# Date 2008-01-16 Time 04:38:44 PST -0800 (1200487124.27 s)
#phil __OFF__

Command line arguments: "../401.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24603
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 401

-------------------------------------------------------------------------------
  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: (69.5475, 46.4607, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


================================== 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: (69.5475, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.98017
Completeness in resolution range: 0.976764
Completeness with d_max=infinity: 0.973657

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8842
                             d_min =   1.9802

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: (69.5475, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.98017
Completeness in resolution range: 0.976764
Completeness with d_max=infinity: 0.973657

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8847 -  4.2364 [2110/2133]  1897   213  10.1%
  bin  2:  4.2364 -  3.3755 [2028/2048]  1827   201   9.9%
  bin  3:  3.3755 -  2.9526 [2002/2021]  1804   198   9.9%
  bin  4:  2.9526 -  2.6843 [1965/1995]  1765   200  10.2%
  bin  5:  2.6843 -  2.4929 [1979/1998]  1780   199  10.1%
  bin  6:  2.4929 -  2.3465 [1954/1979]  1758   196  10.0%
  bin  7:  2.3465 -  2.2294 [1938/1966]  1747   191   9.9%
  bin  8:  2.2294 -  2.1327 [1940/1976]  1747   193   9.9%
  bin  9:  2.1327 -  2.0508 [1940/1982]  1743   197  10.2%
  bin 10:  2.0508 -  1.9802 [1733/1957]  1562   171   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_401/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 25
        2.42 -     3.04: 2233
        3.04 -     3.66: 4745
        3.66 -     4.28: 9144
        4.28 -     4.90: 12437
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.985 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.082 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  2.118 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.127 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28579 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_401/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_401/model_refine_001.geo

CPU time processing inputs: 9.29


============================ 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 = 69.5475 46.4607 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: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3038   r_free= 0.2985   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.997737                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7248 0.99   1375  152 0.2760 0.2722      6.3231      6.2798|
|  2:  4.7248 -  3.7703 0.99   1310  149 0.2334 0.2223      6.3507       6.314|
|  3:  3.7703 -  3.2996 0.99   1291  142 0.2551 0.2491      6.2832      6.3553|
|  4:  3.2996 -  3.0006 0.99   1286  139 0.2707 0.3086      6.1656      6.2824|
|  5:  3.0006 -  2.7870 0.99   1267  145 0.3064 0.2629        6.05      5.9001|
|  6:  2.7870 -  2.6237 0.99   1277  138 0.3112 0.3344      5.9959      5.9463|
|  7:  2.6237 -  2.4929 0.99   1267  146 0.3150 0.2845      5.9347       5.827|
|  8:  2.4929 -  2.3848 0.98   1258  134 0.3342 0.3483      5.9379      5.9934|
|  9:  2.3848 -  2.2934 0.98   1245  143 0.3335 0.3365      5.8809      5.8604|
| 10:  2.2934 -  2.2145 1.00   1251  139 0.3442 0.3135      5.8799      5.7858|
| 11:  2.2145 -  2.1455 0.97   1263  139 0.3438 0.3562      5.8208      5.8616|
| 12:  2.1455 -  2.0843 0.98   1233  138 0.3646 0.3325      5.8203      5.7739|
| 13:  2.0843 -  2.0296 1.00   1258  138 0.3550 0.3344      5.7025      5.6686|
| 14:  2.0296 -  1.9802 0.84   1049  117 0.3784 0.3360      5.7152      5.5328|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.7248  1375   152  0.80  25.20   0.87     0.82      40106.49|
|  2:  4.7248 -  3.7703  1310   149  0.86  20.64   0.99     0.94      41246.78|
|  3:  3.7703 -  3.2996  1291   142  0.83  23.50   1.01     0.98      38984.70|
|  4:  3.2996 -  3.0006  1286   139  0.81  25.44   1.01     0.97      33778.28|
|  5:  3.0006 -  2.7870  1267   145  0.77  29.18   1.01     0.95      26824.18|
|  6:  2.7870 -  2.6237  1277   138  0.77  29.07   1.00     0.96      22777.69|
|  7:  2.6237 -  2.4929  1267   146  0.76  30.40   1.03     0.96      21188.46|
|  8:  2.4929 -  2.3848  1258   134  0.75  31.31   1.03     0.95      20879.45|
|  9:  2.3848 -  2.2934  1245   143  0.74  32.37   1.04     0.95      20069.35|
| 10:  2.2934 -  2.2145  1251   139  0.73  33.34   1.07     0.97      18932.56|
| 11:  2.2145 -  2.1455  1263   139  0.73  33.64   1.05     0.99      18014.40|
| 12:  2.1455 -  2.0843  1233   138  0.72  34.12   1.07     0.99      16488.56|
| 13:  2.0843 -  2.0296  1258   138  0.72  34.52   1.07     0.97      14037.26|
| 14:  2.0296 -  1.9802  1049   117  0.74  32.59   1.06     0.94      10778.45|
|alpha:            min =        0.82 max =            0.99 mean =         0.95|
|beta:             min =    10778.45 max =        41246.78 mean =     24949.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.77|
|phase err.(work): min =        0.00 max =           89.99 mean =        29.55|
|phase err.(test): min =        0.00 max =           89.77 mean =        29.31|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.627068              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.578   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.129   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      213 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2020 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1863 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2882 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4700 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4444 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5673 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6764 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.205 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.652)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3038   r_free= 0.2985   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.997737                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2887   r_free= 0.2817   ksol= 0.33   Bsol= 34.62   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.35,-1.63,0.00,-0.00,-0.00); trace/3= -1.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.971635                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.237316              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.505   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.302044              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.048   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2887      final r-factor (work) = 0.1660          |
| start r-factor (free) = 0.2817      final r-factor (free) = 0.1886          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8544 = 3.24 * 0.50 * 5.9873 + 1.00 * 0.1630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1973 = 3.24 * 0.50 * 5.6437 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1660      final r-factor (work) = 0.1513          |
