# Date 2008-01-16 Time 04:29:09 PST -0800 (1200486549.51 s)
#phil __OFF__

Command line arguments: "../335.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31500
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 335

-------------------------------------------------------------------------------
  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: (69.1963, 47.6339, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


================================== 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: (69.1963, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.903 1.9707
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9030
                             d_min =   1.9707

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: (69.1963, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.903 1.9707
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9034 -  4.2167 [2186/2214]  1964   222  10.2%
  bin  2:  4.2167 -  3.3595 [2084/2107]  1877   207   9.9%
  bin  3:  3.3595 -  2.9386 [2057/2082]  1851   206  10.0%
  bin  4:  2.9386 -  2.6716 [2054/2070]  1848   206  10.0%
  bin  5:  2.6716 -  2.4810 [2022/2061]  1817   205  10.1%
  bin  6:  2.4810 -  2.3353 [2031/2063]  1834   197   9.7%
  bin  7:  2.3353 -  2.2188 [2002/2039]  1800   202  10.1%
  bin  8:  2.2188 -  2.1225 [2007/2049]  1809   198   9.9%
  bin  9:  2.1225 -  2.0410 [1989/2028]  1791   198  10.0%
  bin 10:  2.0410 -  1.9707 [1157/2015]  1039   118  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_335/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: 0.13 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:
        1.59 -     2.25: 13
        2.25 -     2.91: 1462
        2.91 -     3.58: 4493
        3.58 -     4.24: 9178
        4.24 -     4.90: 13157
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.590 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.655 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.764 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.898 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28298 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_335/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_335/model_refine_001.geo

CPU time processing inputs: 7.82


============================ 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 = 69.19625 47.63395 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3758   r_free= 0.3673   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.159698                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9034 -  4.7030 0.99   1411  158 0.3094 0.3327      6.4154      6.4656|
|  2:  4.7030 -  3.7525 0.99   1363  151 0.3028 0.2878      6.5944      6.5612|
|  3:  3.7525 -  3.2840 0.99   1340  148 0.3294 0.3113      6.4771       6.469|
|  4:  3.2840 -  2.9864 0.99   1317  143 0.3559 0.3192      6.3505       6.252|
|  5:  2.9864 -  2.7738 0.98   1321  148 0.3954 0.3643      6.2318      6.1911|
|  6:  2.7738 -  2.6112 0.99   1302  148 0.3940 0.4114      6.1549       6.047|
|  7:  2.6112 -  2.4810 0.99   1303  150 0.4053 0.3681      6.1221      6.0302|
|  8:  2.4810 -  2.3735 0.99   1319  136 0.4099 0.4296      6.0742      6.0818|
|  9:  2.3735 -  2.2824 0.99   1297  148 0.4343 0.4252      6.0405      6.0832|
| 10:  2.2824 -  2.2039 0.98   1290  139 0.4199 0.4061      6.0109      5.9888|
| 11:  2.2039 -  2.1352 0.98   1274  148 0.4329 0.4330      5.9633      5.9449|
| 12:  2.1352 -  2.0743 1.00   1295  147 0.4391 0.4302      5.8887       5.949|
| 13:  2.0743 -  2.0199 0.95   1264  131 0.4564 0.4672      5.8325         5.8|
| 14:  2.0199 -  1.9707 0.42    534   64 0.4351 0.4336      5.7931      5.6742|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9034 -  4.7030  1411   158  0.74  30.33   0.86     0.76      55518.84|
|  2:  4.7030 -  3.7525  1363   151  0.80  25.87   0.96     0.88      61682.57|
|  3:  3.7525 -  3.2840  1340   148  0.76  29.82   0.96     0.92      58865.50|
|  4:  3.2840 -  2.9864  1317   143  0.73  33.02   0.97     0.90      49584.84|
|  5:  2.9864 -  2.7738  1321   148  0.67  38.35   0.95     0.86      42091.34|
|  6:  2.7738 -  2.6112  1302   148  0.65  39.83   0.96     0.84      37910.52|
|  7:  2.6112 -  2.4810  1303   150  0.64  40.57   0.98     0.83      35598.70|
|  8:  2.4810 -  2.3735  1319   136  0.62  42.58   0.98     0.82      34354.12|
|  9:  2.3735 -  2.2824  1297   148  0.60  44.43   0.96     0.82      32840.59|
| 10:  2.2824 -  2.2039  1290   139  0.58  45.54   0.99     0.80      31664.96|
| 11:  2.2039 -  2.1352  1274   148  0.56  47.30   0.99     0.80      30987.12|
| 12:  2.1352 -  2.0743  1295   147  0.52  50.33   1.00     0.79      30585.98|
| 13:  2.0743 -  2.0199  1264   131  0.49  53.04   0.97     0.73      27759.23|
| 14:  2.0199 -  1.9707   534    64  0.48  53.35   1.02     0.64      23283.59|
|alpha:            min =        0.64 max =            0.92 mean =         0.82|
|beta:             min =    23283.59 max =        61682.57 mean =     40459.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.97 mean =        40.29|
|phase err.(test): min =        0.00 max =           89.91 mean =        40.71|
|-----------------------------------------------------------------------------|

