
peak=    3.073 closest distance to " O   HOH Z  88 " =    2.977
peak=    3.070 closest distance to " N   ASN A 252 " =    1.382
peak=    3.061 closest distance to " O   HOH Z 392 " =    2.063
peak=    3.057 closest distance to " O   HOH Z 422 " =    2.701
peak=    3.025 closest distance to " CB  ALA A 114 " =    1.212

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.567 - 5.651
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 202
   mapped sites are within: 0.705 - 5.651

peak=   -4.732 closest distance to " CB  PRO A 243 " =    2.622
peak=   -4.618 closest distance to " O   HOH Z 266 " =    4.731
peak=   -4.482 closest distance to " CD  ARG A 156 " =    2.039
peak=   -4.471 closest distance to " O   VAL A  67 " =    2.752
peak=   -4.393 closest distance to " O   HOH Z 290 " =    1.251
peak=   -4.245 closest distance to " O   ILE A 109 " =    2.642
peak=   -4.135 closest distance to " O   HOH Z 372 " =    2.499
peak=   -4.123 closest distance to " SG  CYS A 254 " =    3.349
peak=   -4.118 closest distance to " OE1 GLN A 223 " =    1.950
peak=   -4.079 closest distance to " O   HOH Z  10 " =    1.562
peak=   -4.061 closest distance to " N   ALA A  43 " =    2.576
peak=   -4.010 closest distance to " O   HOH Z  52 " =    1.380
peak=   -4.000 closest distance to " CD1 PHE A  59 " =    1.866
peak=   -3.949 closest distance to " O   HOH Z 198 " =    2.254
peak=   -3.946 closest distance to " O   HOH Z 231 " =    2.255
peak=   -3.938 closest distance to " O   HOH Z 126 " =    1.901
peak=   -3.918 closest distance to " CE2 TYR A  30 " =    2.768
peak=   -3.903 closest distance to " C   HIS A 108 " =    1.135
peak=   -3.876 closest distance to " O   HOH Z 311 " =    3.691
peak=   -3.874 closest distance to " O   HOH Z 118 " =    3.185
peak=   -3.847 closest distance to " CD1 LEU A 228 " =    2.369
peak=   -3.840 closest distance to " O   HOH Z 389 " =    1.823
peak=   -3.830 closest distance to " ND2 ASN A  45 " =    1.732
peak=   -3.827 closest distance to " CZ3 TRP A 179 " =    1.127
peak=   -3.819 closest distance to " SG ACYS A 201 " =    1.939
peak=   -3.804 closest distance to " NH2AARG A 275 " =    5.422
peak=   -3.803 closest distance to " O   HOH Z  43 " =    1.519
peak=   -3.795 closest distance to " CD1 LEU A 101 " =    2.441
peak=   -3.788 closest distance to " CG1 VAL A 112 " =    2.785
peak=   -3.780 closest distance to " O   PRO A 198 " =    1.294
peak=   -3.778 closest distance to " OG  SER A  97 " =    2.194
peak=   -3.773 closest distance to " O   HOH Z 211 " =    1.621
peak=   -3.769 closest distance to " O   HOH Z 353 " =    2.183
peak=   -3.754 closest distance to " CB  ALA A 291 " =    2.294
peak=   -3.742 closest distance to " O   HOH Z 377 " =    2.131
peak=   -3.739 closest distance to " OG BSER A 134 " =    1.788
peak=   -3.723 closest distance to " CG  PHE A 283 " =    2.784
peak=   -3.722 closest distance to " O   HOH Z 185 " =    2.382
peak=   -3.709 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.705 closest distance to " CD  ARG A 139 " =    1.643
peak=   -3.691 closest distance to " CE2 PHE A 218 " =    2.449
peak=   -3.682 closest distance to " CG1 VAL A 112 " =    2.928
peak=   -3.682 closest distance to " O   PRO A 163 " =    2.108
peak=   -3.680 closest distance to " O   HOH Z 198 " =    1.233
peak=   -3.673 closest distance to " CB  ALA A  43 " =    2.490
peak=   -3.660 closest distance to " CD2 LEU A 300 " =    2.858
