# Date 2008-01-16 Time 06:05:40 PST -0800 (1200492340.49 s)
#phil __OFF__

Command line arguments: "../1005.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5670
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1005

-------------------------------------------------------------------------------
  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, 46.4607, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


================================== 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, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.98157
Completeness in resolution range: 0.959728
Completeness with d_max=infinity: 0.956868

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9816

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, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.98157
Completeness in resolution range: 0.959728
Completeness with d_max=infinity: 0.956868

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2408 [2136/2162]  1926   210   9.8%
  bin  2:  4.2408 -  3.3784 [2067/2087]  1857   210  10.2%
  bin  3:  3.3784 -  2.9549 [2032/2051]  1828   204  10.0%
  bin  4:  2.9549 -  2.6864 [2014/2044]  1814   200   9.9%
  bin  5:  2.6864 -  2.4948 [2017/2036]  1818   199   9.9%
  bin  6:  2.4948 -  2.3482 [1991/2016]  1784   207  10.4%
  bin  7:  2.3482 -  2.2310 [1973/2001]  1778   195   9.9%
  bin  8:  2.2310 -  2.1342 [1981/2017]  1783   198  10.0%
  bin  9:  2.1342 -  2.0522 [1959/2001]  1765   194   9.9%
  bin 10:  2.0522 -  1.9816 [1419/1996]  1277   142  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1005/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2188
        3.04 -     3.66: 4705
        3.66 -     4.28: 9067
        4.28 -     4.90: 12307
  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 204 " - " O   HOH Z 296 "  2.187 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.195 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.231 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28281 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_1005/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1005/model_refine_001.geo

CPU time processing inputs: 9.38


============================ 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 46.4607 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3436   r_free= 0.3432   ksol= 0.00   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.084070                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7303 0.99   1392  156 0.2962 0.2881      6.3684      6.3202|
|  2:  4.7303 -  3.7738 0.99   1338  146 0.2730 0.2711      6.4932      6.4443|
|  3:  3.7738 -  3.3024 0.99   1321  144 0.2929 0.2589      6.3608      6.4264|
|  4:  3.3024 -  3.0030 0.99   1307  153 0.3149 0.3501      6.2739      6.2941|
|  5:  3.0030 -  2.7892 0.99   1295  142 0.3560 0.3525      6.1521      6.1796|
|  6:  2.7892 -  2.6256 0.99   1293  142 0.3518 0.3561      6.0666      6.0297|
|  7:  2.6256 -  2.4948 0.99   1297  140 0.3730 0.3593      6.0667      6.0887|
|  8:  2.4948 -  2.3866 0.98   1253  144 0.3785 0.3692      6.0023      5.9699|
|  9:  2.3866 -  2.2950 0.98   1290  148 0.3761 0.3684      5.9502      5.9388|
| 10:  2.2950 -  2.2161 1.00   1279  138 0.3892 0.4191      5.9414      5.9629|
| 11:  2.2161 -  2.1470 0.98   1270  136 0.4042 0.4011      5.9244      5.9311|
| 12:  2.1470 -  2.0858 0.98   1251  145 0.4116 0.4149      5.8707      5.8994|
| 13:  2.0858 -  2.0310 1.00   1284  137 0.4030 0.4128      5.7613      5.6855|
| 14:  2.0310 -  1.9816 0.59    760   88 0.4198 0.4247      5.7446      5.7185|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7303  1392   156  0.79  26.01   0.86     0.82      42811.34|
|  2:  4.7303 -  3.7738  1338   146  0.84  22.79   0.97     0.91      49185.39|
|  3:  3.7738 -  3.3024  1321   144  0.78  27.95   0.99     0.94      51332.39|
|  4:  3.3024 -  3.0030  1307   153  0.75  31.55   0.98     0.92      47591.02|
|  5:  3.0030 -  2.7892  1295   142  0.68  37.48   0.97     0.87      41175.22|
|  6:  2.7892 -  2.6256  1293   142  0.67  37.79   0.99     0.87      35287.37|
|  7:  2.6256 -  2.4948  1297   140  0.68  37.19   0.99     0.87      31486.23|
|  8:  2.4948 -  2.3866  1253   144  0.67  38.20   0.99     0.88      28580.57|
|  9:  2.3866 -  2.2950  1290   148  0.67  38.63   1.01     0.88      26868.18|
| 10:  2.2950 -  2.2161  1279   138  0.65  40.07   1.03     0.88      25992.22|
| 11:  2.2161 -  2.1470  1270   136  0.63  41.63   1.04     0.88      25615.33|
| 12:  2.1470 -  2.0858  1251   145  0.63  42.07   1.01     0.87      23598.54|
| 13:  2.0858 -  2.0310  1284   137  0.60  44.22   1.01     0.85      20794.96|
| 14:  2.0310 -  1.9816   760    88  0.62  42.92   1.03     0.83      17131.35|
|alpha:            min =        0.82 max =            0.94 mean =         0.88|
|beta:             min =    17131.35 max =        51332.39 mean =     34072.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.87 mean =        35.98|
|phase err.(test): min =        0.00 max =           89.82 mean =        36.00|
|-----------------------------------------------------------------------------|