| start r-factor (free) = 0.1886      final r-factor (free) = 0.1976          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7105 = 0.30 * 1.00 * 5.6437 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6304 = 0.30 * 1.00 * 5.3705 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.652)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.51    67.07   17.02    None  None   None       |
|    all(noH): 2823   0      0.51    67.07   17.02    None  None   None       |
|    Sol.    : 438    0      8.07    67.07   38.70    None  None   None       |
|    Mac.    : 2385   0      0.51    66.73   13.04    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:     0.506 -   7.162:  351   |   5:    33.786 -  40.443:  112        |
|      1:     7.162 -  13.818: 1319   |   6:    40.443 -  47.099:   90        |
|      2:    13.818 -  20.474:  512   |   7:    47.099 -  53.755:   85        |
|      3:    20.474 -  27.130:  178   |   8:    53.755 -  60.411:   56        |
|      4:    27.130 -  33.786:   99   |   9:    60.411 -  67.067:   21        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1513 r_free = 0.1976             target_work(ml) = 5.389         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1510 r_free = 0.1975             target_work(ml) = 5.387         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1510   r_free= 0.1975   ksol= 0.33   Bsol= 34.62   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.35,-1.63,0.00,-0.00,-0.00); trace/3= -1.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.387475                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1497   r_free= 0.1953   ksol= 0.32   Bsol= 40.52   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.97,-1.72,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.380871                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.493917              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.112  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.091955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.377  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1497      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1953      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7743 = 2.49 * 0.50 * 5.3829 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6402 = 2.49 * 0.50 * 5.2811 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4939 = 0.09 * 1.00 * 5.2811 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4819 = 0.09 * 1.00 * 5.1733 + 1.00 * 0.0061                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.652)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.32    67.33   16.60    None  None   None       |
|    all(noH): 2823   0      2.32    67.33   16.60    None  None   None       |
|    Sol.    : 438    0      5.91    67.33   36.77    None  None   None       |
|    Mac.    : 2385   0      2.32    66.02   12.90    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:     2.322 -   8.823:  627   |   5:    34.827 -  41.328:  122        |
|      1:     8.823 -  15.324: 1262   |   6:    41.328 -  47.829:   79        |
|      2:    15.324 -  21.825:  382   |   7:    47.829 -  54.329:   68        |
|      3:    21.825 -  28.326:  123   |   8:    54.329 -  60.830:   37        |
|      4:    28.326 -  34.827:  110   |   9:    60.830 -  67.331:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1553             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1554             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1554   ksol= 0.32   Bsol= 40.52   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.97,-1.72,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1552   ksol= 0.32   Bsol= 41.21   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.41,-1.38,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149970                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.098704              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.347  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.795948              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.304  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1512          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4823 = 2.10 * 0.50 * 5.1721 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4346 = 2.10 * 0.50 * 5.1232 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.3302 = 2.80 * 1.00 * 5.1232 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.2557 = 2.80 * 1.00 * 5.0956 + 1.00 * 0.0087                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.652)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    78.83   17.09    None  None   None       |
|    all(noH): 2823   0      0.72    78.83   17.09    None  None   None       |
|    Sol.    : 438    0      4.36    75.55   39.57    None  None   None       |
|    Mac.    : 2385   0      0.72    78.83   12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.715 -   8.526:  645   |   5:    39.770 -  47.581:  114        |
|      1:     8.526 -  16.337: 1324   |   6:    47.581 -  55.392:   74        |
|      2:    16.337 -  24.148:  341   |   7:    55.392 -  63.203:   61        |
|      3:    24.148 -  31.959:  125   |   8:    63.203 -  71.014:   26        |
|      4:    31.959 -  39.770:  104   |   9:    71.014 -  78.825:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1516             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1516             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1516   ksol= 0.32   Bsol= 41.21   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.41,-1.38,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099365                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1515   ksol= 0.32   Bsol= 44.59   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.38,-1.20,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.098762                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.396289              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.890  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.508776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.977  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1072      final r-factor (work) = 0.1053          |
| start r-factor (free) = 0.1515      final r-factor (free) = 0.1518          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1639 = 2.40 * 0.50 * 5.0957 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1596 = 2.40 * 0.50 * 5.0910 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1053      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5989 = 0.51 * 1.00 * 5.0910 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5991 = 0.51 * 1.00 * 5.0913 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.652)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.77    80.26   16.88    None  None   None       |
|    all(noH): 2823   0      0.77    80.26   16.88    None  None   None       |
|    Sol.    : 438    0      5.73    76.56   39.26    None  None   None       |
|    Mac.    : 2385   0      0.77    80.26   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:     0.774 -   8.723:  738   |   5:    40.517 -  48.465:  104        |
|      1:     8.723 -  16.671: 1270   |   6:    48.465 -  56.414:   76        |
|      2:    16.671 -  24.620:  312   |   7:    56.414 -  64.362:   57        |