peak=   -3.656 closest distance to " O   HOH Z 407 " =    3.316
peak=   -3.638 closest distance to " C   ALA A 158 " =    1.321
peak=   -3.633 closest distance to " O   HOH Z  73 " =    2.238
peak=   -3.633 closest distance to " CG1 VAL A 250 " =    2.684
peak=   -3.627 closest distance to " O   HOH Z 351 " =    1.537
peak=   -3.626 closest distance to " CD  GLN A  58 " =    1.031
peak=   -3.622 closest distance to " O   VAL A  67 " =    2.611
peak=   -3.614 closest distance to " O   HOH Z 435 " =    2.722
peak=   -3.612 closest distance to " C   ASN A 285 " =    2.522
peak=   -3.586 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.572 closest distance to " O   HOH Z 313 " =    2.061
peak=   -3.567 closest distance to " OG BSER A 134 " =    1.229
peak=   -3.562 closest distance to " CG1 VAL A 197 " =    2.256
peak=   -3.550 closest distance to " OXT GLY A 302 " =    2.835
peak=   -3.533 closest distance to " O   HOH Z 196 " =    2.076
peak=   -3.526 closest distance to " OD1 ASN A 148 " =    1.659
peak=   -3.521 closest distance to " CG2 ILE A 263 " =    2.319
peak=   -3.514 closest distance to " ND2 ASN A  45 " =    1.049
peak=   -3.508 closest distance to " OG  SER A  62 " =    1.580
peak=   -3.506 closest distance to " O   HOH Z  38 " =    1.447
peak=   -3.505 closest distance to " O   HOH Z 111 " =    2.170
peak=   -3.499 closest distance to " NH2 ARG A 159 " =    2.382
peak=   -3.499 closest distance to " ND2 ASN A 249 " =    2.118
peak=   -3.498 closest distance to " O   HOH Z 292 " =    4.575
peak=   -3.496 closest distance to " CG  ARG A 269 " =    2.419
peak=   -3.495 closest distance to " N   ALA A 226 " =    2.150
peak=   -3.493 closest distance to " O   HOH Z  76 " =    1.928
peak=   -3.492 closest distance to " CB  PRO A 163 " =    2.576
peak=   -3.492 closest distance to " O   GLY A 211 " =    1.551
peak=   -3.490 closest distance to " CB  ASN A  39 " =    2.232
peak=   -3.490 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.486 closest distance to " CD  ARG A 195 " =    5.256
peak=   -3.482 closest distance to " NH1 ARG A 195 " =    2.566
peak=   -3.480 closest distance to " N   SER A 212 " =    2.078
peak=   -3.477 closest distance to " O   HOH Z 394 " =    1.442
peak=   -3.471 closest distance to " CA  GLY A 241 " =    3.108
peak=   -3.470 closest distance to " CG  TRP A 266 " =    1.798
peak=   -3.467 closest distance to " CD1 LEU A 297 " =    2.471
peak=   -3.467 closest distance to " O   HOH Z  11 " =    1.785
peak=   -3.459 closest distance to " CZ  PHE A  59 " =    1.634
peak=   -3.457 closest distance to " CD2 PHE A 192 " =    2.131
peak=   -3.453 closest distance to " O   HOH Z  60 " =    2.504
peak=   -3.452 closest distance to " CZ  TYR A 169 " =    1.699
peak=   -3.451 closest distance to " CB  ALA A 291 " =    2.236
peak=   -3.443 closest distance to " CA  GLY A 203 " =    2.301
peak=   -3.442 closest distance to " CG  ARG A  66 " =    2.293
peak=   -3.434 closest distance to " O   VAL A 189 " =    2.590
peak=   -3.433 closest distance to " NH2 ARG A  79 " =    1.904
peak=   -3.401 closest distance to " OD1 ASP A 171 " =    1.597
peak=   -3.396 closest distance to " CB  ASP A 286 " =    2.154
peak=   -3.390 closest distance to " O   HOH Z  13 " =    1.590
peak=   -3.388 closest distance to " CB  TRP A  85 " =    2.544
peak=   -3.383 closest distance to " OH  TYR A 247 " =    2.100
peak=   -3.381 closest distance to " N   GLN A  58 " =    1.608