============================== 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 = 8.833647              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.928   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.882631              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.745   (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 |  1.590 -  1.921:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.921 -  2.252:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.252 -  2.583:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.583 -  2.914:     1425 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.914 -  3.245:     1911 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.245 -  3.576:     2582 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.576 -  3.907:     4700 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.907 -  4.238:     4478 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.238 -  4.569:     5994 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.569 -  4.900:     7163 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| 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  1.590 |       0.307 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    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: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3758   r_free= 0.3673   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.159698                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3647   r_free= 0.3542   ksol= 0.30   Bsol= 30.59   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,2.95,-1.69,0.00,-0.00,-0.00); trace/3= -0.05                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.142658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.054489              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.747   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.489870              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.496   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3647      final r-factor (work) = 0.2021          |
| start r-factor (free) = 0.3542      final r-factor (free) = 0.2245          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.9312 = 8.05 * 0.50 * 6.1481 + 1.00 * 0.1712                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7428 = 8.05 * 0.50 * 5.8670 + 1.00 * 0.1152                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2021      final r-factor (work) = 0.1839          |
| start r-factor (free) = 0.2245      final r-factor (free) = 0.2295          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8803 = 0.49 * 1.00 * 5.8670 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7363 = 0.49 * 1.00 * 5.5558 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.04   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    64.04   16.96    None  None   None       |
|    Sol.    : 438    0      7.16    64.04   38.22    None  None   None       |
|    Mac.    : 2385   0      0.00    58.88   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.404:  330   |   5:    32.021 -  38.425:  109        |
|      1:     6.404 -  12.808: 1145   |   6:    38.425 -  44.829:  106        |
|      2:    12.808 -  19.212:  600   |   7:    44.829 -  51.233:   91        |
|      3:    19.212 -  25.617:  238   |   8:    51.233 -  57.637:   64        |
|      4:    25.617 -  32.021:  121   |   9:    57.637 -  64.041:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1839 r_free = 0.2295             target_work(ml) = 5.568         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1836 r_free = 0.2300             target_work(ml) = 5.568         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1836   r_free= 0.2300   ksol= 0.30   Bsol= 30.59   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,2.95,-1.69,0.00,-0.00,-0.00); trace/3= -0.05                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.567786                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1803   r_free= 0.2260   ksol= 0.32   Bsol= 50.62   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-0.36,-1.62,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.555872                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.035625              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.371   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.209844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.606   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1803      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.2260      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3449 = 4.04 * 0.50 * 5.5653 + 1.00 * 0.1152                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0289 = 4.04 * 0.50 * 5.4335 + 1.00 * 0.0652                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1546 = 0.21 * 1.00 * 5.4335 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1097 = 0.21 * 1.00 * 5.2521 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.00    76.55   16.70    None  None   None       |
|    all(noH): 2823   0      2.00    76.55   16.70    None  None   None       |
|    Sol.    : 438    0      6.05    67.78   38.07    None  None   None       |
|    Mac.    : 2385   0      2.00    76.55   12.77    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:     2.001 -   9.457:  891   |   5:    39.277 -  46.733:  115        |
|      1:     9.457 -  16.912: 1118   |   6:    46.733 -  54.188:   92        |
|      2:    16.912 -  24.367:  302   |   7:    54.188 -  61.643:   46        |
|      3:    24.367 -  31.822:  130   |   8:    61.643 -  69.098:   17        |
|      4:    31.822 -  39.277:  111   |   9:    69.098 -  76.553:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1245 r_free = 0.1651             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1650             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1650   ksol= 0.32   Bsol= 50.62   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-0.36,-1.62,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.219745                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1636   ksol= 0.32   Bsol= 51.87   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-1.27,-1.28,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218048                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.900073              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.755  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206231              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.986  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6817 = 2.90 * 0.50 * 5.2526 + 1.00 * 0.0652                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5754 = 2.90 * 0.50 * 5.1763 + 1.00 * 0.0696                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0750 = 0.21 * 1.00 * 5.1763 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0682 = 0.21 * 1.00 * 5.1434 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.02    78.47   16.51    None  None   None       |
|    all(noH): 2823   0      2.02    78.47   16.51    None  None   None       |
|    Sol.    : 438    0      5.22    69.40   37.75    None  None   None       |
|    Mac.    : 2385   0      2.02    78.47   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.019 -   9.664:  967   |   5:    40.242 -  47.887:  107        |
|      1:     9.664 -  17.308: 1098   |   6:    47.887 -  55.532:   97        |
|      2:    17.308 -  24.953:  271   |   7:    55.532 -  63.176:   30        |
|      3:    24.953 -  32.598:  124   |   8:    63.176 -  70.821:   14        |
|      4:    32.598 -  40.242:  114   |   9:    70.821 -  78.466:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1553             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1554             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1554   ksol= 0.32   Bsol= 51.87   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-1.27,-1.28,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138995                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1553   ksol= 0.33   Bsol= 51.87   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.49,-1.11,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138848                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.355698              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.456  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.699  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5559 = 1.36 * 0.50 * 5.1431 + 1.00 * 0.0696                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5443 = 1.36 * 0.50 * 5.1533 + 1.00 * 0.0511                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0034 = 0.58 * 1.00 * 5.1533 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0030 = 0.58 * 1.00 * 5.1506 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    82.33   16.58    None  None   None       |
|    all(noH): 2823   0      1.01    82.33   16.58    None  None   None       |
|    Sol.    : 438    0      5.30    72.41   38.58    None  None   None       |
|    Mac.    : 2385   0      1.01    82.33   12.54    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:     1.009 -   9.141:  878   |   5:    41.668 -  49.800:  115        |