|      3:    24.620 -  32.568:  122   |   8:    64.362 -  72.311:   20        |
|      4:    32.568 -  40.517:  117   |   9:    72.311 -  80.259:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1051 r_free = 0.1520             target_work(ml) = 5.092         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1051 r_free = 0.1520             target_work(ml) = 5.092         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1051   r_free= 0.1520   ksol= 0.32   Bsol= 44.59   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.38,-1.20,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.092470                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1520   ksol= 0.32   Bsol= 45.34   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.21,-0.96,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.092493                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.262455              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.684  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.292180              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.006  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1050      final r-factor (work) = 0.1049          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8205 = 2.26 * 0.50 * 5.0924 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8184 = 2.26 * 0.50 * 5.0925 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1049      final r-factor (work) = 0.1052          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4967 = 0.29 * 1.00 * 5.0925 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4971 = 0.29 * 1.00 * 5.0967 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.652)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    81.78   16.47    None  None   None       |
|    all(noH): 2823   0      1.03    81.78   16.47    None  None   None       |
|    Sol.    : 438    0      6.22    78.08   37.91    None  None   None       |
|    Mac.    : 2385   0      1.03    81.78   12.53    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:     1.029 -   9.104:  876   |   5:    41.405 -  49.480:  100        |
|      1:     9.104 -  17.179: 1196   |   6:    49.480 -  57.555:   70        |
|      2:    17.179 -  25.255:  270   |   7:    57.555 -  65.630:   32        |
|      3:    25.255 -  33.330:  130   |   8:    65.630 -  73.705:   13        |
|      4:    33.330 -  41.405:  131   |   9:    73.705 -  81.781:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1052 r_free = 0.1525             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1052 r_free = 0.1525             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1525   ksol= 0.32   Bsol= 45.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.21,-0.96,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095421                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7248 0.99   1375  152 0.0979 0.1253      5.3678      5.5081|
|  2:  4.7248 -  3.7703 0.99   1310  149 0.0829 0.1113      5.4209      5.6265|
|  3:  3.7703 -  3.2996 0.99   1291  142 0.1013 0.1505       5.447      5.8512|
|  4:  3.2996 -  3.0006 0.99   1286  139 0.1124 0.1482      5.4028      5.5406|
|  5:  3.0006 -  2.7870 0.99   1267  145 0.1219 0.1685       5.276       5.524|
|  6:  2.7870 -  2.6237 0.99   1277  138 0.1124 0.1798      5.1684      5.4171|
|  7:  2.6237 -  2.4929 0.99   1267  146 0.1174 0.1578      5.1167      5.3277|
|  8:  2.4929 -  2.3848 0.98   1258  134 0.1098 0.1678      5.0237      5.3191|
|  9:  2.3848 -  2.2934 0.98   1245  143 0.1081 0.1675        4.97      5.2294|
| 10:  2.2934 -  2.2145 1.00   1251  139 0.1042 0.1667      4.9111      5.1916|
| 11:  2.2145 -  2.1455 0.97   1263  139 0.1049 0.1658      4.8946      5.1885|
| 12:  2.1455 -  2.0843 0.98   1233  138 0.1059 0.1631      4.8304      5.2011|
| 13:  2.0843 -  2.0296 1.00   1258  138 0.1022 0.1617      4.7434      5.0202|
| 14:  2.0296 -  1.9802 0.84   1049  117 0.0961 0.1672      4.6199      4.8998|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.7248  1375   152  0.94   9.07   0.98     0.95       6918.93|
|  2:  4.7248 -  3.7703  1310   149  0.95   7.74   1.02     1.01       8853.40|
|  3:  3.7703 -  3.2996  1291   142  0.94  10.66   1.03     1.02       9829.45|
|  4:  3.2996 -  3.0006  1286   139  0.93  12.66   1.01     0.99       9475.31|
|  5:  3.0006 -  2.7870  1267   145  0.91  14.68   1.00     0.97       7590.60|
|  6:  2.7870 -  2.6237  1277   138  0.91  15.26   0.99     0.96       6590.79|
|  7:  2.6237 -  2.4929  1267   146  0.91  14.92   0.99     0.96       5731.11|
|  8:  2.4929 -  2.3848  1258   134  0.92  13.83   0.99     0.97       4752.72|
|  9:  2.3848 -  2.2934  1245   143  0.92  14.38   1.01     0.99       4523.02|
| 10:  2.2934 -  2.2145  1251   139  0.91  14.43   1.00     0.96       3913.98|
| 11:  2.2145 -  2.1455  1263   139  0.91  15.26   1.00     0.97       4127.31|
| 12:  2.1455 -  2.0843  1233   138  0.91  14.61   1.01     0.99       3598.08|
| 13:  2.0843 -  2.0296  1258   138  0.91  14.63   1.00     0.99       3072.25|
| 14:  2.0296 -  1.9802  1049   117  0.93  13.36   0.98     0.95       2337.99|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2337.99 max =         9829.45 mean =      5885.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.87 mean =        13.20|
|phase err.(test): min =        0.00 max =           89.50 mean =        12.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1525   ksol= 0.32   Bsol= 44.33   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.04,-0.75,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1525   ksol= 0.32   Bsol= 44.33   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.04,-0.75,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095600                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7248 0.99   1375  152 0.0979 0.1254       5.369      5.5097|
|  2:  4.7248 -  3.7703 0.99   1310  149 0.0828 0.1111      5.4205      5.6255|
|  3:  3.7703 -  3.2996 0.99   1291  142 0.1012 0.1505      5.4466      5.8513|
|  4:  3.2996 -  3.0006 0.99   1286  139 0.1124 0.1483      5.4029      5.5411|
|  5:  3.0006 -  2.7870 0.99   1267  145 0.1220 0.1686      5.2764      5.5244|
|  6:  2.7870 -  2.6237 0.99   1277  138 0.1125 0.1798      5.1688      5.4173|
|  7:  2.6237 -  2.4929 0.99   1267  146 0.1175 0.1580      5.1171      5.3282|
|  8:  2.4929 -  2.3848 0.98   1258  134 0.1098 0.1679      5.0238      5.3193|
|  9:  2.3848 -  2.2934 0.98   1245  143 0.1081 0.1674      4.9702       5.229|
| 10:  2.2934 -  2.2145 1.00   1251  139 0.1042 0.1668      4.9113      5.1925|
| 11:  2.2145 -  2.1455 0.97   1263  139 0.1049 0.1659       4.895      5.1887|
| 12:  2.1455 -  2.0843 0.98   1233  138 0.1058 0.1631      4.8304      5.2014|
| 13:  2.0843 -  2.0296 1.00   1258  138 0.1022 0.1616      4.7433      5.0198|
| 14:  2.0296 -  1.9802 0.84   1049  117 0.0962 0.1671      4.6199      4.8995|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.7248  1375   152  0.94   9.09   0.98     0.96       6938.83|
|  2:  4.7248 -  3.7703  1310   149  0.95   7.75   1.02     1.01       8860.21|
|  3:  3.7703 -  3.2996  1291   142  0.94  10.65   1.03     1.03       9823.34|
|  4:  3.2996 -  3.0006  1286   139  0.93  12.66   1.01     0.99       9478.64|