peak=   -3.372 closest distance to " CE  MET A  93 " =    1.283
peak=   -3.368 closest distance to " CD1 ILE A 239 " =    2.085
peak=   -3.368 closest distance to " C   LEU A 143 " =    1.166
peak=   -3.359 closest distance to " CB  ASP A 132 " =    2.300
peak=   -3.358 closest distance to " O   HOH Z 298 " =    2.698
peak=   -3.356 closest distance to " CD2 PHE A  61 " =    2.438
peak=   -3.355 closest distance to " O   HOH Z 222 " =    1.271
peak=   -3.346 closest distance to " NE2 GLN A  88 " =    1.839
peak=   -3.343 closest distance to " O   HOH Z 174 " =    3.103
peak=   -3.342 closest distance to " CB  CYS A 201 " =    2.712
peak=   -3.340 closest distance to " N   THR A 157 " =    1.606
peak=   -3.330 closest distance to " O   HOH Z 253 " =    3.991
peak=   -3.329 closest distance to " CE  MET A 105 " =    2.048
peak=   -3.323 closest distance to " NH2 ARG A  79 " =    1.609
peak=   -3.321 closest distance to " O   HOH Z  37 " =    1.989
peak=   -3.314 closest distance to " NE2 GLN A 103 " =    1.643
peak=   -3.314 closest distance to " OD2 ASP A 171 " =    1.847
peak=   -3.303 closest distance to " O   HOH Z 393 " =    1.416
peak=   -3.297 closest distance to " CG  PRO A 163 " =    2.577
peak=   -3.295 closest distance to " CD1 LEU A 101 " =    2.915
peak=   -3.289 closest distance to " O   VAL A 125 " =    2.360
peak=   -3.287 closest distance to " CG  MET A 105 " =    0.963
peak=   -3.287 closest distance to " O   HOH Z  98 " =    2.238
peak=   -3.285 closest distance to " O   HOH Z 241 " =    1.287
peak=   -3.279 closest distance to " CH2 TRP A 177 " =    2.120
peak=   -3.277 closest distance to " CE3 TRP A 274 " =    2.501
peak=   -3.271 closest distance to " O   GLY A 196 " =    1.108
peak=   -3.268 closest distance to " O   HOH Z 436 " =    1.414
peak=   -3.266 closest distance to " OG BSER A 210 " =    2.153
peak=   -3.262 closest distance to " O   HOH Z  51 " =    1.382
peak=   -3.261 closest distance to " CG2 VAL A 189 " =    2.092
peak=   -3.255 closest distance to " CG2 THR A 221 " =    2.238
peak=   -3.255 closest distance to " O   HOH Z 426 " =    1.625
peak=   -3.254 closest distance to " O   HOH Z  93 " =    1.802
peak=   -3.254 closest distance to " O   ASN A 301 " =    1.484
peak=   -3.250 closest distance to " OD1 ASP A 191 " =    1.754
peak=   -3.249 closest distance to " C   ILE A 234 " =    1.309
peak=   -3.244 closest distance to " O   HOH Z 166 " =    1.524
peak=   -3.243 closest distance to " CD2 TYR A 293 " =    2.028
peak=   -3.241 closest distance to " ND2 ASN A  60 " =    1.395
peak=   -3.240 closest distance to " O   HOH Z 417 " =    2.525
peak=   -3.239 closest distance to " CG  GLU A 152 " =    0.831
peak=   -3.232 closest distance to " CD2 LEU A 237 " =    2.696
peak=   -3.231 closest distance to " O   HOH Z 166 " =    1.747
peak=   -3.231 closest distance to " CB  CYS A 254 " =    2.406
peak=   -3.228 closest distance to " O   HOH Z  88 " =    2.200
peak=   -3.226 closest distance to " O   SER A 135 " =    1.520
peak=   -3.223 closest distance to " O   HOH Z 234 " =    4.298
peak=   -3.220 closest distance to " CG  GLU A  53 " =    1.585
peak=   -3.220 closest distance to " O   HOH Z 348 " =    2.270
peak=   -3.219 closest distance to " CB  ASP A 132 " =    2.336
peak=   -3.204 closest distance to " NH2 ARG A  66 " =    2.068
peak=   -3.203 closest distance to " OG  SER A  26 " =    1.206