|      1:     9.141 -  17.273: 1183   |   6:    49.800 -  57.931:   93        |
|      2:    17.273 -  25.404:  275   |   7:    57.931 -  66.063:   28        |
|      3:    25.404 -  33.536:  133   |   8:    66.063 -  74.195:   10        |
|      4:    33.536 -  41.668:  106   |   9:    74.195 -  82.326:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1578             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1578             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1578   ksol= 0.33   Bsol= 51.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.49,-1.11,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157367                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1578   ksol= 0.32   Bsol= 51.87   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.40,-0.91,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157420                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.263019              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.996  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.918596              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.379  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4552 = 3.26 * 0.50 * 5.1511 + 1.00 * 0.0511                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4496 = 3.26 * 0.50 * 5.1348 + 1.00 * 0.0721                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 25.2645 = 4.92 * 1.00 * 5.1348 + 1.00 * 0.0086                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 25.2119 = 4.92 * 1.00 * 5.1237 + 1.00 * 0.0103                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    97.90   16.84    None  None   None       |
|    all(noH): 2823   0      0.45    97.90   16.84    None  None   None       |
|    Sol.    : 438    0      5.30    90.56   40.35    None  None   None       |
|    Mac.    : 2385   0      0.45    97.90   12.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.449 -  10.194: 1196   |   5:    49.174 -  58.919:   90        |
|      1:    10.194 -  19.939: 1000   |   6:    58.919 -  68.663:   59        |
|      2:    19.939 -  29.684:  202   |   7:    68.663 -  78.408:   13        |
|      3:    29.684 -  39.429:  127   |   8:    78.408 -  88.153:    5        |
|      4:    39.429 -  49.174:  126   |   9:    88.153 -  97.898:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1070 r_free = 0.1574             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1069 r_free = 0.1574             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1574   ksol= 0.32   Bsol= 51.87   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.40,-0.91,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126622                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9034 -  4.7030 0.99   1411  158 0.0937 0.1263       5.352      5.5302|
|  2:  4.7030 -  3.7525 0.99   1363  151 0.0803 0.1063      5.3938      5.6024|
|  3:  3.7525 -  3.2840 0.99   1340  148 0.1014 0.1478      5.4359      5.8295|
|  4:  3.2840 -  2.9864 0.99   1317  143 0.1164 0.1529      5.4248      5.6008|
|  5:  2.9864 -  2.7738 0.98   1321  148 0.1271 0.1709      5.2975      5.5067|
|  6:  2.7738 -  2.6112 0.99   1302  148 0.1200 0.2069      5.2025      5.4777|
|  7:  2.6112 -  2.4810 0.99   1303  150 0.1180 0.1584      5.1329      5.3354|
|  8:  2.4810 -  2.3735 0.99   1319  136 0.1098 0.1663      5.0535      5.2862|
|  9:  2.3735 -  2.2824 0.99   1297  148 0.1136 0.1899      5.0107      5.3496|
| 10:  2.2824 -  2.2039 0.98   1290  139 0.1057 0.1671      4.9398       5.179|
| 11:  2.2039 -  2.1352 0.98   1274  148 0.1084 0.1855      4.9126      5.2278|
| 12:  2.1352 -  2.0743 1.00   1295  147 0.1053 0.1652      4.8312      5.1259|
| 13:  2.0743 -  2.0199 0.95   1264  131 0.1087 0.1746      4.7748      5.0416|
| 14:  2.0199 -  1.9707 0.42    534   64 0.1014 0.1840      4.6882      4.9382|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9034 -  4.7030  1411   158  0.94   8.96   0.97     0.95       6948.42|
|  2:  4.7030 -  3.7525  1363   151  0.95   7.87   1.01     1.00       8626.44|
|  3:  3.7525 -  3.2840  1340   148  0.94  11.02   1.02     1.01       9841.62|
|  4:  3.2840 -  2.9864  1317   143  0.92  13.54   1.01     1.00      10132.50|
|  5:  2.9864 -  2.7738  1321   148  0.90  15.99   1.00     0.97       8181.62|
|  6:  2.7738 -  2.6112  1302   148  0.90  16.24   0.97     0.94       7030.21|
|  7:  2.6112 -  2.4810  1303   150  0.91  15.16   0.98     0.95       5998.00|
|  8:  2.4810 -  2.3735  1319   136  0.91  15.23   0.99     0.96       5426.07|
|  9:  2.3735 -  2.2824  1297   148  0.90  15.85   0.99     0.95       4920.51|
| 10:  2.2824 -  2.2039  1290   139  0.90  15.76   0.98     0.95       4451.82|
| 11:  2.2039 -  2.1352  1274   148  0.90  15.99   0.99     0.95       4327.73|
| 12:  2.1352 -  2.0743  1295   147  0.91  15.19   0.99     0.97       3720.11|
| 13:  2.0743 -  2.0199  1264   131  0.90  16.26   0.98     0.97       3354.51|
| 14:  2.0199 -  1.9707   534    64  0.91  15.21   0.95     0.92       2757.70|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2757.70 max =        10132.50 mean =      6307.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.05|
|phase err.(test): min =        0.00 max =           89.68 mean =        13.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1573   ksol= 0.32   Bsol= 53.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.13,-0.61,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.126609                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1573   ksol= 0.32   Bsol= 53.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.13,-0.61,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.126609                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9034 -  4.7030 0.99   1411  158 0.0937 0.1269      5.3523      5.5325|
|  2:  4.7030 -  3.7525 0.99   1363  151 0.0806 0.1062      5.3958      5.6038|
|  3:  3.7525 -  3.2840 0.99   1340  148 0.1015 0.1478      5.4367      5.8297|
|  4:  3.2840 -  2.9864 0.99   1317  143 0.1163 0.1527      5.4241      5.6002|
|  5:  2.9864 -  2.7738 0.98   1321  148 0.1269 0.1708      5.2964      5.5057|
|  6:  2.7738 -  2.6112 0.99   1302  148 0.1198 0.2068      5.2018      5.4768|
|  7:  2.6112 -  2.4810 0.99   1303  150 0.1180 0.1585      5.1325      5.3354|
|  8:  2.4810 -  2.3735 0.99   1319  136 0.1097 0.1662      5.0534      5.2858|
|  9:  2.3735 -  2.2824 0.99   1297  148 0.1136 0.1900      5.0109      5.3499|
| 10:  2.2824 -  2.2039 0.98   1290  139 0.1056 0.1671      4.9398      5.1791|
| 11:  2.2039 -  2.1352 0.98   1274  148 0.1084 0.1853      4.9125      5.2277|
| 12:  2.1352 -  2.0743 1.00   1295  147 0.1053 0.1652      4.8309      5.1258|
| 13:  2.0743 -  2.0199 0.95   1264  131 0.1087 0.1744      4.7746      5.0408|
| 14:  2.0199 -  1.9707 0.42    534   64 0.1014 0.1840      4.6883      4.9379|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9034 -  4.7030  1411   158  0.94   8.97   0.98     0.95       6951.02|
|  2:  4.7030 -  3.7525  1363   151  0.95   7.89   1.02     1.00       8648.98|
|  3:  3.7525 -  3.2840  1340   148  0.94  11.04   1.03     1.02       9864.11|
|  4:  3.2840 -  2.9864  1317   143  0.92  13.54   1.02     1.01      10121.21|
|  5:  2.9864 -  2.7738  1321   148  0.90  15.98   1.00     0.98       8164.92|
|  6:  2.7738 -  2.6112  1302   148  0.90  16.23   0.98     0.95       7017.98|
|  7:  2.6112 -  2.4810  1303   150  0.91  15.15   0.99     0.96       5990.08|
|  8:  2.4810 -  2.3735  1319   136  0.91  15.23   1.00     0.97       5423.02|
|  9:  2.3735 -  2.2824  1297   148  0.90  15.86   1.00     0.96       4920.31|
| 10:  2.2824 -  2.2039  1290   139  0.90  15.76   1.00     0.96       4449.93|
| 11:  2.2039 -  2.1352  1274   148  0.90  15.99   1.00     0.97       4324.94|
| 12:  2.1352 -  2.0743  1295   147  0.91  15.19   1.01     0.99       3717.39|
| 13:  2.0743 -  2.0199  1264   131  0.90  16.25   1.00     0.98       3351.87|
| 14:  2.0199 -  1.9707   534    64  0.91  15.20   0.97     0.93       2755.22|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2755.22 max =        10121.21 mean =      6306.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.05|
|phase err.(test): min =        0.00 max =           89.68 mean =        13.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.44    97.88   16.82    None  None   None       |
|    all(noH): 2823   0      0.44    97.88   16.82    None  None   None       |
|    Sol.    : 438    0      5.29    90.55   40.33    None  None   None       |
|    Mac.    : 2385   0      0.44    97.88   12.51    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:     0.435 -  10.180: 1196   |   5:    49.160 -  58.905:   90        |
|      1:    10.180 -  19.925: 1000   |   6:    58.905 -  68.650:   59        |
|      2:    19.925 -  29.670:  202   |   7:    68.650 -  78.394:   13        |
|      3:    29.670 -  39.415:  127   |   8:    78.394 -  88.139:    5        |
|      4:    39.415 -  49.160:  126   |   9:    88.139 -  97.884:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 275         
Filter by distance & map next to the model:
   mapped sites are within: 0.438 - 4.626
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 271 from: 275
   mapped sites are within: 0.760 - 4.626