|  5:  3.0006 -  2.7870  1267   145  0.91  14.69   1.01     0.98       7594.22|
|  6:  2.7870 -  2.6237  1277   138  0.91  15.27   0.99     0.96       6595.82|
|  7:  2.6237 -  2.4929  1267   146  0.91  14.93   0.99     0.96       5736.34|
|  8:  2.4929 -  2.3848  1258   134  0.92  13.83   1.00     0.98       4753.95|
|  9:  2.3848 -  2.2934  1245   143  0.92  14.38   1.01     0.99       4524.61|
| 10:  2.2934 -  2.2145  1251   139  0.91  14.43   1.01     0.96       3914.89|
| 11:  2.2145 -  2.1455  1263   139  0.91  15.26   1.01     0.98       4131.14|
| 12:  2.1455 -  2.0843  1233   138  0.91  14.62   1.02     1.00       3598.76|
| 13:  2.0843 -  2.0296  1258   138  0.91  14.63   1.01     1.00       3071.89|
| 14:  2.0296 -  1.9802  1049   117  0.93  13.36   0.99     0.95       2337.23|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2337.23 max =         9823.34 mean =      5888.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.20|
|phase err.(test): min =        0.00 max =           89.55 mean =        12.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.652)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    81.74   16.43    None  None   None       |
|    all(noH): 2823   0      0.99    81.74   16.43    None  None   None       |
|    Sol.    : 438    0      6.18    78.05   37.88    None  None   None       |
|    Mac.    : 2385   0      0.99    81.74   12.49    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:     0.994 -   9.069:  876   |   5:    41.369 -  49.444:  100        |
|      1:     9.069 -  17.144: 1196   |   6:    49.444 -  57.519:   70        |
|      2:    17.144 -  25.219:  270   |   7:    57.519 -  65.595:   32        |
|      3:    25.219 -  33.294:  130   |   8:    65.595 -  73.670:   13        |
|      4:    33.294 -  41.369:  131   |   9:    73.670 -  81.745:    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)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.481 - 4.607
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 277 from: 281
   mapped sites are within: 0.706 - 4.607

peak=    5.736 closest distance to " NE2 GLN A  11 " =    1.189
peak=    5.606 closest distance to " O   HOH Z 144 " =    1.789
peak=    5.498 closest distance to " O   HOH Z 126 " =    1.914
peak=    5.383 closest distance to " CB  ARG A 275 " =    0.928
peak=    5.371 closest distance to " NH2 ARG A  56 " =    2.115
peak=    5.335 closest distance to " CG  PRO A  54 " =    1.286
peak=    5.057 closest distance to " O   HOH Z 232 " =    2.378
peak=    4.983 closest distance to " CG  PRO A 213 " =    1.252
peak=    4.931 closest distance to " CB  GLN A 223 " =    1.464
peak=    4.734 closest distance to " CB  SER A  63 " =    1.140
peak=    4.686 closest distance to " CB  ARG A  79 " =    1.399
peak=    4.672 closest distance to " CB  GLU A 152 " =    1.246
peak=    4.655 closest distance to " CB  GLN A 183 " =    1.183
peak=    4.610 closest distance to " O   HOH Z 236 " =    2.161
peak=    4.609 closest distance to " ND2 ASN A 187 " =    1.525
peak=    4.582 closest distance to " O   HOH Z 427 " =    2.812
peak=    4.568 closest distance to " C   PRO A 198 " =    1.426
peak=    4.533 closest distance to " CB  PRO A  54 " =    0.970
peak=    4.520 closest distance to " O   HOH Z 303 " =    2.132
peak=    4.513 closest distance to " O   HOH Z  78 " =    1.812
peak=    4.439 closest distance to " O   HOH Z 369 " =    2.073
peak=    4.436 closest distance to " O   HOH Z  15 " =    2.311
peak=    4.423 closest distance to " O   HOH Z 209 " =    2.249
peak=    4.392 closest distance to " CG2 VAL A 257 " =    0.857
peak=    4.348 closest distance to " O   HOH Z 272 " =    1.810
peak=    4.320 closest distance to " CB  VAL A 265 " =    1.281
peak=    4.301 closest distance to " O   HOH Z 158 " =    2.989
peak=    4.290 closest distance to " CA  TYR A  30 " =    0.910
peak=    4.257 closest distance to " O   HOH Z 193 " =    1.852
peak=    4.216 closest distance to " O   HOH Z 234 " =    3.607
peak=    4.215 closest distance to " CG  PRO A 243 " =    1.061
peak=    4.167 closest distance to " O   HOH Z 250 " =    1.481
peak=    4.151 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.126 closest distance to " O   HOH Z 346 " =    1.697
peak=    4.123 closest distance to " O   HOH Z 402 " =    1.416
peak=    4.112 closest distance to " O   HOH Z  61 " =    1.655
peak=    4.103 closest distance to " O   HOH Z 371 " =    1.697
peak=    4.093 closest distance to " CD2 TRP A 179 " =    1.325
peak=    4.091 closest distance to " CB  ARG A 190 " =    1.656
peak=    4.087 closest distance to " O   HOH Z 298 " =    1.857
peak=    4.086 closest distance to " O   HOH Z 132 " =    2.319
peak=    4.070 closest distance to " CG  PRO A  90 " =    1.131
peak=    4.054 closest distance to " O   SER A  87 " =    2.127
peak=    4.049 closest distance to " CA  ASN A 215 " =    1.104
peak=    4.020 closest distance to " O   HOH Z 389 " =    1.823
peak=    4.009 closest distance to " NZ  LYS A 117 " =    3.197
peak=    4.002 closest distance to " O   HOH Z 189 " =    2.051
peak=    3.993 closest distance to " O   HOH Z 261 " =    2.158
peak=    3.976 closest distance to " O   HOH Z 203 " =    1.745
peak=    3.976 closest distance to " OG ASER A 258 " =    3.066
peak=    3.924 closest distance to " O   HOH Z  40 " =    1.552
peak=    3.923 closest distance to " CG  PRO A 198 " =    1.251
peak=    3.917 closest distance to " O   HOH Z 128 " =    2.124
peak=    3.911 closest distance to " O   HOH Z 407 " =    2.298
peak=    3.903 closest distance to " O   HOH Z 419 " =    2.136
peak=    3.900 closest distance to " OD1 ASN A  69 " =    2.616
peak=    3.891 closest distance to " CB  SER A   3 " =    1.312
peak=    3.891 closest distance to " O   HOH Z   9 " =    2.051
peak=    3.876 closest distance to " CZ  PHE A 218 " =    1.035
peak=    3.874 closest distance to " O   HOH Z  44 " =    1.727
peak=    3.869 closest distance to " O   HOH Z  93 " =    2.432
peak=    3.869 closest distance to " O   HOH Z 392 " =    3.100
peak=    3.852 closest distance to " CB  TRP A 266 " =    1.049
peak=    3.846 closest distance to " CB  LEU A 228 " =    1.093
peak=    3.837 closest distance to " O   HOH Z 327 " =    1.567
peak=    3.837 closest distance to " O   HOH Z 368 " =    1.992
peak=    3.820 closest distance to " O   HOH Z   1 " =    2.006
peak=    3.817 closest distance to " O   HOH Z  61 " =    1.476
peak=    3.806 closest distance to " CG  ARG A  66 " =    2.396
peak=    3.803 closest distance to " CG1 ILE A  33 " =    1.254
peak=    3.784 closest distance to " CB  TYR A 169 " =    0.710
peak=    3.771 closest distance to " O   HOH Z 245 " =    1.353
peak=    3.762 closest distance to " OG BSER A 164 " =    2.295
peak=    3.754 closest distance to " O   HOH Z 403 " =    1.619
peak=    3.739 closest distance to " O   HOH Z 344 " =    3.244
peak=    3.738 closest distance to " O   HOH Z 425 " =    2.094
peak=    3.729 closest distance to " CG2 ILE A 120 " =    1.137
peak=    3.726 closest distance to " O   HOH Z  10 " =    1.882
peak=    3.718 closest distance to " CB  GLU A 128 " =    1.006
peak=    3.718 closest distance to " CE  LYS A  76 " =    0.820
peak=    3.708 closest distance to " O   HOH Z  66 " =    2.122
peak=    3.706 closest distance to " O   HOH Z 353 " =    2.593