peak=   -3.200 closest distance to " C   MET A 188 " =    1.502
peak=   -3.197 closest distance to " CE BMET A  47 " =    2.267
peak=   -3.196 closest distance to " OG1 THR A 178 " =    1.298
peak=   -3.193 closest distance to " O   HOH Z 359 " =    2.988
peak=   -3.189 closest distance to " O   PRO A 198 " =    1.292
peak=   -3.179 closest distance to " CD1 ILE A 239 " =    2.358
peak=   -3.177 closest distance to " O   HOH Z 191 " =    5.651
peak=   -3.177 closest distance to " O   MET A  40 " =    2.846
peak=   -3.171 closest distance to " O   HOH Z 275 " =    1.547
peak=   -3.170 closest distance to " CD  GLU A 236 " =    1.001
peak=   -3.169 closest distance to " O   HOH Z 207 " =    2.192
peak=   -3.167 closest distance to " CA  GLY A 241 " =    2.794
peak=   -3.166 closest distance to " CE  LYS A  76 " =    2.773
peak=   -3.163 closest distance to " NH2BARG A 275 " =    1.987
peak=   -3.161 closest distance to " O   HOH Z 317 " =    2.345
peak=   -3.159 closest distance to " CB  ALA A 248 " =    1.996
peak=   -3.158 closest distance to " CD  GLN A  11 " =    0.705
peak=   -3.155 closest distance to " CB  ALA A 248 " =    2.445
peak=   -3.153 closest distance to " C   SER A 206 " =    1.489
peak=   -3.152 closest distance to " O   GLN A 240 " =    2.401
peak=   -3.148 closest distance to " OE1 GLN A  88 " =    1.285
peak=   -3.148 closest distance to " CB  TYR A  15 " =    2.192
peak=   -3.143 closest distance to " O   HOH Z 396 " =    1.877
peak=   -3.135 closest distance to " CD2 LEU A 237 " =    2.230
peak=   -3.129 closest distance to " O   HOH Z 128 " =    2.564
peak=   -3.122 closest distance to " OD2 ASP A  50 " =    2.309
peak=   -3.122 closest distance to " O   HOH Z 184 " =    1.804
peak=   -3.119 closest distance to " OE2 GLU A   2 " =    1.748
peak=   -3.118 closest distance to " O   HOH Z  19 " =    2.462
peak=   -3.115 closest distance to " CD  GLN A  88 " =    0.746
peak=   -3.111 closest distance to " O   HOH Z   6 " =    1.542
peak=   -3.111 closest distance to " O   HOH Z 377 " =    1.275
peak=   -3.110 closest distance to " O   HOH Z 281 " =    2.670
peak=   -3.109 closest distance to " O   HOH Z 323 " =    1.234
peak=   -3.100 closest distance to " CG  ASN A 301 " =    1.957
peak=   -3.098 closest distance to " CA  SER A 135 " =    1.356
peak=   -3.098 closest distance to " CB  ASP A 132 " =    2.252
peak=   -3.095 closest distance to " CA  GLY A  98 " =    1.978
peak=   -3.090 closest distance to " NE2 GLN A  58 " =    1.172
peak=   -3.084 closest distance to " O   ALA A  10 " =    1.708
peak=   -3.075 closest distance to " N   ALA A 248 " =    1.608
peak=   -3.070 closest distance to " O   PHE A 218 " =    1.606
peak=   -3.063 closest distance to " O   HOH Z 390 " =    2.371
peak=   -3.039 closest distance to " O   HOH Z 193 " =    1.834
peak=   -3.035 closest distance to " O   LYS A 289 " =    2.994
peak=   -3.034 closest distance to " CD1 ILE A 199 " =    2.530

================= 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    :  0.3204 0.3228   6.022927e+00   6.031832e+00
   1_bss:  0.3082 0.3117   6.004685e+00   6.006025e+00
   1_xyz:  0.1796 0.2010   5.514202e+00   5.619114e+00
   1_adp:  0.1678 0.2042   5.467905e+00   5.636127e+00
   1_occ:  0.1672 0.2042   5.465355e+00   5.633554e+00
   2_bss:  0.1660 0.2018   5.464299e+00   5.631295e+00
   2_xyz:  0.1234 0.1629   5.212404e+00   5.426247e+00