peak=    5.729 closest distance to " NH2 ARG A  56 " =    2.333
peak=    5.396 closest distance to " CB  ARG A 275 " =    0.948
peak=    5.221 closest distance to " CB  GLN A 183 " =    1.313
peak=    5.215 closest distance to " CG  PRO A  54 " =    1.225
peak=    4.980 closest distance to " CB  GLN A 223 " =    1.401
peak=    4.836 closest distance to " O   HOH Z 403 " =    1.784
peak=    4.816 closest distance to " CA  TYR A  30 " =    0.918
peak=    4.703 closest distance to " CB  SER A  63 " =    1.140
peak=    4.650 closest distance to " O   HOH Z 232 " =    2.365
peak=    4.606 closest distance to " CB  ARG A 190 " =    1.699
peak=    4.598 closest distance to " O   HOH Z 142 " =    1.593
peak=    4.542 closest distance to " CB  ARG A  79 " =    1.341
peak=    4.541 closest distance to " C   PRO A 198 " =    1.456
peak=    4.495 closest distance to " O   HOH Z 234 " =    3.669
peak=    4.465 closest distance to " CG  PRO A 213 " =    1.208
peak=    4.462 closest distance to " O   HOH Z 193 " =    1.768
peak=    4.457 closest distance to " O   HOH Z 298 " =    1.775
peak=    4.442 closest distance to " CB  GLU A 152 " =    1.171
peak=    4.406 closest distance to " O   HOH Z  15 " =    2.071
peak=    4.376 closest distance to " NE2 GLN A  11 " =    1.014
peak=    4.335 closest distance to " O   HOH Z 272 " =    1.833
peak=    4.332 closest distance to " O   HOH Z  97 " =    1.934
peak=    4.324 closest distance to " O   SER A  87 " =    2.176
peak=    4.303 closest distance to " O   HOH Z 203 " =    1.740
peak=    4.291 closest distance to " O   HOH Z 369 " =    2.354
peak=    4.266 closest distance to " O   HOH Z 287 " =    2.009
peak=    4.260 closest distance to " O   HOH Z 209 " =    2.228
peak=    4.239 closest distance to " NZ  LYS A 117 " =    3.162
peak=    4.227 closest distance to " O   HOH Z  44 " =    2.053
peak=    4.210 closest distance to " CD2 TRP A 179 " =    1.397
peak=    4.197 closest distance to " O   HOH Z  43 " =    2.110
peak=    4.181 closest distance to " O   HOH Z 402 " =    1.448
peak=    4.168 closest distance to " O   HOH Z 126 " =    1.812
peak=    4.125 closest distance to " O   HOH Z 368 " =    2.101
peak=    4.116 closest distance to " CB  TYR A 169 " =    0.891
peak=    4.111 closest distance to " CG  ARG A  66 " =    2.624
peak=    4.091 closest distance to " NH2BARG A 145 " =    2.102
peak=    4.060 closest distance to " O   HOH Z 158 " =    3.034
peak=    4.057 closest distance to " O   HOH Z 284 " =    2.968
peak=    4.054 closest distance to " CG1 ILE A  33 " =    1.166
peak=    4.053 closest distance to " O   HOH Z 132 " =    2.520
peak=    4.034 closest distance to " O   HOH Z 346 " =    1.658
peak=    3.986 closest distance to " O   HOH Z  59 " =    2.209
peak=    3.964 closest distance to " O   HOH Z  97 " =    2.395
peak=    3.961 closest distance to " CB  PRO A  54 " =    0.901
peak=    3.961 closest distance to " CG  PRO A  90 " =    1.128
peak=    3.955 closest distance to " O   HOH Z  40 " =    1.951
peak=    3.946 closest distance to " CB  GLU A 277 " =    3.599
peak=    3.945 closest distance to " CA  ALA A  21 " =    1.290
peak=    3.930 closest distance to " O   HOH Z 389 " =    1.875
peak=    3.926 closest distance to " O   HOH Z 245 " =    1.339
peak=    3.924 closest distance to " CA  ARG A  36 " =    1.026
peak=    3.923 closest distance to " CB  ASN A 148 " =    1.491
peak=    3.922 closest distance to " O   HOH Z 128 " =    1.955
peak=    3.905 closest distance to " O   HOH Z  63 " =    1.956
peak=    3.898 closest distance to " O   HOH Z 265 " =    2.137
peak=    3.888 closest distance to " CB  ASP A 140 " =    1.065
peak=    3.883 closest distance to " O   HOH Z 250 " =    1.421
peak=    3.869 closest distance to " O   HOH Z  78 " =    1.641
peak=    3.851 closest distance to " CB  GLU A 128 " =    1.127
peak=    3.846 closest distance to " O   HOH Z 371 " =    3.335
peak=    3.846 closest distance to " CD  ARG A 269 " =    0.962
peak=    3.828 closest distance to " CG  PRO A 243 " =    1.142
peak=    3.826 closest distance to " O   HOH Z  54 " =    1.725
peak=    3.826 closest distance to " N   HIS A 108 " =    1.894
peak=    3.824 closest distance to " O   HOH Z 359 " =    1.502
peak=    3.821 closest distance to " O   HOH Z 261 " =    1.765
peak=    3.818 closest distance to " CG1BVAL A  72 " =    1.716
peak=    3.818 closest distance to " CA  LYS A 117 " =    1.282
peak=    3.815 closest distance to " O   HOH Z 327 " =    1.599
peak=    3.811 closest distance to " OD1 ASN A  69 " =    2.491
peak=    3.810 closest distance to " O   HOH Z 291 " =    1.516
peak=    3.809 closest distance to " O   HOH Z 303 " =    2.187
peak=    3.793 closest distance to " CA  ASN A 176 " =    1.213
peak=    3.790 closest distance to " CG2 ILE A 120 " =    1.078
peak=    3.783 closest distance to " O   HOH Z 427 " =    2.850
peak=    3.783 closest distance to " OD2 ASP A 298 " =    3.864
peak=    3.781 closest distance to " O   HOH Z 423 " =    2.024
peak=    3.779 closest distance to " O   HOH Z 380 " =    1.901
peak=    3.779 closest distance to " CB  TRP A 179 " =    1.270
peak=    3.777 closest distance to " O   HOH Z 185 " =    1.793
peak=    3.775 closest distance to " O   HOH Z  80 " =    1.678
peak=    3.767 closest distance to " O   HOH Z 345 " =    2.872
peak=    3.764 closest distance to " O   HOH Z 147 " =    1.775
peak=    3.764 closest distance to " O   HOH Z 108 " =    2.654
peak=    3.763 closest distance to " O   HOH Z 126 " =    1.731
peak=    3.752 closest distance to " O   HOH Z 345 " =    1.644
peak=    3.750 closest distance to " O   HOH Z 189 " =    2.332
peak=    3.750 closest distance to " O   HOH Z 227 " =    1.622
peak=    3.749 closest distance to " CD2 LEU A 297 " =    0.897
peak=    3.735 closest distance to " ND2 ASN A 187 " =    1.460
peak=    3.731 closest distance to " O   HOH Z 197 " =    2.681
peak=    3.731 closest distance to " O   HOH Z  61 " =    1.531
peak=    3.730 closest distance to " O   HOH Z 421 " =    1.780
peak=    3.728 closest distance to " O   HOH Z 316 " =    3.039
peak=    3.718 closest distance to " CG2 ILE A  20 " =    1.374
peak=    3.714 closest distance to " N   ASN A  39 " =    1.319
peak=    3.712 closest distance to " CB  SER A   3 " =    1.234
peak=    3.707 closest distance to " CG  PRO A 198 " =    1.212
peak=    3.697 closest distance to " O   HOH Z 102 " =    1.275
peak=    3.691 closest distance to " CB  VAL A 265 " =    1.222
peak=    3.686 closest distance to " CB  TRP A 266 " =    0.988
peak=    3.684 closest distance to " O   HOH Z 357 " =    2.014
peak=    3.683 closest distance to " O   HOH Z 214 " =    2.312
peak=    3.678 closest distance to " O   HOH Z 406 " =    1.490
peak=    3.671 closest distance to " O   HOH Z 134 " =    1.271
peak=    3.669 closest distance to " CB  ARG A 139 " =    0.925
peak=    3.663 closest distance to " OE1 GLU A   2 " =    2.215
peak=    3.658 closest distance to " O   HOH Z 411 " =    3.755
peak=    3.642 closest distance to " OD2 ASP A 286 " =    2.814
peak=    3.637 closest distance to " O   HOH Z 279 " =    2.152
peak=    3.637 closest distance to " O   HOH Z 299 " =    4.297
peak=    3.631 closest distance to " O   HOH Z 417 " =    2.913
peak=    3.628 closest distance to " O   HOH Z  35 " =    2.368
peak=    3.628 closest distance to " O   HOH Z 183 " =    1.492
peak=    3.613 closest distance to " O   HOH Z 426 " =    1.481
peak=    3.609 closest distance to " CD  LYS A 166 " =    1.376
peak=    3.608 closest distance to " O   HOH Z 163 " =    1.460
peak=    3.607 closest distance to " CB  ALA A 248 " =    1.338
peak=    3.605 closest distance to " CB  VAL A 202 " =    1.508
peak=    3.604 closest distance to " O   HOH Z 422 " =    2.638
peak=    3.604 closest distance to " CA  ALA A  51 " =    0.941
peak=    3.594 closest distance to " CG  GLN A  58 " =    2.659
peak=    3.590 closest distance to " CB  SER A  26 " =    1.752
peak=    3.587 closest distance to " O   HOH Z 128 " =    2.281
peak=    3.586 closest distance to " O   HOH Z 325 " =    2.219
peak=    3.585 closest distance to " CA  ALA A 291 " =    0.810
peak=    3.581 closest distance to " O   HOH Z  68 " =    1.858
peak=    3.573 closest distance to " CA  ARG A 195 " =    1.331
peak=    3.558 closest distance to " CA  ALA A  84 " =    1.174
peak=    3.558 closest distance to " O   HOH Z 180 " =    2.359
peak=    3.556 closest distance to " O   HOH Z 173 " =    2.061
peak=    3.548 closest distance to " CB  SER A 141 " =    1.005
peak=    3.538 closest distance to " CG2 THR A 221 " =    1.270
peak=    3.534 closest distance to " O   HOH Z 416 " =    2.881
peak=    3.534 closest distance to " O   HOH Z  21 " =    1.797