peak=    3.699 closest distance to " CB  VAL A 202 " =    1.577
peak=    3.697 closest distance to " O   HOH Z 368 " =    3.604
peak=    3.690 closest distance to " O   HOH Z 291 " =    1.466
peak=    3.680 closest distance to " CB  ASP A 140 " =    0.964
peak=    3.679 closest distance to " O   HOH Z 214 " =    2.134
peak=    3.674 closest distance to " O   HOH Z 133 " =    2.694
peak=    3.673 closest distance to " O   HOH Z 128 " =    2.059
peak=    3.667 closest distance to " OD2 ASP A 286 " =    2.765
peak=    3.666 closest distance to " O   HOH Z 248 " =    1.563
peak=    3.657 closest distance to " CB  SER A  62 " =    1.306
peak=    3.650 closest distance to " O   HOH Z  88 " =    2.540
peak=    3.643 closest distance to " NH1AARG A 145 " =    1.203
peak=    3.639 closest distance to " O   HOH Z 423 " =    1.904
peak=    3.633 closest distance to " O   HOH Z 406 " =    1.624
peak=    3.630 closest distance to " O   HOH Z 371 " =    3.002
peak=    3.628 closest distance to " CG1BVAL A  72 " =    1.466
peak=    3.626 closest distance to " O   HOH Z 173 " =    1.908
peak=    3.626 closest distance to " O   HOH Z 193 " =    1.908
peak=    3.626 closest distance to " CB  ARG A 139 " =    0.979
peak=    3.618 closest distance to " O   HOH Z  40 " =    1.985
peak=    3.616 closest distance to " CB  SER A  26 " =    1.624
peak=    3.572 closest distance to " CA  ALA A  84 " =    1.267
peak=    3.569 closest distance to " NH2BARG A 145 " =    2.017
peak=    3.558 closest distance to " O  BHOH Z 338 " =    2.346
peak=    3.554 closest distance to " O   HOH Z   1 " =    1.637
peak=    3.540 closest distance to " CB  ALA A  34 " =    1.121
peak=    3.540 closest distance to " CB  TYR A 116 " =    0.809
peak=    3.536 closest distance to " O   HOH Z 433 " =    1.829
peak=    3.534 closest distance to " CB  SER A 212 " =    1.104
peak=    3.533 closest distance to " O   HOH Z 207 " =    1.739
peak=    3.526 closest distance to " CG  GLN A  11 " =    1.917
peak=    3.525 closest distance to " O   HOH Z 337 " =    3.575
peak=    3.523 closest distance to " O   HOH Z 219 " =    2.140
peak=    3.521 closest distance to " O   HOH Z 305 " =    3.596
peak=    3.518 closest distance to " O   HOH Z  64 " =    2.343
peak=    3.518 closest distance to " O   HOH Z 417 " =    3.284
peak=    3.518 closest distance to " CB  TRP A 179 " =    1.301
peak=    3.518 closest distance to " O   HOH Z  21 " =    1.776
peak=    3.497 closest distance to " N   ASN A  39 " =    1.196
peak=    3.496 closest distance to " O   HOH Z 234 " =    1.870
peak=    3.496 closest distance to " CB  GLU A 277 " =    3.507
peak=    3.496 closest distance to " O   HOH Z 284 " =    3.006
peak=    3.494 closest distance to " CB  TYR A 169 " =    0.706
peak=    3.492 closest distance to " CD1 ILE A 106 " =    0.837
peak=    3.492 closest distance to " O   HOH Z  43 " =    1.947
peak=    3.485 closest distance to " CB  GLN A  89 " =    1.395
peak=    3.484 closest distance to " CB  THR A 157 " =    1.089
peak=    3.482 closest distance to " O   HOH Z 180 " =    2.193
peak=    3.478 closest distance to " CB  ILE A 120 " =    1.242
peak=    3.477 closest distance to " O   HOH Z 172 " =    3.252
peak=    3.477 closest distance to " O   HOH Z 193 " =    1.639
peak=    3.476 closest distance to " O   HOH Z  59 " =    1.697
peak=    3.476 closest distance to " O   HOH Z 325 " =    3.854
peak=    3.475 closest distance to " CD  ARG A  66 " =    2.394
peak=    3.474 closest distance to " O   HOH Z   6 " =    2.100
peak=    3.468 closest distance to " CB  LYS A 117 " =    1.241
peak=    3.463 closest distance to " CA  ASP A 162 " =    1.053
peak=    3.459 closest distance to " O   HOH Z 213 " =    1.881
peak=    3.455 closest distance to " N   ARG A 156 " =    1.295
peak=    3.454 closest distance to " O   HOH Z 147 " =    1.786
peak=    3.454 closest distance to " O   HOH Z  88 " =    2.464
peak=    3.452 closest distance to " O   HOH Z 265 " =    2.357
peak=    3.452 closest distance to " O   HOH Z 421 " =    1.835
peak=    3.450 closest distance to " O   HOH Z 313 " =    1.942
peak=    3.449 closest distance to " O   HOH Z  89 " =    2.118
peak=    3.444 closest distance to " CA  ALA A  21 " =    1.106
peak=    3.442 closest distance to " O   HOH Z  54 " =    1.643
peak=    3.441 closest distance to " CA  ALA A 233 " =    1.075
peak=    3.439 closest distance to " CB  ASN A 110 " =    1.090
peak=    3.431 closest distance to " CB  ASN A  39 " =    0.841
peak=    3.431 closest distance to " O   HOH Z  97 " =    1.957
peak=    3.428 closest distance to " ND1 HIS A  86 " =    1.782
peak=    3.423 closest distance to " CG AARG A 275 " =    1.088
peak=    3.415 closest distance to " O   HOH Z 261 " =    2.278
peak=    3.415 closest distance to " CB  ASN A 142 " =    1.010
peak=    3.414 closest distance to " O   HOH Z 380 " =    1.905
peak=    3.413 closest distance to " CD  ARG A 269 " =    0.992
peak=    3.407 closest distance to " CA  THR A 264 " =    0.860
peak=    3.403 closest distance to " N   PHE A 130 " =    1.240
peak=    3.401 closest distance to " CA  SER A 146 " =    1.743
peak=    3.399 closest distance to " O   HOH Z 365 " =    2.840
peak=    3.399 closest distance to " O   HOH Z  85 " =    2.284
peak=    3.395 closest distance to " O   HOH Z 359 " =    1.475
peak=    3.391 closest distance to " CA  PHE A 283 " =    1.276
peak=    3.388 closest distance to " NH1BARG A 145 " =    1.288
peak=    3.383 closest distance to " CD2 LEU A 297 " =    0.917
peak=    3.381 closest distance to " O   HOH Z 336 " =    1.883
peak=    3.379 closest distance to " CD1 ILE A 263 " =    1.366
peak=    3.375 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.371 closest distance to " CA  ARG A  36 " =    0.999
peak=    3.369 closest distance to " CD BLYS A 290 " =    1.202
peak=    3.368 closest distance to " OG  SER A  62 " =    2.806
peak=    3.366 closest distance to " CG  LYS A  76 " =    0.942
peak=    3.363 closest distance to " CB  GLN A  88 " =    1.166
peak=    3.361 closest distance to " CB  GLN A 278 " =    0.810
peak=    3.359 closest distance to " O   ALA A   1 " =    1.676
peak=    3.358 closest distance to " CA  ARG A 195 " =    1.255
peak=    3.357 closest distance to " CG  MET A 113 " =    1.129
peak=    3.357 closest distance to " O   ASN A  74 " =    1.580
peak=    3.352 closest distance to " NE2 GLN A  73 " =    3.736
peak=    3.349 closest distance to " CG  LEU A 167 " =    1.237
peak=    3.344 closest distance to " O   HOH Z 126 " =    1.559
peak=    3.342 closest distance to " CB  ALA A 291 " =    1.297
peak=    3.340 closest distance to " O   HOH Z 148 " =    3.389
peak=    3.335 closest distance to " O   HOH Z 298 " =    2.503
peak=    3.325 closest distance to " O   HOH Z 345 " =    3.321
peak=    3.322 closest distance to " O   HOH Z 286 " =    2.230
peak=    3.321 closest distance to " NE2 GLN A  77 " =    3.136
peak=    3.319 closest distance to " CA  MET A  40 " =    1.088
peak=    3.316 closest distance to " O   HOH Z 426 " =    1.890
peak=    3.315 closest distance to " OD1BASN A 224 " =    2.271
peak=    3.314 closest distance to " CG1 VAL A 153 " =    0.911
peak=    3.313 closest distance to " OG  SER A  22 " =    2.648
peak=    3.309 closest distance to " N   TYR A 116 " =    1.557