   2_adp:  0.1199 0.1597   5.187243e+00   5.405504e+00
   2_occ:  0.1196 0.1597   5.186486e+00   5.405525e+00
   3_bss:  0.1198 0.1594   5.186921e+00   5.405013e+00
   3_xyz:  0.1146 0.1572   5.159237e+00   5.389794e+00
   3_adp:  0.1104 0.1554   5.136980e+00   5.379019e+00
   3_occ:  0.1103 0.1554   5.136995e+00   5.379295e+00
   4_bss:  0.1103 0.1554   5.136975e+00   5.379247e+00
   4_xyz:  0.1098 0.1562   5.137710e+00   5.382849e+00
   4_adp:  0.1089 0.1569   5.135132e+00   5.385011e+00
   4_occ:  0.1088 0.1569   5.135307e+00   5.385428e+00
   5_bss:  0.1088 0.1569   5.135408e+00   5.385505e+00
   5_xyz:  0.1066 0.1577   5.127557e+00   5.387595e+00
   5_adp:  0.1076 0.1568   5.128202e+00   5.383110e+00
   5_occ:  0.1075 0.1568   5.128304e+00   5.383401e+00
   5_bss:  0.1075 0.1569   5.128359e+00   5.383438e+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:  0.310  44.627   0.015  -1.824  -0.557  -0.000  -0.000  -0.000
   1_xyz:  0.310  44.627   0.015  -1.824  -0.557  -0.000  -0.000  -0.000
   1_adp:  0.310  44.627   0.015  -1.824  -0.557  -0.000  -0.000  -0.000
   1_occ:  0.310  44.627   0.015  -1.824  -0.557  -0.000  -0.000  -0.000
   2_bss:  0.332  57.847  -2.010  -2.583  -1.768  -0.000  -0.000  -0.000
   2_xyz:  0.332  57.847  -2.010  -2.583  -1.768  -0.000  -0.000  -0.000
   2_adp:  0.332  57.847  -2.010  -2.583  -1.768  -0.000  -0.000  -0.000
   2_occ:  0.332  57.847  -2.010  -2.583  -1.768  -0.000  -0.000  -0.000
   3_bss:  0.332  57.847  -2.281  -2.521  -1.764  -0.000  -0.000  -0.000
   3_xyz:  0.332  57.847  -2.281  -2.521  -1.764  -0.000  -0.000  -0.000
   3_adp:  0.332  57.847  -2.281  -2.521  -1.764  -0.000  -0.000  -0.000
   3_occ:  0.332  57.847  -2.281  -2.521  -1.764  -0.000  -0.000  -0.000
   4_bss:  0.332  57.847  -2.282  -2.354  -1.693  -0.000  -0.000  -0.000
   4_xyz:  0.332  57.847  -2.282  -2.354  -1.693  -0.000  -0.000  -0.000
   4_adp:  0.332  57.847  -2.282  -2.354  -1.693  -0.000  -0.000  -0.000
   4_occ:  0.332  57.847  -2.282  -2.354  -1.693  -0.000  -0.000  -0.000
   5_bss:  0.332  57.847  -2.108  -2.139  -1.499  -0.000  -0.000  -0.000
   5_xyz:  0.332  57.847  -2.108  -2.139  -1.499  -0.000  -0.000  -0.000
   5_adp:  0.332  57.847  -2.108  -2.139  -1.499  -0.000  -0.000  -0.000
   5_occ:  0.332  57.847  -2.108  -2.139  -1.499  -0.000  -0.000  -0.000
   5_bss:  0.332  57.801  -1.967  -1.967  -1.322  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.472 0.7217  0.8966    29425.436
   1_bss:  32.244 0.7335  0.8917    26518.325
   1_xyz:  18.858 0.8740  1.0038    10356.212
   1_adp:  19.432 0.8681  0.9986    10726.387
   1_occ:  19.388 0.8684  0.9988    10650.400
   2_bss:  19.280 0.8694  0.9531    10570.926
   2_xyz:  14.879 0.9077  0.9739     6966.554
   2_adp:  14.425 0.9115  0.9752     6708.230
   2_occ:  14.427 0.9115  0.9749     6715.669
   3_bss:  14.437 0.9114  0.9718     6713.030
   3_xyz:  13.974 0.9155  0.9723     6440.312
   3_adp:  13.793 0.9169  0.9692     6239.578
   3_occ:  13.800 0.9169  0.9692     6242.749
   4_bss:  13.801 0.9168  0.9718     6241.425
   4_xyz:  13.875 0.9162  0.9708     6284.430
   4_adp:  13.924 0.9158  0.9657     6296.753
   4_occ:  13.932 0.9157  0.9656     6302.658
   5_bss:  13.936 0.9157  0.9723     6303.660
   5_xyz:  13.959 0.9155  0.9720     6335.356
   5_adp:  13.843 0.9165  0.9677     6294.283
   5_occ:  13.848 0.9165  0.9676     6296.699
   5_bss:  13.849 0.9165  0.9716     6296.847