============================== 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 = 5.749359              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.002   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.855937              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.433   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      202 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1986 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1862 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2843 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4646 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4421 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5607 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6700 |
|-----------------------------------------------------------------------------|
|-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 |   4.111    4.900  1.806 |       0.167 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3436   r_free= 0.3432   ksol= 0.00   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.084070                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3316   r_free= 0.3318   ksol= 0.34   Bsol= 50.00   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.21,-1.44,-0.00,-0.00,-0.00); trace/3= -0.50                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.066675                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.052229              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.312   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.425431              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.257   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3316      final r-factor (work) = 0.1805          |
| start r-factor (free) = 0.3318      final r-factor (free) = 0.2048          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4981 = 5.05 * 0.50 * 6.0711 + 1.00 * 0.1618                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6742 = 5.05 * 0.50 * 5.7821 + 1.00 * 0.0678                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1805      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2048      final r-factor (free) = 0.2102          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4660 = 0.43 * 1.00 * 5.7821 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3276 = 0.43 * 1.00 * 5.4490 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.38   17.28    None  None   None       |
|    all(noH): 2823   0      0.00    75.38   17.28    None  None   None       |
|    Sol.    : 438    0      5.67    75.38   40.01    None  None   None       |
|    Mac.    : 2385   0      0.00    72.07   13.11    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 -   7.538:  445   |   5:    37.691 -  45.229:  119        |
|      1:     7.538 -  15.076: 1349   |   6:    45.229 -  52.767:   83        |
|      2:    15.076 -  22.615:  463   |   7:    52.767 -  60.305:   55        |
|      3:    22.615 -  30.153:  152   |   8:    60.305 -  67.844:   41        |
|      4:    30.153 -  37.691:  103   |   9:    67.844 -  75.382:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1648 r_free = 0.2102             target_work(ml) = 5.463         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1644 r_free = 0.2104             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1644   r_free= 0.2104   ksol= 0.34   Bsol= 50.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.21,-1.44,-0.00,-0.00,-0.00); trace/3= -0.50                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.461755                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1628   r_free= 0.2079   ksol= 0.33   Bsol= 54.22   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.36,-1.92,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.457830                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.327843              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.152832              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.211  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1628      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.2079      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4390 = 2.33 * 0.50 * 5.4740 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2877 = 2.33 * 0.50 * 5.3569 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8281 = 0.15 * 1.00 * 5.3569 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8079 = 0.15 * 1.00 * 5.2397 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    73.21   16.92    None  None   None       |
|    all(noH): 2823   0      2.09    73.21   16.92    None  None   None       |
|    Sol.    : 438    0      5.92    73.21   38.19    None  None   None       |
|    Mac.    : 2385   0      2.09    73.07   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.092 -   9.204:  711   |   5:    37.652 -  44.764:  104        |
|      1:     9.204 -  16.316: 1246   |   6:    44.764 -  51.876:   83        |
|      2:    16.316 -  23.428:  348   |   7:    51.876 -  58.988:   53        |
|      3:    23.428 -  30.540:  129   |   8:    58.988 -  66.100:   25        |
|      4:    30.540 -  37.652:  111   |   9:    66.100 -  73.212:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1641             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1641             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1641   ksol= 0.33   Bsol= 54.22   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.36,-1.92,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.211243                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1634   ksol= 0.33   Bsol= 54.22   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.72,-1.76,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.209843                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.346525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.638  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.322540              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.591  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8185 = 3.35 * 0.50 * 5.2387 + 1.00 * 0.0527                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7080 = 3.35 * 0.50 * 5.1616 + 1.00 * 0.0712                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6718 = 0.32 * 1.00 * 5.1616 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6597 = 0.32 * 1.00 * 5.1217 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.41    77.38   17.00    None  None   None       |
|    all(noH): 2823   0      1.41    77.38   17.00    None  None   None       |
|    Sol.    : 438    0      5.08    74.76   38.74    None  None   None       |
|    Mac.    : 2385   0      1.41    77.38   13.01    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:     1.408 -   9.005:  716   |   5:    39.394 -  46.992:  112        |
|      1:     9.005 -  16.602: 1262   |   6:    46.992 -  54.589:   84        |
|      2:    16.602 -  24.200:  336   |   7:    54.589 -  62.186:   49        |
|      3:    24.200 -  31.797:  129   |   8:    62.186 -  69.784:   16        |
|      4:    31.797 -  39.394:  109   |   9:    69.784 -  77.381:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1544             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1544             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1544   ksol= 0.33   Bsol= 54.22   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.72,-1.76,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.120177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1544   ksol= 0.33   Bsol= 54.22   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.72,-1.65,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.120103                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.128326              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.625  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206216              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.194  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0822 = 3.13 * 0.50 * 5.1216 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0700 = 3.13 * 0.50 * 5.1139 + 1.00 * 0.0710                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0623 = 0.21 * 1.00 * 5.1139 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0620 = 0.21 * 1.00 * 5.1144 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    78.37   16.74    None  None   None       |
|    all(noH): 2823   0      1.71    78.37   16.74    None  None   None       |
|    Sol.    : 438    0      6.00    75.70   37.80    None  None   None       |
|    Mac.    : 2385   0      1.71    78.37   12.87    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:     1.709 -   9.375:  842   |   5:    40.040 -  47.706:   97        |
|      1:     9.375 -  17.041: 1177   |   6:    47.706 -  55.372:   85        |
|      2:    17.041 -  24.707:  314   |   7:    55.372 -  63.038:   39        |