peak=    3.528 closest distance to " O   HOH Z 365 " =    2.727
peak=    3.528 closest distance to " O   HOH Z 361 " =    3.522
peak=    3.525 closest distance to " O   HOH Z 374 " =    3.027
peak=    3.521 closest distance to " CA  ALA A 160 " =    0.859
peak=    3.517 closest distance to " O   HOH Z 250 " =    1.636
peak=    3.514 closest distance to " CB  ASN A  39 " =    0.796
peak=    3.512 closest distance to " CA  ASN A 215 " =    1.133
peak=    3.509 closest distance to " NE2 GLN A  77 " =    3.150
peak=    3.505 closest distance to " O   HOH Z 305 " =    3.583
peak=    3.504 closest distance to " O   HOH Z 258 " =    2.192
peak=    3.500 closest distance to " CA  THR A 221 " =    0.986
peak=    3.500 closest distance to " NH2AARG A 275 " =    3.645
peak=    3.495 closest distance to " O   HOH Z 374 " =    2.597
peak=    3.493 closest distance to " O   HOH Z  88 " =    3.411
peak=    3.493 closest distance to " CG2 VAL A 197 " =    1.169
peak=    3.486 closest distance to " CZ  PHE A 218 " =    1.103
peak=    3.485 closest distance to " O   HOH Z 126 " =    1.536
peak=    3.483 closest distance to " O   HOH Z 130 " =    2.397
peak=    3.483 closest distance to " OG BSER A 164 " =    2.276
peak=    3.482 closest distance to " ND1 HIS A  81 " =    1.553
peak=    3.481 closest distance to " CE  LYS A  76 " =    0.835
peak=    3.476 closest distance to " O   HOH Z 132 " =    2.573
peak=    3.475 closest distance to " CD  LYS A  76 " =    1.963
peak=    3.474 closest distance to " N   TYR A 116 " =    1.586
peak=    3.473 closest distance to " NH1AARG A 145 " =    1.274
peak=    3.461 closest distance to " CD  ARG A 159 " =    0.760
peak=    3.443 closest distance to " CB  SER A  62 " =    0.811
peak=    3.442 closest distance to " CB  LEU A 228 " =    1.137
peak=    3.438 closest distance to " CA  ALA A 248 " =    1.243
peak=    3.428 closest distance to " O   HOH Z 171 " =    1.888
peak=    3.428 closest distance to " CB  TYR A 169 " =    0.991
peak=    3.428 closest distance to " O   HOH Z 281 " =    4.626
peak=    3.423 closest distance to " O   HOH Z  85 " =    1.340
peak=    3.414 closest distance to " NZ  LYS A  48 " =    1.234
peak=    3.413 closest distance to " O   HOH Z 403 " =    1.450
peak=    3.409 closest distance to " CB  THR A  31 " =    1.724
peak=    3.409 closest distance to " O   HOH Z 344 " =    3.074
peak=    3.409 closest distance to " O   HOH Z 109 " =    2.325
peak=    3.407 closest distance to " O   HOH Z 193 " =    2.179
peak=    3.406 closest distance to " O   HOH Z 427 " =    3.062
peak=    3.400 closest distance to " OG  SER A  62 " =    2.829
peak=    3.396 closest distance to " CG  ARG A  66 " =    0.956
peak=    3.387 closest distance to " O   HOH Z 298 " =    2.392
peak=    3.374 closest distance to " CA  TYR A 116 " =    1.420
peak=    3.371 closest distance to " CG2BVAL A  41 " =    0.856
peak=    3.363 closest distance to " O   ALA A 165 " =    1.382
peak=    3.360 closest distance to " O   HOH Z 261 " =    1.903
peak=    3.357 closest distance to " CE  LYS A 119 " =    1.129
peak=    3.356 closest distance to " CD1 LEU A  96 " =    0.762
peak=    3.355 closest distance to " O   HOH Z  19 " =    1.577
peak=    3.352 closest distance to " O   HOH Z   1 " =    2.251
peak=    3.350 closest distance to " CA  ASP A 140 " =    1.138
peak=    3.350 closest distance to " OG1 THR A 294 " =    2.374
peak=    3.348 closest distance to " CB  GLN A  88 " =    1.124
peak=    3.348 closest distance to " O   HOH Z 425 " =    1.952
peak=    3.345 closest distance to " O   HOH Z 148 " =    3.234
peak=    3.342 closest distance to " CB  ALA A 291 " =    1.280
peak=    3.336 closest distance to " O   HOH Z 247 " =    1.328
peak=    3.325 closest distance to " CB  MET A  47 " =    0.996
peak=    3.323 closest distance to " CA  SER A  32 " =    1.571
peak=    3.315 closest distance to " O   HOH Z 336 " =    1.612
peak=    3.315 closest distance to " CD1 ILE A 106 " =    0.915
peak=    3.313 closest distance to " CD1 LEU A 300 " =    1.236
peak=    3.302 closest distance to " CA  ASP A 162 " =    1.157
peak=    3.295 closest distance to " CG  ARG A 219 " =    1.183
peak=    3.285 closest distance to " O   HOH Z  61 " =    1.503
peak=    3.281 closest distance to " CE1 TYR A 186 " =    1.245
peak=    3.276 closest distance to " O   HOH Z  66 " =    2.161
peak=    3.276 closest distance to " CG  LEU A 167 " =    1.211
peak=    3.272 closest distance to " CA  VAL A 125 " =    1.128
peak=    3.270 closest distance to " CA  MET A 105 " =    1.112
peak=    3.268 closest distance to " CA  MET A  40 " =    1.066
peak=    3.265 closest distance to " O   HOH Z  89 " =    2.150
peak=    3.261 closest distance to " CG  MET A 185 " =    1.139
peak=    3.258 closest distance to " ND2 ASN A 110 " =    1.505
peak=    3.251 closest distance to " O   HOH Z 383 " =    2.109
peak=    3.249 closest distance to " O   HOH Z 353 " =    2.851
peak=    3.246 closest distance to " CB  ASN A 215 " =    1.193
peak=    3.241 closest distance to " N   CYS A 260 " =    0.822
peak=    3.237 closest distance to " CB  ASN A 285 " =    0.960
peak=    3.236 closest distance to " CZ2 TRP A 179 " =    1.699
peak=    3.231 closest distance to " O   HOH Z  88 " =    2.646
peak=    3.227 closest distance to " O   HOH Z 350 " =    1.922
peak=    3.227 closest distance to " CZ  PHE A  38 " =    1.330
peak=    3.222 closest distance to " O   HOH Z  94 " =    2.331
peak=    3.215 closest distance to " O   HOH Z 421 " =    2.423
peak=    3.213 closest distance to " CB  ILE A 120 " =    1.328
peak=    3.212 closest distance to " NH2 ARG A 156 " =    1.162
peak=    3.210 closest distance to " CB  GLU A  46 " =    1.012
peak=    3.208 closest distance to " CD1 LEU A 228 " =    1.609
peak=    3.201 closest distance to " O   HOH Z 251 " =    1.553
peak=    3.195 closest distance to " O   SER A  26 " =    1.646
peak=    3.193 closest distance to " CB  THR A  52 " =    0.776
peak=    3.191 closest distance to " O   HOH Z 435 " =    2.996
peak=    3.183 closest distance to " O   ALA A 242 " =    1.079
peak=    3.182 closest distance to " CD  ARG A  66 " =    2.807
peak=    3.180 closest distance to " CA  LEU A  83 " =    1.278
peak=    3.177 closest distance to " O   HOH Z  49 " =    2.293
peak=    3.176 closest distance to " O   HOH Z 189 " =    2.435
peak=    3.175 closest distance to " CB  GLN A 103 " =    0.840
peak=    3.171 closest distance to " O   HOH Z 124 " =    1.247
peak=    3.170 closest distance to " O   HOH Z 380 " =    1.890
peak=    3.166 closest distance to " OH  TYR A 116 " =    1.074
peak=    3.165 closest distance to " CD  PRO A  54 " =    1.117
peak=    3.164 closest distance to " OG BSER A 134 " =    2.950
peak=    3.162 closest distance to " O   HOH Z  63 " =    2.278
peak=    3.162 closest distance to " O   HOH Z 367 " =    3.510
peak=    3.160 closest distance to " CA  ARG A 275 " =    1.872
peak=    3.156 closest distance to " CA  ALA A 299 " =    0.963
peak=    3.156 closest distance to " O   HOH Z 135 " =    1.764
peak=    3.155 closest distance to " CD  ARG A  79 " =    2.091
peak=    3.148 closest distance to " CB  ALA A   9 " =    1.585
peak=    3.139 closest distance to " CB  TYR A 116 " =    0.785
peak=    3.134 closest distance to " OE1 GLN A  11 " =    1.919
peak=    3.126 closest distance to " OG BSER A 134 " =    2.894
peak=    3.123 closest distance to " O   HOH Z 423 " =    3.388
peak=    3.122 closest distance to " O   HOH Z 438 " =    1.893
peak=    3.122 closest distance to " C   TYR A 214 " =    1.375
peak=    3.121 closest distance to " O   HOH Z 419 " =    1.556
peak=    3.118 closest distance to " CD  GLN A 194 " =    1.544
peak=    3.113 closest distance to " CB  SER A 212 " =    1.046
peak=    3.111 closest distance to " CG2 VAL A 257 " =    0.775
peak=    3.109 closest distance to " CG BARG A 102 " =    1.750
peak=    3.108 closest distance to " O   HOH Z 425 " =    1.222
peak=    3.105 closest distance to " CA  ASP A 191 " =    0.909
peak=    3.099 closest distance to " O   HOH Z 213 " =    1.783
peak=    3.088 closest distance to " O   HOH Z  30 " =    2.037
peak=    3.075 closest distance to " CA  GLU A 152 " =    0.836
peak=    3.073 closest distance to " O   HOH Z  88 " =    3.049
peak=    3.072 closest distance to " CD1AILE A 234 " =    0.909
peak=    3.067 closest distance to " CD  GLN A 240 " =    1.457
peak=    3.066 closest distance to " O   HOH Z 329 " =    3.998
peak=    3.059 closest distance to " CB  ALA A 227 " =    1.130
peak=    3.050 closest distance to " CA  SER A  87 " =    1.027
peak=    3.041 closest distance to " CA  GLY A  80 " =    0.784