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6246e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6246e-01
   1_xyz:   1.082  0.008  0.068 14.869  0.004  4.115   6.6313e-02
   1_adp:   1.082  0.008  0.068 14.869  0.004  4.115   6.6313e-02
   1_occ:   1.082  0.008  0.068 14.869  0.004  4.115   6.6313e-02
   2_bss:   1.082  0.008  0.068 14.869  0.004  4.115   6.6313e-02
   2_xyz:   1.105  0.009  0.080 14.796  0.004  4.127   7.0857e-02
   2_adp:   1.105  0.009  0.080 14.796  0.004  4.127   7.0857e-02
   2_occ:   1.105  0.009  0.080 14.796  0.004  4.127   7.0857e-02
   3_bss:   1.105  0.009  0.080 14.796  0.004  4.127   7.0857e-02
   3_xyz:   1.063  0.009  0.080 14.781  0.004  4.130   6.7678e-02
   3_adp:   1.063  0.009  0.080 14.781  0.004  4.130   6.7678e-02
   3_occ:   1.063  0.009  0.080 14.781  0.004  4.130   6.7678e-02
   4_bss:   1.063  0.009  0.080 14.781  0.004  4.130   6.7678e-02
   4_xyz:   1.026  0.008  0.077 14.648  0.004  4.131   6.2627e-02
   4_adp:   1.026  0.008  0.077 14.648  0.004  4.131   6.2627e-02
   4_occ:   1.026  0.008  0.077 14.648  0.004  4.131   6.2627e-02
   5_bss:   1.026  0.008  0.077 14.648  0.004  4.131   6.2627e-02
   5_xyz:   1.098  0.010  0.082 14.841  0.004  4.132   7.1625e-02
   5_adp:   1.098  0.010  0.082 14.841  0.004  4.132   7.1625e-02
   5_occ:   1.098  0.010  0.082 14.841  0.004  4.132   7.1625e-02
   5_bss:   1.098  0.010  0.082 14.841  0.004  4.132   7.1625e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4176e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4176e-01
   1_xyz:   8.967  0.045  0.269 84.764  0.031  2.306   1.0345e-01
   1_adp:   8.967  0.045  0.269 84.764  0.031  2.306   1.0345e-01
   1_occ:   8.967  0.045  0.269 84.764  0.031  2.306   1.0345e-01
   2_bss:   8.967  0.045  0.269 84.764  0.031  2.306   1.0345e-01
   2_xyz:   7.178  0.060  0.244 83.983  0.041  2.301   5.8507e-02
   2_adp:   7.178  0.060  0.244 83.983  0.041  2.301   5.8507e-02
   2_occ:   7.178  0.060  0.244 83.983  0.041  2.301   5.8507e-02
   3_bss:   7.178  0.060  0.244 83.983  0.041  2.301   5.8507e-02
   3_xyz:   7.347  0.044  0.256 82.227  0.038  2.304   5.2094e-02
   3_adp:   7.347  0.044  0.256 82.227  0.038  2.304   5.2094e-02
   3_occ:   7.347  0.044  0.256 82.227  0.038  2.304   5.2094e-02
   4_bss:   7.347  0.044  0.256 82.227  0.038  2.304   5.2094e-02
   4_xyz:   7.141  0.041  0.240 83.435  0.038  2.338   4.3364e-02
   4_adp:   7.141  0.041  0.240 83.435  0.038  2.338   4.3364e-02
   4_occ:   7.141  0.041  0.240 83.435  0.038  2.338   4.3364e-02
   5_bss:   7.141  0.041  0.240 83.435  0.038  2.338   4.3364e-02
   5_xyz:   7.172  0.045  0.257 82.819  0.040  2.275   5.5286e-02
   5_adp:   7.172  0.045  0.257 82.819  0.040  2.275   5.5286e-02
   5_occ:   7.172  0.045  0.257 82.819  0.040  2.275   5.5286e-02
   5_bss:   7.172  0.045  0.257 82.819  0.040  2.275   5.5286e-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:  77.94   0.00  16.50  77.94   0.00  12.66  63.02   6.22  37.42
   1_occ:  77.94   0.00  16.50  77.94   0.00  12.66  63.02   6.22  37.42
   2_bss:  77.94   0.00  16.50  77.94   0.00  12.66  63.02   6.22  37.42
   2_xyz:  77.94   0.00  16.50  77.94   0.00  12.66  63.02   6.22  37.42
   2_adp:  68.93   0.00  16.53  68.93   0.00  12.67  63.10   4.51  37.54
   2_occ:  68.93   0.00  16.53  68.93   0.00  12.67  63.10   4.51  37.54
   3_bss:  68.93   0.00  16.53  68.93   0.00  12.67  63.10   4.51  37.54