|      3:    24.707 -  32.373:  129   |   8:    63.038 -  70.704:   12        |
|      4:    32.373 -  40.040:  121   |   9:    70.704 -  78.370:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1547             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1071 r_free = 0.1547             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1547   ksol= 0.33   Bsol= 54.22   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.72,-1.65,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114321                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1548   ksol= 0.33   Bsol= 54.22   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.62,-1.48,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114359                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.621432              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.911  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.121659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.981  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2177 = 1.62 * 0.50 * 5.1148 + 1.00 * 0.0710                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2116 = 1.62 * 0.50 * 5.1275 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1102      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6311 = 0.12 * 1.00 * 5.1275 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6314 = 0.12 * 1.00 * 5.1375 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.99    76.10   16.37    None  None   None       |
|    all(noH): 2823   0      1.99    76.10   16.37    None  None   None       |
|    Sol.    : 438    0      6.57    75.70   36.25    None  None   None       |
|    Mac.    : 2385   0      1.99    76.10   12.71    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:     1.990 -   9.401:  852   |   5:    39.045 -  46.455:   93        |
|      1:     9.401 -  16.812: 1171   |   6:    46.455 -  53.866:   83        |
|      2:    16.812 -  24.223:  313   |   7:    53.866 -  61.277:   32        |
|      3:    24.223 -  31.634:  131   |   8:    61.277 -  68.688:    8        |
|      4:    31.634 -  39.045:  132   |   9:    68.688 -  76.099:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1559             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1559             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1559   ksol= 0.33   Bsol= 54.22   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.62,-1.48,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138152                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7303 0.99   1392  156 0.1013 0.1278      5.4031      5.5466|
|  2:  4.7303 -  3.7738 0.99   1338  146 0.0895 0.1134      5.4705        5.64|
|  3:  3.7738 -  3.3024 0.99   1321  144 0.1077 0.1532      5.4865      5.8739|
|  4:  3.3024 -  3.0030 0.99   1307  153 0.1186 0.1565      5.4523      5.5754|
|  5:  3.0030 -  2.7892 0.99   1295  142 0.1350 0.1777      5.3321      5.5725|
|  6:  2.7892 -  2.6256 0.99   1293  142 0.1202 0.1763      5.2013      5.4362|
|  7:  2.6256 -  2.4948 0.99   1297  140 0.1252 0.1554      5.1661      5.3302|
|  8:  2.4948 -  2.3866 0.98   1253  144 0.1141 0.1771      5.0213      5.3537|
|  9:  2.3866 -  2.2950 0.98   1290  148 0.1131 0.1673      5.0056      5.2625|
| 10:  2.2950 -  2.2161 1.00   1279  138 0.1110 0.1735      4.9258      5.2256|
| 11:  2.2161 -  2.1470 0.98   1270  136 0.1118 0.1759      4.9397      5.2491|
| 12:  2.1470 -  2.0858 0.98   1251  145 0.1073 0.1575      4.8543      5.1162|
| 13:  2.0858 -  2.0310 1.00   1284  137 0.1130 0.1754      4.7679      5.0657|
| 14:  2.0310 -  1.9816 0.59    760   88 0.1039 0.1532      4.6361      4.8539|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7303  1392   156  0.94   9.09   0.98     0.95       7194.33|
|  2:  4.7303 -  3.7738  1338   146  0.95   8.12   1.01     1.00       9377.47|
|  3:  3.7738 -  3.3024  1321   144  0.93  11.35   1.01     1.01      10435.15|
|  4:  3.3024 -  3.0030  1307   153  0.92  13.57   1.00     0.97      10303.54|
|  5:  3.0030 -  2.7892  1295   142  0.90  16.04   0.99     0.96       8305.58|
|  6:  2.7892 -  2.6256  1293   142  0.90  15.52   0.98     0.96       6881.38|
|  7:  2.6256 -  2.4948  1297   140  0.91  15.12   0.99     0.97       6107.68|
|  8:  2.4948 -  2.3866  1253   144  0.91  14.45   0.98     0.96       4695.50|
|  9:  2.3866 -  2.2950  1290   148  0.92  14.49   1.00     0.97       4615.33|
| 10:  2.2950 -  2.2161  1279   138  0.91  14.75   1.00     0.97       4019.17|
| 11:  2.2161 -  2.1470  1270   136  0.90  15.78   0.99     0.94       4206.13|
| 12:  2.1470 -  2.0858  1251   145  0.92  14.50   1.01     1.01       3780.84|
| 13:  2.0858 -  2.0310  1284   137  0.91  15.46   1.00     0.99       3148.39|
| 14:  2.0310 -  1.9816   760    88  0.92  13.89   0.98     0.94       2352.13|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2352.13 max =        10435.15 mean =      6254.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.67|
|phase err.(test): min =        0.00 max =           89.85 mean =        13.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1559   ksol= 0.33   Bsol= 54.15   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.53,-1.36,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138163                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1559   ksol= 0.33   Bsol= 54.15   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.53,-1.36,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138163                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7303 0.99   1392  156 0.1013 0.1278      5.4033      5.5467|
|  2:  4.7303 -  3.7738 0.99   1338  146 0.0895 0.1134      5.4705      5.6399|
|  3:  3.7738 -  3.3024 0.99   1321  144 0.1078 0.1532      5.4864      5.8737|
|  4:  3.3024 -  3.0030 0.99   1307  153 0.1186 0.1565      5.4523      5.5754|
|  5:  3.0030 -  2.7892 0.99   1295  142 0.1350 0.1777      5.3322      5.5727|
|  6:  2.7892 -  2.6256 0.99   1293  142 0.1202 0.1762      5.2013      5.4357|
|  7:  2.6256 -  2.4948 0.99   1297  140 0.1252 0.1554      5.1659      5.3301|
|  8:  2.4948 -  2.3866 0.98   1253  144 0.1140 0.1772      5.0212      5.3537|
|  9:  2.3866 -  2.2950 0.98   1290  148 0.1131 0.1673      5.0056      5.2623|
| 10:  2.2950 -  2.2161 1.00   1279  138 0.1110 0.1735      4.9258       5.226|
| 11:  2.2161 -  2.1470 0.98   1270  136 0.1118 0.1760      4.9398      5.2494|
| 12:  2.1470 -  2.0858 0.98   1251  145 0.1073 0.1576      4.8545      5.1165|
| 13:  2.0858 -  2.0310 1.00   1284  137 0.1131 0.1755      4.7679      5.0658|
| 14:  2.0310 -  1.9816 0.59    760   88 0.1039 0.1533      4.6358      4.8534|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7303  1392   156  0.94   9.09   0.98     0.95       7195.44|
|  2:  4.7303 -  3.7738  1338   146  0.95   8.12   1.01     1.00       9376.57|
|  3:  3.7738 -  3.3024  1321   144  0.93  11.35   1.02     1.01      10432.45|
|  4:  3.3024 -  3.0030  1307   153  0.92  13.58   1.00     0.97      10304.36|
|  5:  3.0030 -  2.7892  1295   142  0.90  16.04   0.99     0.96       8304.55|
|  6:  2.7892 -  2.6256  1293   142  0.90  15.52   0.98     0.96       6880.29|
|  7:  2.6256 -  2.4948  1297   140  0.91  15.12   0.99     0.97       6105.85|
|  8:  2.4948 -  2.3866  1253   144  0.91  14.45   0.99     0.96       4694.91|
|  9:  2.3866 -  2.2950  1290   148  0.92  14.49   1.00     0.97       4614.85|
| 10:  2.2950 -  2.2161  1279   138  0.91  14.75   1.00     0.98       4019.72|
| 11:  2.2161 -  2.1470  1270   136  0.90  15.79   0.99     0.94       4207.85|
| 12:  2.1470 -  2.0858  1251   145  0.92  14.51   1.01     1.01       3783.21|
| 13:  2.0858 -  2.0310  1284   137  0.91  15.46   1.00     0.99       3148.34|
| 14:  2.0310 -  1.9816   760    88  0.92  13.89   0.98     0.95       2350.33|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2350.33 max =        10432.45 mean =      6254.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.67|
|phase err.(test): min =        0.00 max =           89.85 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.92    76.03   16.29    None  None   None       |
|    all(noH): 2823   0      1.92    76.03   16.29    None  None   None       |
|    Sol.    : 438    0      6.49    75.62   36.18    None  None   None       |
|    Mac.    : 2385   0      1.92    76.03   12.64    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:     1.919 -   9.329:  852   |   5:    38.973 -  46.384:   93        |
|      1:     9.329 -  16.740: 1171   |   6:    46.384 -  53.795:   83        |
|      2:    16.740 -  24.151:  313   |   7:    53.795 -  61.206:   32        |
|      3:    24.151 -  31.562:  131   |   8:    61.206 -  68.616:    8        |
|      4:    31.562 -  38.973:  132   |   9:    68.616 -  76.027:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 298         
Filter by distance & map next to the model:
   mapped sites are within: 0.529 - 4.631
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 291 from: 298
   mapped sites are within: 0.707 - 4.631