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.853 - 5.576
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.853 - 5.576

peak=   -4.895 closest distance to " O   HOH Z 266 " =    4.815
peak=   -4.582 closest distance to " C   HIS A 108 " =    1.120
peak=   -4.477 closest distance to " CD  ARG A 156 " =    2.065
peak=   -4.442 closest distance to " CD  GLN A  58 " =    1.126
peak=   -4.294 closest distance to " O   HOH Z 377 " =    2.198
peak=   -4.293 closest distance to " SG  CYS A 254 " =    3.388
peak=   -4.267 closest distance to " O   HOH Z  13 " =    1.739
peak=   -4.245 closest distance to " OXT GLY A 302 " =    2.854
peak=   -4.224 closest distance to " O   VAL A  67 " =    2.694
peak=   -4.208 closest distance to " CD1 LEU A 101 " =    2.420
peak=   -4.177 closest distance to " CA  ASP A 298 " =    1.041
peak=   -4.102 closest distance to " OE1 GLN A 223 " =    2.159
peak=   -4.087 closest distance to " CB  PRO A 243 " =    2.685
peak=   -4.083 closest distance to " OG  SER A  97 " =    2.239
peak=   -4.080 closest distance to " CB  ALA A 184 " =    2.353
peak=   -4.036 closest distance to " OG BSER A 134 " =    1.380
peak=   -3.990 closest distance to " O   HOH Z 372 " =    2.335
peak=   -3.981 closest distance to " O   VAL A  67 " =    2.921
peak=   -3.966 closest distance to " CG  ASP A 132 " =    2.323
peak=   -3.921 closest distance to " O   HOH Z 198 " =    2.022
peak=   -3.913 closest distance to " CB  ALA A 291 " =    2.297
peak=   -3.893 closest distance to " O   HOH Z 353 " =    2.242
peak=   -3.891 closest distance to " O   PHE A 218 " =    1.575
peak=   -3.842 closest distance to " O   PRO A 163 " =    2.131
peak=   -3.838 closest distance to " O   HOH Z 165 " =    1.902
peak=   -3.836 closest distance to " CB  ALA A 161 " =    2.577
peak=   -3.835 closest distance to " O   HOH Z  10 " =    1.552
peak=   -3.826 closest distance to " CB  PHE A 192 " =    2.047
peak=   -3.800 closest distance to " O   HOH Z 292 " =    4.538
peak=   -3.785 closest distance to " O   HOH Z 196 " =    1.983
peak=   -3.771 closest distance to " N   ALA A 248 " =    1.756
peak=   -3.761 closest distance to " ND2 ASN A 187 " =    1.543
peak=   -3.722 closest distance to " CZ3 TRP A 179 " =    1.262
peak=   -3.721 closest distance to " CG1 VAL A 112 " =    2.720
peak=   -3.713 closest distance to " CD  ARG A 139 " =    1.607
peak=   -3.712 closest distance to " O   HOH Z 394 " =    1.545
peak=   -3.711 closest distance to " NE2 GLN A  88 " =    1.731
peak=   -3.691 closest distance to " CD1 PHE A  59 " =    1.983
peak=   -3.684 closest distance to " ND2 ASN A  45 " =    1.111
peak=   -3.668 closest distance to " O   HOH Z 166 " =    1.656
peak=   -3.663 closest distance to " CD2 LEU A 237 " =    2.520
peak=   -3.660 closest distance to " O   HOH Z  71 " =    1.909
peak=   -3.657 closest distance to " CZ  TYR A 169 " =    1.844
peak=   -3.654 closest distance to " OG BSER A 134 " =    1.775
peak=   -3.652 closest distance to " CD1 LEU A  25 " =    2.497
peak=   -3.652 closest distance to " O   HOH Z 114 " =    3.317
peak=   -3.631 closest distance to " OD2 ASP A 171 " =    2.477
peak=   -3.621 closest distance to " O   SER A 210 " =    1.899
peak=   -3.621 closest distance to " CB  ASN A  39 " =    2.347
peak=   -3.617 closest distance to " O   PRO A 198 " =    1.320
peak=   -3.617 closest distance to " CG1AVAL A  41 " =    2.683
peak=   -3.616 closest distance to " O   HOH Z 389 " =    1.777
peak=   -3.605 closest distance to " O   HOH Z 407 " =    2.860
peak=   -3.602 closest distance to " CB  ALA A 248 " =    2.212
peak=   -3.594 closest distance to " O   HOH Z  11 " =    2.065
peak=   -3.592 closest distance to " O   HOH Z 395 " =    5.149
peak=   -3.592 closest distance to " CE2 TYR A  30 " =    2.670
peak=   -3.590 closest distance to " CB  PHE A 208 " =    2.283
peak=   -3.589 closest distance to " N   THR A 235 " =    1.395
peak=   -3.576 closest distance to " O   HOH Z 351 " =    1.497
peak=   -3.574 closest distance to " N   ALA A 248 " =    2.076
peak=   -3.565 closest distance to " O   HOH Z 252 " =    3.511
peak=   -3.560 closest distance to " OD1 ASP A 171 " =    1.592
peak=   -3.544 closest distance to " OD1 ASN A  39 " =    2.251
peak=   -3.543 closest distance to " O   HOH Z 123 " =    2.341
peak=   -3.533 closest distance to " OE1 GLN A 223 " =    1.937
peak=   -3.531 closest distance to " OD1 ASN A 148 " =    1.514
peak=   -3.520 closest distance to " CG2 ILE A 263 " =    2.250
peak=   -3.519 closest distance to " CG2 ILE A  49 " =    2.669
peak=   -3.515 closest distance to " N   THR A  52 " =    1.717
peak=   -3.509 closest distance to " CD  LYS A 289 " =    2.410
peak=   -3.508 closest distance to " O   HOH Z 234 " =    4.057
peak=   -3.505 closest distance to " O   ALA A  34 " =    2.138
peak=   -3.497 closest distance to " O   HOH Z 111 " =    2.021
peak=   -3.491 closest distance to " O   LEU A 167 " =    1.574
peak=   -3.488 closest distance to " O   HOH Z 102 " =    1.621
peak=   -3.487 closest distance to " O   GLY A  80 " =    2.466
peak=   -3.486 closest distance to " CG1 VAL A 112 " =    2.816
peak=   -3.481 closest distance to " O   HOH Z 126 " =    1.849
peak=   -3.472 closest distance to " CG1 VAL A  67 " =    3.203
peak=   -3.471 closest distance to " CB  ALA A  43 " =    2.438
peak=   -3.470 closest distance to " CB  ALA A  10 " =    2.258
peak=   -3.470 closest distance to " CG1 VAL A  78 " =    2.727
peak=   -3.466 closest distance to " CE1 TYR A 247 " =    2.694
peak=   -3.452 closest distance to " CD2 TYR A 247 " =    2.386
peak=   -3.450 closest distance to " O   HOH Z 414 " =    1.358
peak=   -3.439 closest distance to " O   HOH Z  15 " =    1.475
peak=   -3.438 closest distance to " O   VAL A 174 " =    2.176
peak=   -3.434 closest distance to " O   HOH Z 283 " =    2.124
peak=   -3.429 closest distance to " CG2 VAL A 189 " =    2.180
peak=   -3.422 closest distance to " O   HOH Z 422 " =    1.521
peak=   -3.421 closest distance to " O   HOH Z  52 " =    1.573
peak=   -3.415 closest distance to " O   HOH Z 377 " =    1.764
peak=   -3.415 closest distance to " O   HOH Z 171 " =    2.127
peak=   -3.414 closest distance to " O   HOH Z 435 " =    2.668
peak=   -3.401 closest distance to " OG  SER A  26 " =    1.298
peak=   -3.397 closest distance to " CD2 PHE A 225 " =    1.315
peak=   -3.392 closest distance to " OE1 GLN A 183 " =    1.481
peak=   -3.391 closest distance to " O   PRO A 198 " =    1.312
peak=   -3.389 closest distance to " O   HOH Z 243 " =    2.056
peak=   -3.387 closest distance to " OD2 ASP A 191 " =    1.494
peak=   -3.387 closest distance to " O   TRP A  92 " =    1.840
peak=   -3.377 closest distance to " NH2 ARG A  79 " =    2.080