peak=    3.306 closest distance to " CB  SER A 216 " =    0.772
peak=    3.302 closest distance to " O   HOH Z 423 " =    2.819
peak=    3.299 closest distance to " O   HOH Z 128 " =    2.039
peak=    3.298 closest distance to " O   HOH Z 357 " =    1.881
peak=    3.298 closest distance to " O   HOH Z 329 " =    3.872
peak=    3.297 closest distance to " CA  ALA A 291 " =    0.819
peak=    3.297 closest distance to " O   HOH Z  66 " =    2.096
peak=    3.296 closest distance to " CG  MET A 185 " =    1.172
peak=    3.296 closest distance to " CG2 VAL A 197 " =    1.095
peak=    3.289 closest distance to " CA  THR A 221 " =    1.014
peak=    3.281 closest distance to " O   HOH Z 175 " =    2.111
peak=    3.275 closest distance to " O   HOH Z 123 " =    2.191
peak=    3.263 closest distance to " O   HOH Z  44 " =    3.000
peak=    3.260 closest distance to " O   HOH Z 273 " =    2.691
peak=    3.259 closest distance to " CB  ALA A   9 " =    1.560
peak=    3.258 closest distance to " CB  MET A  47 " =    1.119
peak=    3.253 closest distance to " O   HOH Z 188 " =    1.854
peak=    3.243 closest distance to " O   HOH Z 411 " =    3.762
peak=    3.243 closest distance to " CG2 THR A 294 " =    1.690
peak=    3.241 closest distance to " CB  THR A  31 " =    1.683
peak=    3.240 closest distance to " CD  LYS A 166 " =    1.239
peak=    3.240 closest distance to " CB  THR A 279 " =    1.704
peak=    3.236 closest distance to " CD  PRO A 243 " =    1.480
peak=    3.235 closest distance to " O   HOH Z 185 " =    1.787
peak=    3.232 closest distance to " O   HOH Z 302 " =    1.930
peak=    3.229 closest distance to " O   HOH Z  92 " =    2.492
peak=    3.226 closest distance to " NE  ARG A  24 " =    1.943
peak=    3.221 closest distance to " O   HOH Z 109 " =    2.519
peak=    3.220 closest distance to " O   HOH Z 391 " =    2.883
peak=    3.213 closest distance to " CD1 LEU A 300 " =    1.349
peak=    3.208 closest distance to " O   HOH Z 291 " =    1.805
peak=    3.207 closest distance to " O   HOH Z 261 " =    1.543
peak=    3.206 closest distance to " CB  SER A 141 " =    1.021
peak=    3.201 closest distance to " O   HOH Z 285 " =    2.752
peak=    3.201 closest distance to " O   HOH Z 437 " =    1.461
peak=    3.198 closest distance to " CG  GLU A 277 " =    2.089
peak=    3.195 closest distance to " CZ2 TRP A 179 " =    1.701
peak=    3.190 closest distance to " CB  HIS A 108 " =    0.785
peak=    3.189 closest distance to " O   HOH Z  50 " =    1.539
peak=    3.188 closest distance to " O   HOH Z 294 " =    1.431
peak=    3.184 closest distance to " O   MET A 105 " =    1.847
peak=    3.180 closest distance to " O   HOH Z 153 " =    1.612
peak=    3.178 closest distance to " ND2 ASN A 249 " =    0.875
peak=    3.177 closest distance to " O   HOH Z 257 " =    2.158
peak=    3.177 closest distance to " CA  SER A  87 " =    1.001
peak=    3.172 closest distance to " CA  ALA A 299 " =    0.911
peak=    3.171 closest distance to " CB  ALA A 248 " =    1.372
peak=    3.166 closest distance to " CB  ALA A   1 " =    4.607
peak=    3.164 closest distance to " O   HOH Z 380 " =    1.681
peak=    3.161 closest distance to " CG2 THR A 221 " =    1.088
peak=    3.161 closest distance to " CA  ALA A 158 " =    1.237
peak=    3.160 closest distance to " CB  SER A 273 " =    0.837
peak=    3.147 closest distance to " OG1 THR A 294 " =    2.397
peak=    3.144 closest distance to " CB  MET A  40 " =    0.845
peak=    3.134 closest distance to " CG BARG A 102 " =    1.721
peak=    3.127 closest distance to " N   ASN A 127 " =    1.266
peak=    3.124 closest distance to " O   HOH Z 271 " =    2.241
peak=    3.119 closest distance to " NH1 ARG A 138 " =    1.167
peak=    3.117 closest distance to " CH2 TRP A  92 " =    2.127
peak=    3.114 closest distance to " CA  ALA A  51 " =    0.898
peak=    3.105 closest distance to " O   HOH Z 332 " =    1.467
peak=    3.103 closest distance to " NE2 HIS A 207 " =    1.363
peak=    3.100 closest distance to " O  BHOH Z  74 " =    1.360
peak=    3.098 closest distance to " O   HOH Z 124 " =    2.111
peak=    3.093 closest distance to " CG  GLN A  77 " =    2.120
peak=    3.092 closest distance to " CB  LEU A 255 " =    0.797
peak=    3.092 closest distance to " CB  ASN A 215 " =    1.103
peak=    3.087 closest distance to " N   SER A 135 " =    1.218
peak=    3.085 closest distance to " OG BSER A 134 " =    2.883
peak=    3.083 closest distance to " O   HOH Z  47 " =    1.798
peak=    3.082 closest distance to " O   HOH Z 132 " =    3.339
peak=    3.074 closest distance to " CE AMET A  47 " =    1.384
peak=    3.073 closest distance to " CA  MET A 105 " =    0.939
peak=    3.071 closest distance to " O   HOH Z 409 " =    2.658
peak=    3.067 closest distance to " CD1 LEU A 228 " =    1.576
peak=    3.049 closest distance to " N   ASP A 162 " =    1.202
peak=    3.042 closest distance to " O   HOH Z 153 " =    3.768
peak=    3.035 closest distance to " CB  LYS A 290 " =    1.150
peak=    3.034 closest distance to " O   HOH Z 361 " =    3.116
peak=    3.034 closest distance to " CA  ARG A 102 " =    1.024
peak=    3.031 closest distance to " CD1AILE A 234 " =    0.896

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.777 - 5.936
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.777 - 5.936

peak=   -4.754 closest distance to " CB  PRO A 243 " =    2.642
peak=   -4.712 closest distance to " O   HOH Z 266 " =    4.950
peak=   -4.519 closest distance to " CD  ARG A 156 " =    2.079
peak=   -4.421 closest distance to " C   HIS A 108 " =    1.145
peak=   -4.417 closest distance to " CG  GLN A 223 " =    1.875
peak=   -4.395 closest distance to " O   HOH Z 377 " =    2.058
peak=   -4.376 closest distance to " OG BSER A 134 " =    1.254
peak=   -4.300 closest distance to " O   VAL A  67 " =    2.674
peak=   -4.270 closest distance to " O   HOH Z 290 " =    1.132
peak=   -4.216 closest distance to " CG1 VAL A 112 " =    2.823
peak=   -4.213 closest distance to " CG  GLN A  58 " =    1.082
peak=   -4.190 closest distance to " CA  VAL A  67 " =    2.880
peak=   -4.166 closest distance to " ND2 ASN A  45 " =    1.597
peak=   -4.143 closest distance to " SG  CYS A 254 " =    3.388
peak=   -4.105 closest distance to " O   HOH Z 435 " =    2.788
peak=   -4.076 closest distance to " O   HOH Z 313 " =    1.867
peak=   -4.007 closest distance to " CE2 PHE A 218 " =    2.453
peak=   -3.938 closest distance to " O   HOH Z 185 " =    2.185
peak=   -3.892 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.888 closest distance to " O   HOH Z 389 " =    1.929
peak=   -3.882 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.882 closest distance to " CZ  TYR A 169 " =    1.748
peak=   -3.861 closest distance to " CZ3 TRP A 179 " =    1.195
peak=   -3.860 closest distance to " O   HOH Z 372 " =    2.390
peak=   -3.858 closest distance to " CB  ASN A  39 " =    2.291
peak=   -3.845 closest distance to " O   HOH Z 231 " =    2.334
peak=   -3.836 closest distance to " OXT GLY A 302 " =    2.773
peak=   -3.829 closest distance to " CG  PHE A 283 " =    2.708
peak=   -3.824 closest distance to " CD2 PHE A 192 " =    1.981
peak=   -3.808 closest distance to " O   HOH Z 351 " =    1.502
peak=   -3.787 closest distance to " CD  ARG A 139 " =    1.528
peak=   -3.785 closest distance to " O   HOH Z 198 " =    1.912