peak=    5.638 closest distance to " CG  PRO A  54 " =    1.335
peak=    5.504 closest distance to " O   HOH Z 126 " =    1.960
peak=    5.502 closest distance to " NH2 ARG A  56 " =    2.141
peak=    5.271 closest distance to " NE2 GLN A  11 " =    1.201
peak=    5.259 closest distance to " CB  GLN A 223 " =    1.393
peak=    5.218 closest distance to " O   HOH Z 232 " =    2.340
peak=    5.086 closest distance to " CG  PRO A 213 " =    1.235
peak=    4.945 closest distance to " CB  SER A  63 " =    1.226
peak=    4.765 closest distance to " CB  PRO A  54 " =    0.978
peak=    4.723 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.683 closest distance to " C   PRO A 198 " =    1.532
peak=    4.663 closest distance to " O   HOH Z 236 " =    2.001
peak=    4.639 closest distance to " CB  ASN A 187 " =    1.210
peak=    4.610 closest distance to " CB  GLN A 183 " =    1.144
peak=    4.592 closest distance to " O   HOH Z 298 " =    1.974
peak=    4.540 closest distance to " CB  LEU A 228 " =    1.063
peak=    4.520 closest distance to " O   HOH Z  78 " =    1.764
peak=    4.510 closest distance to " O   HOH Z 369 " =    2.075
peak=    4.495 closest distance to " ND2 ASN A 187 " =    1.498
peak=    4.426 closest distance to " CB  GLU A 128 " =    0.980
peak=    4.388 closest distance to " CB  ASN A 148 " =    1.391
peak=    4.374 closest distance to " CG  PRO A 243 " =    1.085
peak=    4.373 closest distance to " O   HOH Z 144 " =    1.738
peak=    4.360 closest distance to " O   HOH Z  15 " =    2.256
peak=    4.325 closest distance to " CB  ARG A  79 " =    1.393
peak=    4.309 closest distance to " O   HOH Z 193 " =    1.881
peak=    4.306 closest distance to " CB  GLU A 152 " =    1.205
peak=    4.278 closest distance to " CB  SER A 216 " =    0.796
peak=    4.278 closest distance to " O   HOH Z 234 " =    3.755
peak=    4.256 closest distance to " CB  ARG A 190 " =    1.575
peak=    4.252 closest distance to " CG  PRO A  90 " =    1.105
peak=    4.251 closest distance to " O   HOH Z 303 " =    2.150
peak=    4.237 closest distance to " O   HOH Z 132 " =    2.469
peak=    4.232 closest distance to " CG2 VAL A 257 " =    1.024
peak=    4.206 closest distance to " CD  ARG A 159 " =    0.768
peak=    4.181 closest distance to " O   HOH Z  78 " =    2.108
peak=    4.159 closest distance to " CA  TYR A  30 " =    0.964
peak=    4.156 closest distance to " CG  PRO A 198 " =    1.303
peak=    4.058 closest distance to " O   HOH Z 368 " =    1.872
peak=    4.045 closest distance to " O   HOH Z 272 " =    1.853
peak=    4.039 closest distance to " CA  ASN A 215 " =    1.180
peak=    4.032 closest distance to " O   HOH Z 250 " =    1.509
peak=    4.026 closest distance to " CZ  PHE A 218 " =    1.036
peak=    4.010 closest distance to " CB  ASN A  39 " =    0.909
peak=    4.007 closest distance to " O   HOH Z 427 " =    2.885
peak=    3.996 closest distance to " O   HOH Z 158 " =    3.034
peak=    3.996 closest distance to " O   HOH Z  21 " =    1.728
peak=    3.991 closest distance to " CB  VAL A 265 " =    1.281
peak=    3.966 closest distance to " O   HOH Z   1 " =    2.015
peak=    3.959 closest distance to " CB  TRP A 266 " =    0.929
peak=    3.946 closest distance to " O   HOH Z 261 " =    2.181
peak=    3.944 closest distance to " O   HOH Z  40 " =    1.959
peak=    3.943 closest distance to " OD1 ASN A  69 " =    2.674
peak=    3.939 closest distance to " CB  SER A 212 " =    1.194
peak=    3.936 closest distance to " O   HOH Z 214 " =    2.028
peak=    3.912 closest distance to " O   HOH Z 265 " =    2.450
peak=    3.909 closest distance to " CA  SER A  87 " =    0.990
peak=    3.907 closest distance to " O   HOH Z 346 " =    1.684
peak=    3.893 closest distance to " ND1 HIS A  86 " =    1.661
peak=    3.890 closest distance to " CD  ARG A  66 " =    2.180
peak=    3.879 closest distance to " O   HOH Z 219 " =    2.196
peak=    3.878 closest distance to " CB  ASN A 142 " =    0.908
peak=    3.877 closest distance to " CB  ALA A  34 " =    1.035
peak=    3.877 closest distance to " O   HOH Z  68 " =    2.098
peak=    3.876 closest distance to " NH1AARG A 145 " =    1.191
peak=    3.872 closest distance to " O   HOH Z 193 " =    1.749
peak=    3.862 closest distance to " O   HOH Z  10 " =    1.884
peak=    3.861 closest distance to " CA  THR A 264 " =    0.868
peak=    3.850 closest distance to " O   HOH Z 209 " =    2.310
peak=    3.827 closest distance to " O   HOH Z 133 " =    1.690
peak=    3.824 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.817 closest distance to " O   HOH Z  61 " =    1.625
peak=    3.805 closest distance to " CB  SER A   3 " =    1.404
peak=    3.801 closest distance to " O   HOH Z   9 " =    2.025
peak=    3.771 closest distance to " O   HOH Z 389 " =    1.948
peak=    3.765 closest distance to " O   HOH Z 344 " =    3.161
peak=    3.762 closest distance to " OD2 ASP A 286 " =    2.889
peak=    3.755 closest distance to " N   PHE A 130 " =    1.231
peak=    3.749 closest distance to " O   HOH Z 419 " =    2.038
peak=    3.745 closest distance to " O   HOH Z 403 " =    1.677
peak=    3.734 closest distance to " O   HOH Z 217 " =    3.135
peak=    3.717 closest distance to " CB  MET A  40 " =    0.807
peak=    3.711 closest distance to " CG1 ILE A  33 " =    1.270
peak=    3.706 closest distance to " CD2 LEU A 255 " =    1.603
peak=    3.702 closest distance to " O   HOH Z 316 " =    3.062
peak=    3.687 closest distance to " CD1 LEU A 300 " =    1.194
peak=    3.683 closest distance to " CB  ASP A 140 " =    0.845
peak=    3.672 closest distance to " O   HOH Z 189 " =    2.417
peak=    3.669 closest distance to " O   SER A  87 " =    2.167
peak=    3.666 closest distance to " O   ASN A 209 " =    1.325
peak=    3.650 closest distance to " CA  ALA A 233 " =    1.273
peak=    3.642 closest distance to " O   HOH Z 213 " =    1.870
peak=    3.639 closest distance to " O   HOH Z 188 " =    2.081
peak=    3.637 closest distance to " CB  LEU A 143 " =    1.115
peak=    3.636 closest distance to " O   HOH Z 423 " =    1.561
peak=    3.625 closest distance to " O   HOH Z 133 " =    2.378
peak=    3.623 closest distance to " CD  ARG A 219 " =    1.091
peak=    3.617 closest distance to " CG  LEU A 167 " =    1.225
peak=    3.611 closest distance to " O   HOH Z 327 " =    1.803
peak=    3.611 closest distance to " CZ  PHE A 208 " =    1.116
peak=    3.608 closest distance to " O   HOH Z 425 " =    2.083
peak=    3.596 closest distance to " NH2 ARG A 156 " =    1.244
peak=    3.596 closest distance to " CA  ALA A  21 " =    1.186
peak=    3.592 closest distance to " CG2 THR A 221 " =    0.961
peak=    3.571 closest distance to " CD BLYS A 290 " =    1.098
peak=    3.570 closest distance to " O   HOH Z 261 " =    2.178
peak=    3.566 closest distance to " O   HOH Z 371 " =    1.764
peak=    3.564 closest distance to " O   HOH Z 411 " =    3.814
peak=    3.564 closest distance to " O   HOH Z 386 " =    3.105
peak=    3.560 closest distance to " OD1BASN A 224 " =    2.285
peak=    3.556 closest distance to " NH2BARG A 145 " =    2.005
peak=    3.547 closest distance to " CD1 ILE A 106 " =    0.773
peak=    3.546 closest distance to " CD  LYS A 166 " =    1.234
peak=    3.543 closest distance to " N   ARG A 156 " =    1.343
peak=    3.540 closest distance to " O   HOH Z 128 " =    2.151
peak=    3.540 closest distance to " O   HOH Z 368 " =    3.544
peak=    3.531 closest distance to " O   HOH Z   1 " =    1.816
peak=    3.522 closest distance to " O   HOH Z 180 " =    2.075
peak=    3.521 closest distance to " CB  GLU A  46 " =    0.934
peak=    3.515 closest distance to " CD2 TRP A 179 " =    1.295
peak=    3.509 closest distance to " O   HOH Z 402 " =    1.497
peak=    3.507 closest distance to " CG  ARG A 159 " =    0.876
peak=    3.505 closest distance to " CB  ALA A   1 " =    4.631
peak=    3.495 closest distance to " O   HOH Z 437 " =    1.610
peak=    3.493 closest distance to " O   HOH Z 291 " =    1.611
peak=    3.479 closest distance to " CA  THR A 221 " =    0.965
peak=    3.466 closest distance to " O   HOH Z 147 " =    1.808
peak=    3.466 closest distance to " O   HOH Z 207 " =    1.763
peak=    3.462 closest distance to " O   HOH Z  61 " =    1.522
peak=    3.458 closest distance to " O   HOH Z 193 " =    2.016
peak=    3.445 closest distance to " O   HOH Z 248 " =    1.700
peak=    3.445 closest distance to " O   HOH Z 108 " =    2.292
peak=    3.445 closest distance to " O   HOH Z 305 " =    3.604
peak=    3.441 closest distance to " O   HOH Z 273 " =    2.742
peak=    3.438 closest distance to " CB  SER A 210 " =    0.708
peak=    3.437 closest distance to " CB  TRP A 179 " =    1.434
peak=    3.435 closest distance to " CA  TYR A  30 " =    1.062
peak=    3.432 closest distance to " O   HOH Z 329 " =    3.751
peak=    3.432 closest distance to " CD  ARG A 269 " =    0.939
peak=    3.431 closest distance to " NE2 HIS A 207 " =    1.384
peak=    3.431 closest distance to " CA  GLN A 223 " =    1.013
peak=    3.423 closest distance to " O   HOH Z 371 " =    2.868
peak=    3.423 closest distance to " O   HOH Z  88 " =    3.412
peak=    3.423 closest distance to " CB  ILE A 120 " =    1.165
peak=    3.418 closest distance to " OG  SER A  97 " =    3.549
peak=    3.417 closest distance to " O   HOH Z 353 " =    2.705