peak=   -3.376 closest distance to " CG  GLU A  53 " =    1.483
peak=   -3.373 closest distance to " O   SER A 135 " =    1.591
peak=   -3.361 closest distance to " N   SER A 276 " =    1.408
peak=   -3.361 closest distance to " CD  GLN A 223 " =    1.454
peak=   -3.357 closest distance to " O   HOH Z  38 " =    1.690
peak=   -3.357 closest distance to " O   HOH Z 290 " =    1.266
peak=   -3.354 closest distance to " CB  ASP A 286 " =    1.865
peak=   -3.351 closest distance to " CA  ALA A 248 " =    2.622
peak=   -3.351 closest distance to " O   HOH Z   6 " =    1.728
peak=   -3.343 closest distance to " CZ2 TRP A 274 " =    1.148
peak=   -3.343 closest distance to " N   GLN A  58 " =    1.628
peak=   -3.341 closest distance to " O   HOH Z 185 " =    2.424
peak=   -3.341 closest distance to " O   HOH Z 193 " =    1.684
peak=   -3.339 closest distance to " CA  GLY A 203 " =    2.319
peak=   -3.336 closest distance to " ND2 ASN A  45 " =    1.626
peak=   -3.329 closest distance to " CD2 LEU A 237 " =    2.428
peak=   -3.327 closest distance to " CD1 LEU A 228 " =    2.105
peak=   -3.323 closest distance to " CB  ALA A 248 " =    2.067
peak=   -3.320 closest distance to " CB  SER A 258 " =    2.030
peak=   -3.319 closest distance to " O   VAL A 189 " =    1.775
peak=   -3.318 closest distance to " NH2 ARG A  66 " =    1.965
peak=   -3.317 closest distance to " CG1 VAL A 125 " =    2.242
peak=   -3.310 closest distance to " NE2 GLN A 194 " =    1.843
peak=   -3.309 closest distance to " O   HOH Z 177 " =    1.628
peak=   -3.308 closest distance to " CG  GLU A   2 " =    1.809
peak=   -3.305 closest distance to " O   HOH Z 361 " =    3.404
peak=   -3.302 closest distance to " SG ACYS A 201 " =    2.092
peak=   -3.301 closest distance to " CD1 ILE A 239 " =    2.208
peak=   -3.298 closest distance to " O   HOH Z 166 " =    1.731
peak=   -3.297 closest distance to " CG  PRO A 243 " =    1.728
peak=   -3.296 closest distance to " CZ  ARG A  66 " =    1.272
peak=   -3.291 closest distance to " CB  PRO A 163 " =    2.529
peak=   -3.288 closest distance to " O   HOH Z  19 " =    2.123
peak=   -3.287 closest distance to " CA  GLY A 133 " =    2.336
peak=   -3.286 closest distance to " O   ALA A 160 " =    1.483
peak=   -3.283 closest distance to " O   GLY A  75 " =    1.859
peak=   -3.283 closest distance to " CB  GLN A  11 " =    1.861
peak=   -3.282 closest distance to " CE  MET A 105 " =    2.212
peak=   -3.280 closest distance to " CD2 TYR A 293 " =    1.910
peak=   -3.278 closest distance to " O   ILE A 234 " =    1.284
peak=   -3.276 closest distance to " CZ  PHE A  59 " =    1.686
peak=   -3.275 closest distance to " NH2AARG A 275 " =    5.124
peak=   -3.274 closest distance to " O   HOH Z 311 " =    3.701
peak=   -3.272 closest distance to " O   HOH Z  43 " =    1.695
peak=   -3.266 closest distance to " O   VAL A 189 " =    2.618
peak=   -3.257 closest distance to " O   ALA A  10 " =    1.830
peak=   -3.255 closest distance to " ND2 ASN A  69 " =    1.650
peak=   -3.254 closest distance to " O   ALA A   1 " =    1.900
peak=   -3.251 closest distance to " NE2 GLN A 103 " =    1.652
peak=   -3.248 closest distance to " C   LEU A 143 " =    1.031
peak=   -3.247 closest distance to " N   ALA A 226 " =    1.935
peak=   -3.241 closest distance to " CE3 TRP A 150 " =    2.224
peak=   -3.239 closest distance to " OG BSER A 210 " =    2.182
peak=   -3.239 closest distance to " CG2 THR A 178 " =    2.264
peak=   -3.236 closest distance to " CA  GLY A 241 " =    2.388
peak=   -3.233 closest distance to " CB  PHE A  16 " =    2.592
peak=   -3.232 closest distance to " OG  SER A   3 " =    1.810
peak=   -3.227 closest distance to " O   GLY A  80 " =    2.573
peak=   -3.224 closest distance to " NE1 TRP A 266 " =    2.402
peak=   -3.216 closest distance to " NE  ARG A  66 " =    4.287
peak=   -3.214 closest distance to " O   SER A  95 " =    1.571
peak=   -3.212 closest distance to " O   MET A  40 " =    2.729
peak=   -3.209 closest distance to " O   HOH Z 281 " =    2.552
peak=   -3.205 closest distance to " NH2 ARG A  66 " =    5.576
peak=   -3.201 closest distance to " CE  LYS A 166 " =    2.977
peak=   -3.198 closest distance to " CB  ALA A 291 " =    2.332
peak=   -3.191 closest distance to " CG  ASP A 231 " =    0.853
peak=   -3.191 closest distance to " O   HOH Z  11 " =    1.866
peak=   -3.177 closest distance to " O   ASN A  45 " =    1.851
peak=   -3.175 closest distance to " NH1 ARG A 195 " =    2.626
peak=   -3.168 closest distance to " CZ3 TRP A 274 " =    2.447
peak=   -3.166 closest distance to " O   SER A   3 " =    1.132
peak=   -3.166 closest distance to " CG  PHE A 283 " =    2.505
peak=   -3.161 closest distance to " O   HOH Z 211 " =    1.607
peak=   -3.161 closest distance to " O   HOH Z 251 " =    1.513
peak=   -3.160 closest distance to " O   HOH Z 412 " =    4.515
peak=   -3.149 closest distance to " OG1 THR A  82 " =    1.512
peak=   -3.147 closest distance to " O   HOH Z 139 " =    3.221
peak=   -3.143 closest distance to " O   HOH Z 213 " =    1.540
peak=   -3.141 closest distance to " CD2 LEU A 300 " =    2.738
peak=   -3.132 closest distance to " O   HOH Z  37 " =    1.783
peak=   -3.132 closest distance to " O   HOH Z 427 " =    1.446
peak=   -3.130 closest distance to " C   ALA A 158 " =    1.297
peak=   -3.127 closest distance to " CB  TRP A  85 " =    2.540
peak=   -3.125 closest distance to " NE2 GLN A  88 " =    1.080
peak=   -3.117 closest distance to " O   HOH Z 171 " =    2.085
peak=   -3.115 closest distance to " O   HOH Z 351 " =    1.353
peak=   -3.107 closest distance to " O   PRO A 198 " =    1.687
peak=   -3.105 closest distance to " O   HOH Z 250 " =    1.511
peak=   -3.096 closest distance to " C   SER A 206 " =    1.546
peak=   -3.096 closest distance to " ND2 ASN A  39 " =    1.167
peak=   -3.092 closest distance to " O   ASN A 301 " =    1.377
peak=   -3.090 closest distance to " CZ  PHE A  38 " =    2.000
peak=   -3.083 closest distance to " O   HOH Z  41 " =    2.166
peak=   -3.082 closest distance to " O   HOH Z 362 " =    4.274
peak=   -3.075 closest distance to " O   GLU A 152 " =    1.490
peak=   -3.074 closest distance to " CG  GLU A 152 " =    1.729
peak=   -3.052 closest distance to " O   HOH Z 265 " =    2.272
peak=   -3.051 closest distance to " O   HOH Z 174 " =    2.243
peak=   -3.050 closest distance to " O   HOH Z  56 " =    1.315
peak=   -3.048 closest distance to " CB  ALA A   9 " =    2.477
peak=   -3.043 closest distance to " CA  GLY A 241 " =    3.235
peak=   -3.039 closest distance to " N   VAL A 189 " =    1.672
peak=   -3.035 closest distance to " O   HOH Z  77 " =    2.159
peak=   -3.007 closest distance to " O   HOH Z  91 " =    2.239