peak=   -3.784 closest distance to " O   ALA A 161 " =    1.640
peak=   -3.774 closest distance to " N   GLN A  58 " =    1.690
peak=   -3.756 closest distance to " OD1 ASN A 148 " =    1.555
peak=   -3.756 closest distance to " CB  ALA A 248 " =    2.322
peak=   -3.750 closest distance to " N   ALA A  43 " =    2.545
peak=   -3.706 closest distance to " CB  ALA A 291 " =    2.328
peak=   -3.687 closest distance to " O   HOH Z 114 " =    3.056
peak=   -3.686 closest distance to " O   HOH Z 407 " =    2.926
peak=   -3.685 closest distance to " O   ARG A 145 " =    1.523
peak=   -3.671 closest distance to " OG  SER A  97 " =    2.157
peak=   -3.667 closest distance to " CZ  PHE A  59 " =    1.467
peak=   -3.666 closest distance to " O   HOH Z 211 " =    1.674
peak=   -3.660 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.652 closest distance to " O   SER A  95 " =    1.469
peak=   -3.644 closest distance to " CE  MET A 105 " =    2.280
peak=   -3.631 closest distance to " CD1 PHE A  59 " =    1.919
peak=   -3.624 closest distance to " OD2 ASP A 191 " =    1.400
peak=   -3.618 closest distance to " CB  ALA A 161 " =    2.514
peak=   -3.613 closest distance to " CB  ALA A  43 " =    2.356
peak=   -3.609 closest distance to " CB  ALA A 248 " =    2.098
peak=   -3.607 closest distance to " OD1 ASN A 187 " =    1.635
peak=   -3.586 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.584 closest distance to " CA  GLY A  98 " =    1.823
peak=   -3.578 closest distance to " OD2 ASP A 171 " =    2.250
peak=   -3.578 closest distance to " O   HOH Z 353 " =    2.217
peak=   -3.575 closest distance to " N   ALA A 248 " =    1.678
peak=   -3.569 closest distance to " ND2 ASN A 187 " =    1.520
peak=   -3.568 closest distance to " CG2 ILE A 263 " =    2.234
peak=   -3.562 closest distance to " O   PRO A 198 " =    1.234
peak=   -3.552 closest distance to " ND2 ASN A 249 " =    2.176
peak=   -3.551 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.549 closest distance to " CB  PHE A 208 " =    2.228
peak=   -3.545 closest distance to " O   HOH Z 102 " =    1.547
peak=   -3.542 closest distance to " O   HOH Z 198 " =    1.461
peak=   -3.528 closest distance to " O   HOH Z  63 " =    1.722
peak=   -3.520 closest distance to " O   SER A 135 " =    1.427
peak=   -3.492 closest distance to " NH2AARG A 275 " =    5.116
peak=   -3.488 closest distance to " O   HOH Z 362 " =    5.936
peak=   -3.484 closest distance to " CD1 ILE A 239 " =    2.348
peak=   -3.483 closest distance to " CG2 THR A 178 " =    2.269
peak=   -3.480 closest distance to " CG  ASP A 231 " =    0.777
peak=   -3.477 closest distance to " O   HOH Z 395 " =    5.182
peak=   -3.463 closest distance to " C   LEU A 143 " =    1.017
peak=   -3.463 closest distance to " N   SER A 212 " =    2.019
peak=   -3.456 closest distance to " O   HOH Z  13 " =    1.591
peak=   -3.454 closest distance to " CA  GLY A 133 " =    1.969
peak=   -3.454 closest distance to " NE2 GLN A 278 " =    1.706
peak=   -3.453 closest distance to " CA  GLY A 203 " =    2.275
peak=   -3.451 closest distance to " O   HOH Z  60 " =    2.282
peak=   -3.444 closest distance to " O   HOH Z 298 " =    1.269
peak=   -3.443 closest distance to " OD1 ASP A 191 " =    1.531
peak=   -3.438 closest distance to " O   HOH Z 263 " =    2.965
peak=   -3.434 closest distance to " CB  ASP A 132 " =    2.252
peak=   -3.433 closest distance to " NH2BARG A 275 " =    1.923
peak=   -3.430 closest distance to " N   ASP A 286 " =    2.373
peak=   -3.430 closest distance to " CB  ASP A 132 " =    2.391
peak=   -3.415 closest distance to " O   HOH Z  15 " =    1.581
peak=   -3.410 closest distance to " CD1 LEU A 228 " =    2.092
peak=   -3.390 closest distance to " O   HOH Z 126 " =    1.887
peak=   -3.389 closest distance to " O   HOH Z 394 " =    1.403
peak=   -3.378 closest distance to " O   HOH Z  38 " =    1.672
peak=   -3.375 closest distance to " OG BSER A 134 " =    1.660
peak=   -3.374 closest distance to " O   PHE A 218 " =    1.593
peak=   -3.373 closest distance to " OE1 GLN A  88 " =    1.185
peak=   -3.371 closest distance to " O   HOH Z 385 " =    1.985
peak=   -3.364 closest distance to " O   VAL A 174 " =    2.106
peak=   -3.361 closest distance to " OG  SER A  97 " =    1.751
peak=   -3.358 closest distance to " CG  GLU A 277 " =    1.283
peak=   -3.358 closest distance to " O   PRO A 163 " =    2.005
peak=   -3.353 closest distance to " C   MET A 188 " =    1.451
peak=   -3.344 closest distance to " CB  TRP A  85 " =    2.493
peak=   -3.344 closest distance to " O   HOH Z  43 " =    1.822
peak=   -3.338 closest distance to " CA  GLY A 241 " =    2.274
peak=   -3.337 closest distance to " CD2 PHE A 225 " =    1.173
peak=   -3.336 closest distance to " CG  ARG A 269 " =    2.536
peak=   -3.332 closest distance to " CB  ASP A 286 " =    2.081
peak=   -3.330 closest distance to " C   PRO A  90 " =    1.526
peak=   -3.328 closest distance to " O   HOH Z 165 " =    2.069
peak=   -3.327 closest distance to " O   VAL A 189 " =    1.688
peak=   -3.324 closest distance to " CG1 VAL A 230 " =    1.999
peak=   -3.319 closest distance to " O   HOH Z 283 " =    2.368
peak=   -3.317 closest distance to " O   VAL A 189 " =    2.549
peak=   -3.317 closest distance to " O   HOH Z 103 " =    1.720
peak=   -3.316 closest distance to " O   HOH Z 140 " =    1.714
peak=   -3.311 closest distance to " O   ALA A 292 " =    1.974
peak=   -3.294 closest distance to " OE2 GLU A 152 " =    1.185
peak=   -3.291 closest distance to " CA  ASP A 298 " =    1.104
peak=   -3.288 closest distance to " O   HOH Z 339 " =    1.852
peak=   -3.288 closest distance to " CB  PRO A 163 " =    2.447
peak=   -3.287 closest distance to " O   MET A  40 " =    2.777
peak=   -3.285 closest distance to " O   HOH Z  10 " =    1.434
peak=   -3.278 closest distance to " O   HOH Z 166 " =    2.050
peak=   -3.277 closest distance to " O   HOH Z 266 " =    4.742
peak=   -3.273 closest distance to " C   ASP A 231 " =    2.520
peak=   -3.271 closest distance to " O   LEU A 101 " =    2.275
peak=   -3.270 closest distance to " CD2 LEU A 237 " =    2.731
peak=   -3.270 closest distance to " CD  GLU A 236 " =    1.029
peak=   -3.269 closest distance to " O   TRP A  70 " =    1.463
peak=   -3.264 closest distance to " OD2 ASP A  50 " =    1.543
peak=   -3.264 closest distance to " O   ALA A  34 " =    2.417
peak=   -3.263 closest distance to " OD1 ASP A 191 " =    1.783
peak=   -3.257 closest distance to " NH1 ARG A 195 " =    2.608
peak=   -3.256 closest distance to " O   HOH Z 137 " =    1.394
peak=   -3.254 closest distance to " O   SER A  22 " =    2.441
peak=   -3.248 closest distance to " O   GLN A 240 " =    2.000
peak=   -3.246 closest distance to " O   SER A 146 " =    1.123
peak=   -3.240 closest distance to " CE  MET A 105 " =    2.044
peak=   -3.234 closest distance to " O   ALA A  51 " =    1.298
peak=   -3.231 closest distance to " O   HOH Z 421 " =    3.064
peak=   -3.228 closest distance to " ND2 ASN A  69 " =    1.600
peak=   -3.226 closest distance to " O   HOH Z 253 " =    3.822
peak=   -3.226 closest distance to " O   HOH Z 243 " =    1.949
peak=   -3.223 closest distance to " O   HOH Z  90 " =    2.411
peak=   -3.222 closest distance to " C   ALA A 158 " =    1.390