peak=    3.417 closest distance to " N   ASN A  39 " =    1.251
peak=    3.414 closest distance to " O   HOH Z 280 " =    3.078
peak=    3.413 closest distance to " O   HOH Z 245 " =    1.312
peak=    3.401 closest distance to " O   HOH Z 234 " =    1.716
peak=    3.399 closest distance to " CG1 VAL A 153 " =    0.889
peak=    3.399 closest distance to " CA  MET A  40 " =    1.114
peak=    3.396 closest distance to " CA  ILE A 234 " =    0.956
peak=    3.395 closest distance to " CB  ALA A 291 " =    1.288
peak=    3.389 closest distance to " CB  ALA A 248 " =    0.965
peak=    3.378 closest distance to " O   HOH Z 203 " =    1.893
peak=    3.376 closest distance to " CG1 ILE A 151 " =    1.028
peak=    3.376 closest distance to " CB  VAL A 202 " =    1.618
peak=    3.376 closest distance to " CB  ASN A 110 " =    1.081
peak=    3.371 closest distance to " CA  ALA A  51 " =    0.875
peak=    3.371 closest distance to " O   HOH Z 128 " =    2.011
peak=    3.362 closest distance to " NH1 ARG A 138 " =    1.111
peak=    3.361 closest distance to " CB  ARG A 139 " =    0.949
peak=    3.361 closest distance to " O   HOH Z 286 " =    2.280
peak=    3.361 closest distance to " CA  ALA A  84 " =    1.457
peak=    3.359 closest distance to " CZ  PHE A 192 " =    0.865
peak=    3.357 closest distance to " O   HOH Z 285 " =    2.846
peak=    3.356 closest distance to " O   HOH Z 213 " =    2.538
peak=    3.356 closest distance to " CB  ASN A 224 " =    1.061
peak=    3.354 closest distance to " O   HOH Z 407 " =    2.267
peak=    3.352 closest distance to " O   HOH Z 426 " =    1.830
peak=    3.350 closest distance to " CB  GLU A 236 " =    0.980
peak=    3.350 closest distance to " CG1BVAL A  72 " =    1.597
peak=    3.350 closest distance to " N   ASN A 127 " =    1.271
peak=    3.349 closest distance to " CB  TYR A 116 " =    0.838
peak=    3.348 closest distance to " O   HOH Z 116 " =    2.902
peak=    3.346 closest distance to " O   HOH Z  64 " =    2.253
peak=    3.339 closest distance to " O   HOH Z 148 " =    3.299
peak=    3.336 closest distance to " CB  MET A  47 " =    1.019
peak=    3.335 closest distance to " CB  SER A  62 " =    1.145
peak=    3.333 closest distance to " CB  THR A 157 " =    1.128
peak=    3.332 closest distance to " O   HOH Z  49 " =    2.140
peak=    3.326 closest distance to " CB  GLU A 277 " =    3.578
peak=    3.323 closest distance to " N   SER A 134 " =    1.325
peak=    3.320 closest distance to " CG  LYS A  76 " =    0.903
peak=    3.318 closest distance to " CB  HIS A 108 " =    0.755
peak=    3.316 closest distance to " CA  LYS A 290 " =    1.303
peak=    3.316 closest distance to " O   THR A 220 " =    1.350
peak=    3.314 closest distance to " O  BHOH Z 338 " =    2.382
peak=    3.313 closest distance to " CA  ALA A 291 " =    0.944
peak=    3.312 closest distance to " CG  MET A 113 " =    1.257
peak=    3.309 closest distance to " CB  ASP A 132 " =    3.975
peak=    3.306 closest distance to " OG  SER A  22 " =    2.771
peak=    3.306 closest distance to " O   HOH Z 313 " =    1.946
peak=    3.305 closest distance to " CA  ASN A 217 " =    1.277
peak=    3.305 closest distance to " CA  ALA A 154 " =    0.939
peak=    3.303 closest distance to " O   HOH Z 227 " =    2.084
peak=    3.300 closest distance to " O   HOH Z   3 " =    1.892
peak=    3.300 closest distance to " CD  PRO A 243 " =    1.567
peak=    3.300 closest distance to " CA  ARG A 195 " =    1.267
peak=    3.291 closest distance to " O   HOH Z 295 " =    1.549
peak=    3.289 closest distance to " O   HOH Z 282 " =    1.943
peak=    3.288 closest distance to " CE1 TYR A 186 " =    1.414
peak=    3.286 closest distance to " CB  ALA A 184 " =    0.877
peak=    3.283 closest distance to " N   SER A 135 " =    1.237
peak=    3.283 closest distance to " OG  SER A 206 " =    1.216
peak=    3.278 closest distance to " CG2 ILE A 120 " =    1.129
peak=    3.275 closest distance to " O   HOH Z 345 " =    1.764
peak=    3.267 closest distance to " O   HOH Z 302 " =    1.898
peak=    3.266 closest distance to " O   HOH Z 406 " =    1.683
peak=    3.265 closest distance to " CA  ALA A 158 " =    1.161
peak=    3.260 closest distance to " CG AARG A 275 " =    1.211
peak=    3.256 closest distance to " O   HOH Z 128 " =    2.188
peak=    3.255 closest distance to " O   PHE A 192 " =    1.387
peak=    3.255 closest distance to " CB  GLN A  88 " =    1.255
peak=    3.251 closest distance to " N   SER A 146 " =    1.634
peak=    3.246 closest distance to " O   HOH Z 411 " =    1.848
peak=    3.244 closest distance to " O   THR A 251 " =    1.144
peak=    3.240 closest distance to " NE2 GLN A  73 " =    3.775
peak=    3.235 closest distance to " CB  LYS A 117 " =    1.229
peak=    3.233 closest distance to " CG  GLN A 278 " =    1.305
peak=    3.229 closest distance to " CG  GLN A 144 " =    0.939
peak=    3.226 closest distance to " O   HOH Z 294 " =    1.514
peak=    3.224 closest distance to " N   VAL A 126 " =    1.352
peak=    3.223 closest distance to " O   HOH Z 409 " =    2.631
peak=    3.223 closest distance to " O   HOH Z 425 " =    1.265
peak=    3.220 closest distance to " CZ3 TRP A 123 " =    1.335
peak=    3.219 closest distance to " O   HOH Z  44 " =    3.054
peak=    3.214 closest distance to " N   GLN A 278 " =    0.981
peak=    3.213 closest distance to " NH2BARG A 190 " =    1.610
peak=    3.208 closest distance to " O   HOH Z 435 " =    1.961
peak=    3.206 closest distance to " CB  ILE A 234 " =    1.033
peak=    3.205 closest distance to " C   GLN A  88 " =    1.573
peak=    3.202 closest distance to " CE BLYS A 290 " =    1.201
peak=    3.196 closest distance to " CB  ALA A 114 " =    1.131
peak=    3.187 closest distance to " O   HOH Z 332 " =    1.521
peak=    3.181 closest distance to " O   HOH Z  93 " =    2.639
peak=    3.180 closest distance to " O   HOH Z 386 " =    2.858
peak=    3.176 closest distance to " CB  LYS A 193 " =    1.048
peak=    3.173 closest distance to " O   MET A 105 " =    1.690
peak=    3.165 closest distance to " O   HOH Z 271 " =    2.428
peak=    3.164 closest distance to " CB  ALA A 248 " =    1.319
peak=    3.163 closest distance to " O   HOH Z 175 " =    2.146
peak=    3.162 closest distance to " CA  GLY A 267 " =    1.175
peak=    3.161 closest distance to " O   HOH Z 423 " =    2.634
peak=    3.154 closest distance to " CB  TRP A 150 " =    1.468
peak=    3.154 closest distance to " O   HOH Z 172 " =    3.183
peak=    3.154 closest distance to " ND1 HIS A  81 " =    1.661
peak=    3.154 closest distance to " O   HOH Z 379 " =    3.516
peak=    3.153 closest distance to " O   HOH Z 152 " =    2.140
peak=    3.153 closest distance to " CB  ALA A   9 " =    1.587
peak=    3.152 closest distance to " O   HOH Z 211 " =    2.754
peak=    3.151 closest distance to " O   HOH Z 359 " =    4.089
peak=    3.149 closest distance to " O   HOH Z  87 " =    2.140
peak=    3.148 closest distance to " OG1 THR A 294 " =    1.685
peak=    3.147 closest distance to " O   HOH Z 153 " =    1.651
peak=    3.145 closest distance to " O   HOH Z  63 " =    1.399
peak=    3.145 closest distance to " ND2 ASN A 249 " =    0.902
peak=    3.144 closest distance to " OD1 ASN A 217 " =    1.611
peak=    3.143 closest distance to " O   HOH Z 216 " =    2.746
peak=    3.142 closest distance to " CA  TYR A 186 " =    1.571
peak=    3.136 closest distance to " O   HOH Z  49 " =    2.526
peak=    3.135 closest distance to " CB  GLN A 103 " =    0.840
peak=    3.135 closest distance to " CA  ARG A  36 " =    1.093
peak=    3.132 closest distance to " CB  ARG A 138 " =    1.056
peak=    3.132 closest distance to " NH1BARG A 145 " =    1.130
peak=    3.128 closest distance to " N   ASN A 252 " =    1.472
peak=    3.126 closest distance to " O   HOH Z 175 " =    3.568
peak=    3.125 closest distance to " O   HOH Z  97 " =    1.949
peak=    3.125 closest distance to " O   TYR A 116 " =    1.312
peak=    3.119 closest distance to " CG2 ILE A 151 " =    0.711
peak=    3.117 closest distance to " O   HOH Z 345 " =    3.533
peak=    3.111 closest distance to " CG BARG A 102 " =    1.879
peak=    3.107 closest distance to " CB  VAL A 265 " =    1.963
peak=    3.107 closest distance to " O   HOH Z 325 " =    3.853
peak=    3.102 closest distance to " CG2 THR A 220 " =    0.977
peak=    3.100 closest distance to " O   HOH Z 263 " =    1.695
peak=    3.093 closest distance to " CD2 HIS A  81 " =    1.242
peak=    3.092 closest distance to " CA  TYR A 116 " =    1.384
peak=    3.090 closest distance to " O   HOH Z 391 " =    2.929
peak=    3.088 closest distance to " CG  GLN A  89 " =    1.509
peak=    3.086 closest distance to " O   HOH Z 163 " =    1.783
peak=    3.084 closest distance to " CG2 ILE A 106 " =    0.878
peak=    3.081 closest distance to " CG BARG A 275 " =    1.440
peak=    3.080 closest distance to " CB  ALA A 291 " =    0.807
peak=    3.072 closest distance to " O   HOH Z 433 " =    1.822
peak=    3.066 closest distance to " O   HOH Z 281 " =    3.933
peak=    3.045 closest distance to " O   ALA A   1 " =    1.534
peak=    3.028 closest distance to " N   TYR A  15 " =    0.707
peak=    3.026 closest distance to " CB  ASN A 215 " =    1.085
peak=    3.026 closest distance to " O   HOH Z 409 " =    3.044