================= 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    :  0.3758 0.3673   6.159698e+00   6.134097e+00
   1_bss:  0.3647 0.3542   6.142658e+00   6.113175e+00
   1_xyz:  0.2021 0.2245   5.616632e+00   5.714859e+00
   1_adp:  0.1839 0.2295   5.568409e+00   5.744645e+00
   1_occ:  0.1836 0.2300   5.567786e+00   5.744812e+00
   2_bss:  0.1803 0.2260   5.555872e+00   5.730562e+00
   2_xyz:  0.1327 0.1754   5.280906e+00   5.491007e+00
   2_adp:  0.1245 0.1651   5.220421e+00   5.431357e+00
   2_occ:  0.1244 0.1650   5.219745e+00   5.431097e+00
   3_bss:  0.1246 0.1636   5.218048e+00   5.425781e+00
   3_xyz:  0.1126 0.1564   5.150181e+00   5.381720e+00
   3_adp:  0.1112 0.1553   5.139238e+00   5.374045e+00
   3_occ:  0.1112 0.1554   5.138995e+00   5.374191e+00
   4_bss:  0.1111 0.1553   5.138848e+00   5.374107e+00
   4_xyz:  0.1142 0.1559   5.156240e+00   5.379589e+00
   4_adp:  0.1133 0.1578   5.157478e+00   5.389818e+00
   4_occ:  0.1133 0.1578   5.157367e+00   5.389835e+00
   5_bss:  0.1132 0.1578   5.157420e+00   5.389913e+00
   5_xyz:  0.1075 0.1567   5.127789e+00   5.379220e+00
   5_adp:  0.1070 0.1574   5.126722e+00   5.382131e+00
   5_occ:  0.1069 0.1574   5.126622e+00   5.382173e+00
   5_bss:  0.1068 0.1573   5.126609e+00   5.382206e+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:  0.297  30.587  -1.415   2.952  -1.686   0.000  -0.000  -0.000
   1_xyz:  0.297  30.587  -1.415   2.952  -1.686   0.000  -0.000  -0.000
   1_adp:  0.297  30.587  -1.415   2.952  -1.686   0.000  -0.000  -0.000
   1_occ:  0.297  30.587  -1.415   2.952  -1.686   0.000  -0.000  -0.000
   2_bss:  0.321  50.620  -2.805  -0.362  -1.621  -0.000  -0.000  -0.000
   2_xyz:  0.321  50.620  -2.805  -0.362  -1.621  -0.000  -0.000  -0.000
   2_adp:  0.321  50.620  -2.805  -0.362  -1.621  -0.000  -0.000  -0.000
   2_occ:  0.321  50.620  -2.805  -0.362  -1.621  -0.000  -0.000  -0.000
   3_bss:  0.324  51.871  -2.872  -1.273  -1.283  -0.000  -0.000  -0.000
   3_xyz:  0.324  51.871  -2.872  -1.273  -1.283  -0.000  -0.000  -0.000
   3_adp:  0.324  51.871  -2.872  -1.273  -1.283  -0.000  -0.000  -0.000
   3_occ:  0.324  51.871  -2.872  -1.273  -1.283  -0.000  -0.000  -0.000
   4_bss:  0.325  51.871  -2.832  -1.490  -1.108  -0.000  -0.000  -0.000
   4_xyz:  0.325  51.871  -2.832  -1.490  -1.108  -0.000  -0.000  -0.000
   4_adp:  0.325  51.871  -2.832  -1.490  -1.108  -0.000  -0.000  -0.000
   4_occ:  0.325  51.871  -2.832  -1.490  -1.108  -0.000  -0.000  -0.000
   5_bss:  0.324  51.871  -2.658  -1.398  -0.908  -0.000  -0.000  -0.000
   5_xyz:  0.324  51.871  -2.658  -1.398  -0.908  -0.000  -0.000  -0.000
   5_adp:  0.324  51.871  -2.658  -1.398  -0.908  -0.000  -0.000  -0.000
   5_occ:  0.324  51.871  -2.658  -1.398  -0.908  -0.000  -0.000  -0.000
   5_bss:  0.322  53.635  -2.334  -1.132  -0.609  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.336 0.6410  0.8225    40457.146
   1_bss:  39.182 0.6530  0.8368    36991.260
   1_xyz:  22.195 0.8407  1.0057    13158.289
   1_adp:  23.167 0.8299  0.9938    13907.637
   1_occ:  23.188 0.8297  0.9934    13920.378
   2_bss:  22.677 0.8347  0.9481    13381.838
   2_xyz:  16.627 0.8919  0.9815     7816.578
   2_adp:  15.248 0.9044  0.9813     7004.111
   2_occ:  15.241 0.9044  0.9811     6997.528
   3_bss:  15.115 0.9053  0.9746     6880.646
   3_xyz:  14.120 0.9138  0.9788     6330.787
   3_adp:  13.914 0.9157  0.9741     6263.108
   3_occ:  13.910 0.9157  0.9740     6260.240
   4_bss:  13.908 0.9157  0.9743     6259.860
   4_xyz:  13.939 0.9157  0.9735     6290.524
   4_adp:  14.137 0.9142  0.9669     6405.338
   4_occ:  14.134 0.9142  0.9668     6404.041
   5_bss:  14.135 0.9142  0.9722     6403.821
   5_xyz:  13.948 0.9155  0.9734     6290.607
   5_adp:  14.004 0.9151  0.9660     6307.334
   5_occ:  14.003 0.9151  0.9660     6306.692
   5_bss:  14.003 0.9151  0.9759     6305.717
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7120e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7120e-01
   1_xyz:   1.382  0.013  0.083 15.313  0.005  4.113   1.1516e-01
   1_adp:   1.382  0.013  0.083 15.313  0.005  4.113   1.1516e-01
   1_occ:   1.382  0.013  0.083 15.313  0.005  4.113   1.1516e-01
   2_bss:   1.382  0.013  0.083 15.313  0.005  4.113   1.1516e-01
   2_xyz:   1.078  0.008  0.075 14.747  0.005  4.126   6.5204e-02
   2_adp:   1.078  0.008  0.075 14.747  0.005  4.126   6.5204e-02
   2_occ:   1.078  0.008  0.075 14.747  0.005  4.126   6.5204e-02
   3_bss:   1.078  0.008  0.075 14.747  0.005  4.126   6.5204e-02
   3_xyz:   1.094  0.009  0.080 14.893  0.005  4.112   6.9631e-02
   3_adp:   1.094  0.009  0.080 14.893  0.005  4.112   6.9631e-02
   3_occ:   1.094  0.009  0.080 14.893  0.005  4.112   6.9631e-02
   4_bss:   1.094  0.009  0.080 14.893  0.005  4.112   6.9631e-02
   4_xyz:   0.916  0.006  0.070 14.478  0.004  4.112   5.1106e-02
   4_adp:   0.916  0.006  0.070 14.478  0.004  4.112   5.1106e-02
   4_occ:   0.916  0.006  0.070 14.478  0.004  4.112   5.1106e-02
   5_bss:   0.916  0.006  0.070 14.478  0.004  4.112   5.1106e-02
   5_xyz:   1.109  0.009  0.083 14.841  0.005  4.113   7.2092e-02
   5_adp:   1.109  0.009  0.083 14.841  0.005  4.113   7.2092e-02
   5_occ:   1.109  0.009  0.083 14.841  0.005  4.113   7.2092e-02
   5_bss:   1.109  0.009  0.083 14.841  0.005  4.113   7.2092e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.590   2.4128e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.590   2.4128e-01
   1_xyz:   7.867  0.076  0.277 86.417  0.027  2.235   2.6751e-01
   1_adp:   7.867  0.076  0.277 86.417  0.027  2.235   2.6751e-01
   1_occ:   7.867  0.076  0.277 86.417  0.027  2.235   2.6751e-01
   2_bss:   7.867  0.076  0.277 86.417  0.027  2.235   2.6751e-01
   2_xyz:   7.677  0.055  0.264 81.861  0.044  2.303   4.9706e-02
   2_adp:   7.677  0.055  0.264 81.861  0.044  2.303   4.9706e-02
   2_occ:   7.677  0.055  0.264 81.861  0.044  2.303   4.9706e-02
   3_bss:   7.677  0.055  0.264 81.861  0.044  2.303   4.9706e-02
   3_xyz:   8.120  0.050  0.257 82.942  0.037  2.315   5.5380e-02
   3_adp:   8.120  0.050  0.257 82.942  0.037  2.315   5.5380e-02
   3_occ:   8.120  0.050  0.257 82.942  0.037  2.315   5.5380e-02
   4_bss:   8.120  0.050  0.257 82.942  0.037  2.315   5.5380e-02
   4_xyz:   6.795  0.042  0.224 82.010  0.037  2.393   2.8278e-02
   4_adp:   6.795  0.042  0.224 82.010  0.037  2.393   2.8278e-02
   4_occ:   6.795  0.042  0.224 82.010  0.037  2.393   2.8278e-02
   5_bss:   6.795  0.042  0.224 82.010  0.037  2.393   2.8278e-02
   5_xyz:   8.081  0.055  0.273 82.583  0.037  2.285   5.6806e-02
   5_adp:   8.081  0.055  0.273 82.583  0.037  2.285   5.6806e-02
   5_occ:   8.081  0.055  0.273 82.583  0.037  2.285   5.6806e-02
   5_bss:   8.081  0.055  0.273 82.583  0.037  2.285   5.6806e-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:  64.04   0.00  16.96  58.88   0.00  13.06  64.04   7.16  38.22
   1_occ:  64.04   0.00  16.96  58.88   0.00  13.06  64.04   7.16  38.22
   2_bss:  64.04   0.00  16.96  58.88   0.00  13.06  64.04   7.16  38.22
   2_xyz:  64.04   0.00  16.96  58.88   0.00  13.06  64.04   7.16  38.22
   2_adp:  76.55   2.00  16.70  76.55   2.00  12.77  67.78   6.05  38.07
   2_occ:  76.55   2.00  16.70  76.55   2.00  12.77  67.78   6.05  38.07
   3_bss:  76.55   2.00  16.70  76.55   2.00  12.77  67.78   6.05  38.07
   3_xyz:  76.55   2.00  16.70  76.55   2.00  12.77  67.78   6.05  38.07
   3_adp:  78.47   2.02  16.51  78.47   2.02  12.61  69.40   5.22  37.75
   3_occ:  78.47   2.02  16.51  78.47   2.02  12.61  69.40   5.22  37.75
   4_bss:  78.47   2.02  16.51  78.47   2.02  12.61  69.40   5.22  37.75
   4_xyz:  78.47   2.02  16.51  78.47   2.02  12.61  69.40   5.22  37.75
   4_adp:  82.33   1.01  16.58  82.33   1.01  12.54  72.41   5.30  38.58
   4_occ:  82.33   1.01  16.58  82.33   1.01  12.54  72.41   5.30  38.58
   5_bss:  82.33   1.01  16.58  82.33   1.01  12.54  72.41   5.30  38.58
   5_xyz:  82.33   1.01  16.58  82.33   1.01  12.54  72.41   5.30  38.58
   5_adp:  97.90   0.45  16.84  97.90   0.45  12.52  90.56   5.30  40.35
   5_occ:  97.90   0.45  16.84  97.90   0.45  12.52  90.56   5.30  40.35
   5_bss:  97.88   0.44  16.82  97.88   0.44  12.51  90.55   5.29  40.33
------------------------------------------------------------------------
 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:    1.258    0.017    0.428
   1_adp:    1.258    0.017    0.428
   1_occ:    1.258    0.017    0.428
   2_bss:    1.258    0.017    0.428
   2_xyz:    1.053    0.020    0.496
   2_adp:    1.053    0.020    0.496
   2_occ:    1.053    0.020    0.496
   3_bss:    1.053    0.020    0.496
   3_xyz:    1.075    0.037    0.531
   3_adp:    1.075    0.037    0.531
   3_occ:    1.075    0.037    0.531
   4_bss:    1.075    0.037    0.531
   4_xyz:    1.144    0.036    0.536
   4_adp:    1.144    0.036    0.536
   4_occ:    1.144    0.036    0.536
   5_bss:    1.144    0.036    0.536
   5_xyz:    1.202    0.052    0.543
   5_adp:    1.202    0.052    0.543
   5_occ:    1.202    0.052    0.543
   5_bss:    1.202    0.052    0.543
------------------------------------------------------------------------

CPU time actual refinement: 281.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_335/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_335/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_335/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_335/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_335/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 281.27 
  Macro-tasks:
    bulk solvent and scale       = 31.62  
    individual site refinement   = 119.80 
    weights calculation          = 24.18  
    collect and process          = 5.42   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 181.10 
  Micro-tasks:
    mask                            = 1.01   
    f_calc                          = 90.59  
    alpha_beta                      = 6.77   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 99.60  
    fmodel                         = 5.76   
    r_factors                      = 0.13   
    phase_errors                   = 9.03   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 214.11 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.916 micro seconds
Total CPU time: 4.88 minutes
from_scatterers_fft:    672 calls, 90.32 s
gradients_fft:          617 calls, 87.38 s

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

# Date 2008-01-16 Time 04:34:01 PST -0800 (1200486841.09 s)
Start R-work = 0.3758, R-free = 0.3673 (no bulk solvent and anisotropic scale)
Final R-work = 0.1288, R-free = 0.1748 (no bulk solvent and anisotropic scale)

Start R-work = 0.3647, R-free = 0.3542
Final R-work = 0.1068, R-free = 0.1573