   3_xyz:  68.93   0.00  16.53  68.93   0.00  12.67  63.10   4.51  37.54
   3_adp:  72.19   1.39  16.75  72.19   1.39  12.84  66.49   5.73  38.06
   3_occ:  72.19   1.39  16.75  72.19   1.39  12.84  66.49   5.73  38.06
   4_bss:  72.19   1.39  16.75  72.19   1.39  12.84  66.49   5.73  38.06
   4_xyz:  72.19   1.39  16.75  72.19   1.39  12.84  66.49   5.73  38.06
   4_adp:  83.05   0.67  16.88  83.05   0.67  12.84  72.23   6.08  38.92
   4_occ:  83.05   0.67  16.88  83.05   0.67  12.84  72.23   6.08  38.92
   5_bss:  83.05   0.67  16.88  83.05   0.67  12.84  72.23   6.08  38.92
   5_xyz:  83.05   0.67  16.88  83.05   0.67  12.84  72.23   6.08  38.92
   5_adp:  81.73   1.31  16.42  81.73   1.31  12.59  71.78   5.96  37.24
   5_occ:  81.73   1.31  16.42  81.73   1.31  12.59  71.78   5.96  37.24
   5_bss:  81.68   1.27  16.37  81.68   1.27  12.55  71.73   5.92  37.20
------------------------------------------------------------------------
 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:    1.369    0.018    0.289
   1_adp:    1.369    0.018    0.289
   1_occ:    1.369    0.018    0.289
   2_bss:    1.369    0.018    0.289
   2_xyz:    0.792    0.029    0.359
   2_adp:    0.792    0.029    0.359
   2_occ:    0.792    0.029    0.359
   3_bss:    0.792    0.029    0.359
   3_xyz:    0.829    0.047    0.380
   3_adp:    0.829    0.047    0.380
   3_occ:    0.829    0.047    0.380
   4_bss:    0.829    0.047    0.380
   4_xyz:    0.878    0.062    0.390
   4_adp:    0.878    0.062    0.390
   4_occ:    0.878    0.062    0.390
   5_bss:    0.878    0.062    0.390
   5_xyz:    0.909    0.078    0.395
   5_adp:    0.909    0.078    0.395
   5_occ:    0.909    0.078    0.395
   5_bss:    0.909    0.078    0.395
------------------------------------------------------------------------

CPU time actual refinement: 269.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1037/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_1037/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1037/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1037/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1037/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 269.27 
  Macro-tasks:
    bulk solvent and scale       = 31.07  
    individual site refinement   = 110.69 
    weights calculation          = 23.74  
    collect and process          = 5.41   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 170.99 
  Micro-tasks:
    mask                            = 1.00   
    f_calc                          = 85.54  
    alpha_beta                      = 6.71   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 94.27  
    fmodel                         = 5.61   
    r_factors                      = 0.12   
    phase_errors                   = 9.20   
    foms                           = 0.16   
    TOTAL for micro-tasks          = 203.58 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.810 micro seconds
Total CPU time: 4.68 minutes
from_scatterers_fft:    658 calls, 85.25 s
gradients_fft:          603 calls, 82.59 s

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

# Date 2008-01-16 Time 06:15:34 PST -0800 (1200492934.69 s)
Start R-work = 0.3204, R-free = 0.3228 (no bulk solvent and anisotropic scale)
Final R-work = 0.1312, R-free = 0.1760 (no bulk solvent and anisotropic scale)

Start R-work = 0.3082, R-free = 0.3117
Final R-work = 0.1075, R-free = 0.1569