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.186 - 5.613
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 183 from: 188
   mapped sites are within: 0.717 - 5.613

peak=   -4.636 closest distance to " O   HOH Z 290 " =    1.107
peak=   -4.623 closest distance to " CB  PRO A 243 " =    2.615
peak=   -4.528 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.358 closest distance to " O   HOH Z 266 " =    4.921
peak=   -4.319 closest distance to " O   HOH Z 435 " =    2.809
peak=   -4.293 closest distance to " O   HOH Z 389 " =    1.929
peak=   -4.176 closest distance to " O   VAL A  67 " =    2.546
peak=   -4.165 closest distance to " O   HOH Z 351 " =    1.424
peak=   -4.098 closest distance to " CG  GLN A 223 " =    1.713
peak=   -4.064 closest distance to " CB  PRO A 280 " =    2.071
peak=   -4.052 closest distance to " CZ3 TRP A 179 " =    1.100
peak=   -3.978 closest distance to " CG1 VAL A 112 " =    2.937
peak=   -3.953 closest distance to " ND2 ASN A  45 " =    1.572
peak=   -3.936 closest distance to " O   HOH Z 185 " =    2.274
peak=   -3.870 closest distance to " O   PRO A 198 " =    1.239
peak=   -3.841 closest distance to " O   HOH Z 407 " =    3.246
peak=   -3.839 closest distance to " CE2 TYR A  30 " =    2.822
peak=   -3.828 closest distance to " N   ALA A  43 " =    2.572
peak=   -3.798 closest distance to " O   HOH Z  38 " =    1.501
peak=   -3.796 closest distance to " CD  ARG A  14 " =    3.358
peak=   -3.792 closest distance to " OG BSER A 134 " =    1.269
peak=   -3.791 closest distance to " CB  PRO A 163 " =    2.580
peak=   -3.772 closest distance to " CD  GLN A  58 " =    0.948
peak=   -3.766 closest distance to " O   HOH Z 231 " =    2.142
peak=   -3.760 closest distance to " O   HOH Z 313 " =    1.941
peak=   -3.760 closest distance to " CG  ASP A 231 " =    0.717
peak=   -3.725 closest distance to " C   HIS A 108 " =    1.147
peak=   -3.722 closest distance to " CG  MET A 105 " =    0.992
peak=   -3.721 closest distance to " O   HOH Z 372 " =    2.440
peak=   -3.714 closest distance to " CA  GLY A  98 " =    1.919
peak=   -3.690 closest distance to " O   HOH Z  60 " =    2.499
peak=   -3.683 closest distance to " C   ALA A 158 " =    1.459
peak=   -3.681 closest distance to " OG BSER A 134 " =    1.659
peak=   -3.673 closest distance to " CZ  TYR A 169 " =    1.598
peak=   -3.670 closest distance to " O   HOH Z  52 " =    1.157
peak=   -3.669 closest distance to " O   HOH Z 353 " =    2.095
peak=   -3.664 closest distance to " O   HOH Z  43 " =    1.594
peak=   -3.657 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.657 closest distance to " N   ASP A 286 " =    2.447
peak=   -3.655 closest distance to " CD1 PHE A  59 " =    1.834
peak=   -3.647 closest distance to " C   LEU A 222 " =    0.742
peak=   -3.646 closest distance to " CD  ARG A 195 " =    5.196
peak=   -3.646 closest distance to " O   HOH Z 198 " =    1.275
peak=   -3.640 closest distance to " CB  ALA A  43 " =    2.490
peak=   -3.623 closest distance to " CB  ALA A 291 " =    2.191
peak=   -3.616 closest distance to " CA  GLY A 241 " =    2.280
peak=   -3.613 closest distance to " NH2AARG A 275 " =    5.432
peak=   -3.610 closest distance to " CB  TRP A  85 " =    2.441
peak=   -3.607 closest distance to " O   TYR A 247 " =    2.854
peak=   -3.603 closest distance to " CB  PHE A 192 " =    1.981
peak=   -3.593 closest distance to " CB  ALA A 161 " =    2.639
peak=   -3.588 closest distance to " O   HOH Z 126 " =    1.867
peak=   -3.583 closest distance to " CD  ARG A 139 " =    1.592
peak=   -3.578 closest distance to " O   VAL A 189 " =    2.504
peak=   -3.573 closest distance to " O   HOH Z 282 " =    1.011
peak=   -3.569 closest distance to " O   VAL A  67 " =    2.719
peak=   -3.567 closest distance to " CB  ASN A  39 " =    2.197
peak=   -3.556 closest distance to " CE2 PHE A 218 " =    2.481
peak=   -3.549 closest distance to " O   ARG A 145 " =    1.521
peak=   -3.544 closest distance to " CB  CYS A 254 " =    2.283
peak=   -3.543 closest distance to " O   HOH Z 198 " =    2.032
peak=   -3.536 closest distance to " CZ  PHE A  59 " =    1.529
peak=   -3.536 closest distance to " CG  GLU A 152 " =    0.774
peak=   -3.524 closest distance to " O   HOH Z 211 " =    1.628
peak=   -3.521 closest distance to " CZ BARG A 275 " =    1.781
peak=   -3.518 closest distance to " O   HOH Z  10 " =    1.495
peak=   -3.518 closest distance to " OD1 ASN A 148 " =    1.565
peak=   -3.512 closest distance to " N   GLN A  58 " =    1.894
peak=   -3.506 closest distance to " O   HOH Z 118 " =    3.161
peak=   -3.494 closest distance to " O   GLY A 211 " =    1.344
peak=   -3.491 closest distance to " O   PRO A 163 " =    1.985
peak=   -3.489 closest distance to " CG  PHE A 283 " =    2.728
peak=   -3.486 closest distance to " CD  GLN A  88 " =    0.788
peak=   -3.481 closest distance to " ND2 ASN A 249 " =    2.167
peak=   -3.478 closest distance to " CG2 ILE A 263 " =    2.330
peak=   -3.476 closest distance to " CD1 LEU A 101 " =    2.347
peak=   -3.475 closest distance to " CA  GLY A 203 " =    2.240
peak=   -3.475 closest distance to " C   LEU A 143 " =    1.327
peak=   -3.471 closest distance to " O   HOH Z 241 " =    1.158
peak=   -3.461 closest distance to " O   HOH Z  73 " =    2.169
peak=   -3.458 closest distance to " OG  SER A  97 " =    2.194
peak=   -3.453 closest distance to " OD1 ASP A 171 " =    1.609
peak=   -3.452 closest distance to " CD1 LEU A 228 " =    2.371
peak=   -3.446 closest distance to " CG1 VAL A 197 " =    2.215
peak=   -3.432 closest distance to " CE  MET A 105 " =    2.232
peak=   -3.425 closest distance to " N   THR A 157 " =    1.510
peak=   -3.411 closest distance to " O   GLN A 240 " =    2.176
peak=   -3.402 closest distance to " CE3 TRP A 274 " =    1.045
peak=   -3.390 closest distance to " CD1 LEU A 297 " =    2.458
peak=   -3.381 closest distance to " O   HOH Z 359 " =    3.296
peak=   -3.376 closest distance to " O   HOH Z 176 " =    0.752
peak=   -3.376 closest distance to " O   HOH Z 281 " =    2.682
peak=   -3.370 closest distance to " CD1 ILE A 239 " =    2.306
peak=   -3.369 closest distance to " CB  CYS A 201 " =    2.596
peak=   -3.365 closest distance to " CB  ALA A 248 " =    2.039
peak=   -3.362 closest distance to " O   HOH Z 394 " =    1.376
peak=   -3.359 closest distance to " CE BMET A  47 " =    1.911
peak=   -3.355 closest distance to " CB  ALA A 248 " =    2.495
peak=   -3.352 closest distance to " O   HOH Z 298 " =    2.514
peak=   -3.348 closest distance to " CE  LYS A  76 " =    2.677
peak=   -3.345 closest distance to " NH1AARG A 275 " =    1.775
peak=   -3.344 closest distance to " N   SER A 212 " =    1.778
peak=   -3.343 closest distance to " O   HOH Z  51 " =    1.113
peak=   -3.341 closest distance to " NH1 ARG A 195 " =    2.544
peak=   -3.340 closest distance to " OG  SER A   3 " =    1.679
peak=   -3.337 closest distance to " O   HOH Z  98 " =    2.219
peak=   -3.332 closest distance to " OD1 ASP A 191 " =    1.743
peak=   -3.331 closest distance to " CG  TRP A 266 " =    1.820
peak=   -3.326 closest distance to " O   HOH Z 114 " =    0.759
peak=   -3.318 closest distance to " OE1 GLN A  88 " =    1.224
peak=   -3.317 closest distance to " O   PRO A 198 " =    1.236
peak=   -3.317 closest distance to " CG  ARG A 269 " =    2.326
peak=   -3.315 closest distance to " O   HOH Z 317 " =    1.564
peak=   -3.313 closest distance to " CD  GLU A 277 " =    1.087
peak=   -3.309 closest distance to " O   HOH Z 298 " =    1.176
peak=   -3.307 closest distance to " CB  ASP A 286 " =    1.989
peak=   -3.307 closest distance to " O   HOH Z 111 " =    1.175
peak=   -3.303 closest distance to " O   TRP A  70 " =    1.474
peak=   -3.296 closest distance to " O   HOH Z 417 " =    2.871
peak=   -3.294 closest distance to " O   HOH Z  11 " =    1.820
peak=   -3.290 closest distance to " CA  SER A 135 " =    1.370
peak=   -3.280 closest distance to " O   HOH Z 222 " =    1.165
peak=   -3.273 closest distance to " O   HOH Z 191 " =    5.613
peak=   -3.268 closest distance to " O   ALA A 161 " =    1.529
peak=   -3.261 closest distance to " O   HOH Z 322 " =    1.422
peak=   -3.260 closest distance to " O   HOH Z 385 " =    2.074
peak=   -3.259 closest distance to " O   LEU A 101 " =    2.657
peak=   -3.258 closest distance to " N   ASP A 171 " =    2.362
peak=   -3.258 closest distance to " CD2 PHE A  61 " =    1.983
peak=   -3.255 closest distance to " O   HOH Z 266 " =    4.659
peak=   -3.246 closest distance to " O   HOH Z 210 " =    0.900
peak=   -3.245 closest distance to " CG2 THR A  29 " =    2.310
peak=   -3.241 closest distance to " O   ALA A 180 " =    1.224
peak=   -3.238 closest distance to " NH2 ARG A  79 " =    1.614
peak=   -3.235 closest distance to " O   SER A 135 " =    1.441
peak=   -3.226 closest distance to " O   GLY A 196 " =    1.170
peak=   -3.215 closest distance to " CD2 PHE A  61 " =    2.635
peak=   -3.214 closest distance to " O   HOH Z 417 " =    2.505
peak=   -3.208 closest distance to " O   HOH Z 111 " =    1.929
peak=   -3.202 closest distance to " CB  ASP A 132 " =    2.346
peak=   -3.201 closest distance to " O   HOH Z  93 " =    2.465
peak=   -3.194 closest distance to " NE2 GLN A  88 " =    1.804
peak=   -3.193 closest distance to " CG1 VAL A 250 " =    2.691
peak=   -3.190 closest distance to " CD2 TYR A 293 " =    1.966
peak=   -3.187 closest distance to " CH2 TRP A 177 " =    2.103
peak=   -3.186 closest distance to " O   HOH Z 426 " =    1.617
peak=   -3.185 closest distance to " O   SER A  95 " =    1.496
peak=   -3.184 closest distance to " ND2 ASN A  60 " =    1.394
peak=   -3.181 closest distance to " CG1 VAL A 230 " =    2.100
peak=   -3.177 closest distance to " O   HOH Z 311 " =    3.598
peak=   -3.174 closest distance to " NH2 ARG A  79 " =    1.910
peak=   -3.174 closest distance to " O   GLY A  17 " =    1.288
peak=   -3.172 closest distance to " CE1 TYR A 169 " =    2.510
peak=   -3.165 closest distance to " CE3 TRP A 274 " =    2.431
peak=   -3.159 closest distance to " O   HOH Z  63 " =    1.614
peak=   -3.158 closest distance to " O   HOH Z 174 " =    2.659
peak=   -3.155 closest distance to " CB  LEU A  83 " =    2.372
peak=   -3.154 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.150 closest distance to " O   HOH Z 168 " =    1.841
peak=   -3.149 closest distance to " CE3 TRP A 123 " =    1.242
peak=   -3.149 closest distance to " CB  PHE A 208 " =    2.221
peak=   -3.148 closest distance to " O   HOH Z 114 " =    1.693
peak=   -3.147 closest distance to " CA  GLY A 241 " =    3.192
peak=   -3.143 closest distance to " CD1 ILE A 199 " =    2.659
peak=   -3.141 closest distance to " O   HOH Z 137 " =    1.619
peak=   -3.140 closest distance to " N   GLN A 122 " =    1.465
peak=   -3.138 closest distance to " OD2 ASP A 200 " =    1.430
peak=   -3.136 closest distance to " OD2 ASP A 171 " =    2.177
peak=   -3.133 closest distance to " O   ALA A 292 " =    2.098
peak=   -3.130 closest distance to " CG2 THR A 178 " =    2.228
peak=   -3.127 closest distance to " CD1 TRP A 179 " =    0.868
peak=   -3.120 closest distance to " C   MET A 188 " =    1.486
peak=   -3.115 closest distance to " O   HOH Z 282 " =    4.870
peak=   -3.115 closest distance to " SD  MET A 188 " =    2.272
peak=   -3.111 closest distance to " O   HOH Z 390 " =    2.396
peak=   -3.110 closest distance to " O   HOH Z 244 " =    1.949
peak=   -3.097 closest distance to " O   SER A  62 " =    2.127
peak=   -3.096 closest distance to " O   HOH Z 371 " =    1.562
peak=   -3.095 closest distance to " N   GLY A  23 " =    2.298
peak=   -3.078 closest distance to " SG ACYS A 201 " =    2.022
peak=   -3.061 closest distance to " OD1AASN A 224 " =    1.751
peak=   -3.061 closest distance to " O   HOH Z 423 " =    1.099
peak=   -3.021 closest distance to " CB  CYS A 201 " =    2.304

================= 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    :  0.3436 0.3432   6.084070e+00   6.078123e+00
   1_bss:  0.3316 0.3318   6.066675e+00   6.055221e+00
   1_xyz:  0.1805 0.2048   5.517985e+00   5.620429e+00
   1_adp:  0.1648 0.2102   5.462820e+00   5.653114e+00
   1_occ:  0.1644 0.2104   5.461755e+00   5.652873e+00
   2_bss:  0.1628 0.2079   5.457830e+00   5.647512e+00
   2_xyz:  0.1282 0.1723   5.253247e+00   5.479828e+00
   2_adp:  0.1239 0.1641   5.211765e+00   5.430817e+00
   2_occ:  0.1238 0.1641   5.211243e+00   5.431040e+00
   3_bss:  0.1237 0.1634   5.209843e+00   5.428840e+00
   3_xyz:  0.1110 0.1554   5.131692e+00   5.374934e+00
   3_adp:  0.1088 0.1544   5.120110e+00   5.370464e+00
   3_occ:  0.1087 0.1544   5.120177e+00   5.370809e+00
   4_bss:  0.1087 0.1544   5.120103e+00   5.370698e+00
   4_xyz:  0.1071 0.1548   5.114577e+00   5.373535e+00
   4_adp:  0.1072 0.1547   5.114399e+00   5.372979e+00
   4_occ:  0.1071 0.1547   5.114321e+00   5.373138e+00
   5_bss:  0.1071 0.1548   5.114359e+00   5.373142e+00
   5_xyz:  0.1102 0.1557   5.132236e+00   5.380627e+00
   5_adp:  0.1115 0.1559   5.138268e+00   5.382793e+00
   5_occ:  0.1115 0.1559   5.138152e+00   5.382768e+00
   5_bss:  0.1115 0.1559   5.138163e+00   5.382762e+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:  0.336  50.001   0.161  -0.211  -1.444  -0.000  -0.000  -0.000
   1_xyz:  0.336  50.001   0.161  -0.211  -1.444  -0.000  -0.000  -0.000
   1_adp:  0.336  50.001   0.161  -0.211  -1.444  -0.000  -0.000  -0.000
   1_occ:  0.336  50.001   0.161  -0.211  -1.444  -0.000  -0.000  -0.000
   2_bss:  0.331  54.220  -1.858  -2.355  -1.916  -0.000  -0.000  -0.000
   2_xyz:  0.331  54.220  -1.858  -2.355  -1.916  -0.000  -0.000  -0.000
   2_adp:  0.331  54.220  -1.858  -2.355  -1.916  -0.000  -0.000  -0.000
   2_occ:  0.331  54.220  -1.858  -2.355  -1.916  -0.000  -0.000  -0.000
   3_bss:  0.331  54.220  -2.314  -2.718  -1.758  -0.000  -0.000  -0.000
   3_xyz:  0.331  54.220  -2.314  -2.718  -1.758  -0.000  -0.000  -0.000
   3_adp:  0.331  54.220  -2.314  -2.718  -1.758  -0.000  -0.000  -0.000
   3_occ:  0.331  54.220  -2.314  -2.718  -1.758  -0.000  -0.000  -0.000
   4_bss:  0.331  54.220  -2.322  -2.719  -1.651  -0.000  -0.000  -0.000
   4_xyz:  0.331  54.220  -2.322  -2.719  -1.651  -0.000  -0.000  -0.000
   4_adp:  0.331  54.220  -2.322  -2.719  -1.651  -0.000  -0.000  -0.000
   4_occ:  0.331  54.220  -2.322  -2.719  -1.651  -0.000  -0.000  -0.000
   5_bss:  0.331  54.220  -2.221  -2.621  -1.483  -0.000  -0.000  -0.000
   5_xyz:  0.331  54.220  -2.221  -2.621  -1.483  -0.000  -0.000  -0.000
   5_adp:  0.331  54.220  -2.221  -2.621  -1.483  -0.000  -0.000  -0.000
   5_occ:  0.331  54.220  -2.221  -2.621  -1.483  -0.000  -0.000  -0.000
   5_bss:  0.331  54.148  -2.147  -2.531  -1.359  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.982 0.6931  0.8775    34071.673
   1_bss:  34.917 0.7036  0.8775    31232.541
   1_xyz:  18.982 0.8730  1.0164    10605.661
   1_adp:  19.837 0.8644  1.0133    11258.239
   1_occ:  19.840 0.8643  1.0129    11238.156
   2_bss:  19.661 0.8660  0.9602    11084.138
   2_xyz:  15.882 0.8991  0.9808     7590.713
   2_adp:  14.714 0.9093  0.9853     6931.085
   2_occ:  14.717 0.9092  0.9851     6921.737
   3_bss:  14.674 0.9096  0.9772     6874.809
   3_xyz:  13.613 0.9180  0.9804     6144.207
   3_adp:  13.520 0.9189  0.9768     6078.470
   3_occ:  13.524 0.9188  0.9767     6079.465
   4_bss:  13.523 0.9188  0.9779     6078.024
   4_xyz:  13.529 0.9189  0.9768     6127.860
   4_adp:  13.492 0.9193  0.9723     6130.230
   4_occ:  13.496 0.9192  0.9722     6127.285
   5_bss:  13.498 0.9192  0.9765     6127.682
   5_xyz:  13.613 0.9185  0.9760     6210.719
   5_adp:  13.625 0.9184  0.9725     6257.517
   5_occ:  13.626 0.9184  0.9724     6254.646
   5_bss:  13.626 0.9184  0.9733     6254.408
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6176e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6176e-01
   1_xyz:   1.069  0.008  0.076 15.090  0.005  4.112   6.7789e-02
   1_adp:   1.069  0.008  0.076 15.090  0.005  4.112   6.7789e-02
   1_occ:   1.069  0.008  0.076 15.090  0.005  4.112   6.7789e-02
   2_bss:   1.069  0.008  0.076 15.090  0.005  4.112   6.7789e-02
   2_xyz:   0.948  0.006  0.071 14.420  0.004  4.120   5.2744e-02
   2_adp:   0.948  0.006  0.071 14.420  0.004  4.120   5.2744e-02
   2_occ:   0.948  0.006  0.071 14.420  0.004  4.120   5.2744e-02
   3_bss:   0.948  0.006  0.071 14.420  0.004  4.120   5.2744e-02
   3_xyz:   1.085  0.009  0.083 14.968  0.004  4.112   7.1242e-02
   3_adp:   1.085  0.009  0.083 14.968  0.004  4.112   7.1242e-02
   3_occ:   1.085  0.009  0.083 14.968  0.004  4.112   7.1242e-02
   4_bss:   1.085  0.009  0.083 14.968  0.004  4.112   7.1242e-02
   4_xyz:   1.075  0.010  0.081 14.851  0.005  4.113   7.1008e-02
   4_adp:   1.075  0.010  0.081 14.851  0.005  4.113   7.1008e-02
   4_occ:   1.075  0.010  0.081 14.851  0.005  4.113   7.1008e-02
   5_bss:   1.075  0.010  0.081 14.851  0.005  4.113   7.1008e-02
   5_xyz:   0.941  0.007  0.072 14.538  0.004  4.112   5.4630e-02
   5_adp:   0.941  0.007  0.072 14.538  0.004  4.112   5.4630e-02
   5_occ:   0.941  0.007  0.072 14.538  0.004  4.112   5.4630e-02
   5_bss:   0.941  0.007  0.072 14.538  0.004  4.112   5.4630e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4095e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4095e-01
   1_xyz:   8.817  0.070  0.318 85.638  0.048  2.299   7.0669e-02
   1_adp:   8.817  0.070  0.318 85.638  0.048  2.299   7.0669e-02
   1_occ:   8.817  0.070  0.318 85.638  0.048  2.299   7.0669e-02
   2_bss:   8.817  0.070  0.318 85.638  0.048  2.299   7.0669e-02
   2_xyz:   8.146  0.043  0.219 82.083  0.038  2.356   3.5776e-02
   2_adp:   8.146  0.043  0.219 82.083  0.038  2.356   3.5776e-02
   2_occ:   8.146  0.043  0.219 82.083  0.038  2.356   3.5776e-02
   3_bss:   8.146  0.043  0.219 82.083  0.038  2.356   3.5776e-02
   3_xyz:   7.962  0.046  0.261 84.822  0.039  2.241   5.8035e-02
   3_adp:   7.962  0.046  0.261 84.822  0.039  2.241   5.8035e-02
   3_occ:   7.962  0.046  0.261 84.822  0.039  2.241   5.8035e-02
   4_bss:   7.962  0.046  0.261 84.822  0.039  2.241   5.8035e-02
   4_xyz:   7.506  0.048  0.259 84.718  0.040  2.308   6.7124e-02
   4_adp:   7.506  0.048  0.259 84.718  0.040  2.308   6.7124e-02
   4_occ:   7.506  0.048  0.259 84.718  0.040  2.308   6.7124e-02
   5_bss:   7.506  0.048  0.259 84.718  0.040  2.308   6.7124e-02
   5_xyz:   7.594  0.039  0.217 84.720  0.037  2.336   3.5115e-02
   5_adp:   7.594  0.039  0.217 84.720  0.037  2.336   3.5115e-02
   5_occ:   7.594  0.039  0.217 84.720  0.037  2.336   3.5115e-02
   5_bss:   7.594  0.039  0.217 84.720  0.037  2.336   3.5115e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  75.38   0.00  17.28  72.07   0.00  13.11  75.38   5.67  40.01
   1_occ:  75.38   0.00  17.28  72.07   0.00  13.11  75.38   5.67  40.01
   2_bss:  75.38   0.00  17.28  72.07   0.00  13.11  75.38   5.67  40.01
   2_xyz:  75.38   0.00  17.28  72.07   0.00  13.11  75.38   5.67  40.01
   2_adp:  73.21   2.09  16.92  73.07   2.09  13.02  73.21   5.92  38.19
   2_occ:  73.21   2.09  16.92  73.07   2.09  13.02  73.21   5.92  38.19
   3_bss:  73.21   2.09  16.92  73.07   2.09  13.02  73.21   5.92  38.19
   3_xyz:  73.21   2.09  16.92  73.07   2.09  13.02  73.21   5.92  38.19
   3_adp:  77.38   1.41  17.00  77.38   1.41  13.01  74.76   5.08  38.74
   3_occ:  77.38   1.41  17.00  77.38   1.41  13.01  74.76   5.08  38.74
   4_bss:  77.38   1.41  17.00  77.38   1.41  13.01  74.76   5.08  38.74
   4_xyz:  77.38   1.41  17.00  77.38   1.41  13.01  74.76   5.08  38.74
   4_adp:  78.37   1.71  16.74  78.37   1.71  12.87  75.70   6.00  37.80
   4_occ:  78.37   1.71  16.74  78.37   1.71  12.87  75.70   6.00  37.80
   5_bss:  78.37   1.71  16.74  78.37   1.71  12.87  75.70   6.00  37.80
   5_xyz:  78.37   1.71  16.74  78.37   1.71  12.87  75.70   6.00  37.80
   5_adp:  76.10   1.99  16.37  76.10   1.99  12.71  75.70   6.57  36.25
   5_occ:  76.10   1.99  16.37  76.10   1.99  12.71  75.70   6.57  36.25
   5_bss:  76.03   1.92  16.29  76.03   1.92  12.64  75.62   6.49  36.18
------------------------------------------------------------------------
 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:    1.108    0.022    0.344
   1_adp:    1.108    0.022    0.344
   1_occ:    1.108    0.022    0.344
   2_bss:    1.108    0.022    0.344
   2_xyz:    0.764    0.019    0.388
   2_adp:    0.764    0.019    0.388
   2_occ:    0.764    0.019    0.388
   3_bss:    0.764    0.019    0.388
   3_xyz:    0.846    0.068    0.429
   3_adp:    0.846    0.068    0.429
   3_occ:    0.846    0.068    0.429
   4_bss:    0.846    0.068    0.429
   4_xyz:    1.042    0.075    0.438
   4_adp:    1.042    0.075    0.438
   4_occ:    1.042    0.075    0.438
   5_bss:    1.042    0.075    0.438
   5_xyz:    1.110    0.072    0.441
   5_adp:    1.110    0.072    0.441
   5_occ:    1.110    0.072    0.441
   5_bss:    1.110    0.072    0.441
------------------------------------------------------------------------

CPU time actual refinement: 324.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1005/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_1005/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1005/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1005/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1005/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.16 
  Macro-tasks:
    bulk solvent and scale       = 35.65  
    individual site refinement   = 137.75 
    weights calculation          = 29.87  
    collect and process          = 6.70   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 210.10 
  Micro-tasks:
    mask                            = 1.23   
    f_calc                          = 102.39 
    alpha_beta                      = 8.47   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 112.67 
    fmodel                         = 6.84   
    r_factors                      = 0.18   
    phase_errors                   = 10.83  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 244.05 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.553 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    652 calls, 102.06 s
gradients_fft:          597 calls,  98.55 s

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

# Date 2008-01-16 Time 06:11:16 PST -0800 (1200492676.67 s)
Start R-work = 0.3436, R-free = 0.3432 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1777 (no bulk solvent and anisotropic scale)

Start R-work = 0.3316, R-free = 0.3318
Final R-work = 0.1115, R-free = 0.1559