peak=   -3.216 closest distance to " O   ILE A 106 " =    2.092
peak=   -3.215 closest distance to " O   HOH Z  11 " =    1.812
peak=   -3.210 closest distance to " O   HOH Z 359 " =    3.326
peak=   -3.208 closest distance to " CD1 LEU A 297 " =    2.399
peak=   -3.201 closest distance to " CE3 TRP A 274 " =    2.354
peak=   -3.197 closest distance to " CB  GLN A  11 " =    1.770
peak=   -3.196 closest distance to " CD1 LEU A 101 " =    2.256
peak=   -3.193 closest distance to " CA  GLY A 241 " =    3.113
peak=   -3.192 closest distance to " O   HOH Z 166 " =    1.468
peak=   -3.191 closest distance to " NH2 ARG A  79 " =    1.998
peak=   -3.190 closest distance to " O   HOH Z 281 " =    2.661
peak=   -3.188 closest distance to " O   HOH Z 123 " =    2.332
peak=   -3.177 closest distance to " O   HOH Z 134 " =    3.165
peak=   -3.173 closest distance to " N   THR A 235 " =    1.311
peak=   -3.172 closest distance to " SG ACYS A 201 " =    1.750
peak=   -3.172 closest distance to " OG  SER A  62 " =    1.543
peak=   -3.168 closest distance to " CG  GLU A 152 " =    1.002
peak=   -3.168 closest distance to " O   HOH Z 131 " =    4.054
peak=   -3.165 closest distance to " CD2 LEU A 300 " =    2.793
peak=   -3.162 closest distance to " CG1 VAL A 197 " =    2.103
peak=   -3.156 closest distance to " CD  GLN A  88 " =    0.867
peak=   -3.156 closest distance to " O   HOH Z 244 " =    2.046
peak=   -3.156 closest distance to " NE  ARG A  36 " =    1.959
peak=   -3.154 closest distance to " OG1 THR A 246 " =    1.416
peak=   -3.152 closest distance to " O   HOH Z 427 " =    1.435
peak=   -3.152 closest distance to " CG  TRP A 266 " =    1.988
peak=   -3.152 closest distance to " O   ALA A  10 " =    1.650
peak=   -3.151 closest distance to " O   HOH Z 377 " =    0.863
peak=   -3.136 closest distance to " O   HOH Z  24 " =    1.346
peak=   -3.128 closest distance to " CA  GLY A  57 " =    2.149
peak=   -3.127 closest distance to " CA  ASP A  27 " =    2.386
peak=   -3.127 closest distance to " O   ALA A 180 " =    1.024
peak=   -3.125 closest distance to " O   HOH Z 250 " =    1.379
peak=   -3.125 closest distance to " O   HOH Z 111 " =    2.164
peak=   -3.121 closest distance to " CD  PRO A  90 " =    1.762
peak=   -3.117 closest distance to " OE1 GLN A 194 " =    1.690
peak=   -3.114 closest distance to " CA  TRP A 274 " =    1.422
peak=   -3.113 closest distance to " OH  TYR A 214 " =    1.215
peak=   -3.093 closest distance to " O   HOH Z 369 " =    2.220
peak=   -3.090 closest distance to " OD1AASN A 224 " =    1.825
peak=   -3.089 closest distance to " O   HOH Z 298 " =    2.416
peak=   -3.087 closest distance to " O   HOH Z 414 " =    1.715
peak=   -3.084 closest distance to " NH2 ARG A  79 " =    1.618
peak=   -3.081 closest distance to " O   HOH Z 371 " =    1.688
peak=   -3.080 closest distance to " O   HOH Z 371 " =    1.532
peak=   -3.080 closest distance to " O   HOH Z 282 " =    1.166
peak=   -3.075 closest distance to " O   HOH Z  11 " =    2.077
peak=   -3.074 closest distance to " CD2 TYR A 293 " =    1.944
peak=   -3.060 closest distance to " O   ASN A 249 " =    1.431
peak=   -3.055 closest distance to " O   HOH Z 323 " =    1.331
peak=   -3.050 closest distance to " CE  LYS A  76 " =    2.787
peak=   -3.043 closest distance to " O   HOH Z 137 " =    1.510
peak=   -3.037 closest distance to " CG  ARG A 269 " =    2.012
peak=   -3.027 closest distance to " O   HOH Z  51 " =    1.334

================= 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    :  0.3038 0.2985   5.997737e+00   5.964474e+00
   1_bss:  0.2887 0.2817   5.971635e+00   5.930096e+00
   1_xyz:  0.1660 0.1886   5.441010e+00   5.544695e+00
   1_adp:  0.1513 0.1976   5.388792e+00   5.585523e+00
   1_occ:  0.1510 0.1975   5.387475e+00   5.584351e+00
   2_bss:  0.1497 0.1953   5.380871e+00   5.574386e+00
   2_xyz:  0.1193 0.1618   5.181237e+00   5.402404e+00
   2_adp:  0.1170 0.1553   5.152421e+00   5.365154e+00
   2_occ:  0.1168 0.1554   5.151654e+00   5.365095e+00
   3_bss:  0.1168 0.1552   5.149970e+00   5.362425e+00
   3_xyz:  0.1101 0.1512   5.110176e+00   5.341488e+00
   3_adp:  0.1073 0.1516   5.099384e+00   5.345494e+00
   3_occ:  0.1072 0.1516   5.099365e+00   5.345607e+00
   4_bss:  0.1072 0.1515   5.098762e+00   5.344868e+00
   4_xyz:  0.1053 0.1518   5.093104e+00   5.349671e+00
   4_adp:  0.1051 0.1520   5.092498e+00   5.350221e+00
   4_occ:  0.1051 0.1520   5.092470e+00   5.350222e+00
   5_bss:  0.1050 0.1520   5.092493e+00   5.350178e+00
   5_xyz:  0.1049 0.1531   5.096074e+00   5.357774e+00
   5_adp:  0.1052 0.1525   5.095444e+00   5.354836e+00
   5_occ:  0.1052 0.1525   5.095421e+00   5.354865e+00
   5_bss:  0.1052 0.1525   5.095600e+00   5.355075e+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:  0.331  34.615  -1.991   0.348  -1.629   0.000  -0.000  -0.000
   1_xyz:  0.331  34.615  -1.991   0.348  -1.629   0.000  -0.000  -0.000
   1_adp:  0.331  34.615  -1.991   0.348  -1.629   0.000  -0.000  -0.000
   1_occ:  0.331  34.615  -1.991   0.348  -1.629   0.000  -0.000  -0.000
   2_bss:  0.318  40.521  -2.879  -1.971  -1.717  -0.000  -0.000  -0.000
   2_xyz:  0.318  40.521  -2.879  -1.971  -1.717  -0.000  -0.000  -0.000
   2_adp:  0.318  40.521  -2.879  -1.971  -1.717  -0.000  -0.000  -0.000
   2_occ:  0.318  40.521  -2.879  -1.971  -1.717  -0.000  -0.000  -0.000
   3_bss:  0.320  41.209  -2.921  -2.409  -1.382  -0.000  -0.000  -0.000
   3_xyz:  0.320  41.209  -2.921  -2.409  -1.382  -0.000  -0.000  -0.000
   3_adp:  0.320  41.209  -2.921  -2.409  -1.382  -0.000  -0.000  -0.000
   3_occ:  0.320  41.209  -2.921  -2.409  -1.382  -0.000  -0.000  -0.000
   4_bss:  0.321  44.590  -2.772  -2.378  -1.196  -0.000  -0.000  -0.000
   4_xyz:  0.321  44.590  -2.772  -2.378  -1.196  -0.000  -0.000  -0.000
   4_adp:  0.321  44.590  -2.772  -2.378  -1.196  -0.000  -0.000  -0.000
   4_occ:  0.321  44.590  -2.772  -2.378  -1.196  -0.000  -0.000  -0.000
   5_bss:  0.321  45.343  -2.558  -2.205  -0.959  -0.000  -0.000  -0.000
   5_xyz:  0.321  45.343  -2.558  -2.205  -0.959  -0.000  -0.000  -0.000
   5_adp:  0.321  45.343  -2.558  -2.205  -0.959  -0.000  -0.000  -0.000
   5_occ:  0.321  45.343  -2.558  -2.205  -0.959  -0.000  -0.000  -0.000
   5_bss:  0.321  44.330  -2.374  -2.045  -0.754  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  29.525 0.7673  0.9535    24949.137
   1_bss:  28.213 0.7794  0.9299    21609.214
   1_xyz:  17.142 0.8894  1.0127     8844.396
   1_adp:  18.198 0.8793  1.0073     9553.443
   1_occ:  18.173 0.8794  1.0073     9517.764
   2_bss:  17.891 0.8819  0.9708     9261.379
   2_xyz:  14.426 0.9110  0.9850     6485.832
   2_adp:  13.586 0.9180  0.9857     6090.346
   2_occ:  13.584 0.9180  0.9856     6080.339
   3_bss:  13.537 0.9183  0.9845     6037.635
   3_xyz:  13.003 0.9228  0.9856     5749.510
   3_adp:  13.064 0.9225  0.9789     5752.189
   3_occ:  13.066 0.9225  0.9788     5753.801
   4_bss:  13.049 0.9226  0.9835     5744.905
   4_xyz:  13.102 0.9222  0.9830     5813.436
   4_adp:  13.112 0.9221  0.9770     5808.977
   4_occ:  13.113 0.9221  0.9769     5808.449
   5_bss:  13.113 0.9221  0.9844     5808.744
   5_xyz:  13.219 0.9214  0.9840     5910.509
   5_adp:  13.159 0.9219  0.9779     5884.840
   5_occ:  13.160 0.9218  0.9778     5884.976
   5_bss:  13.165 0.9218  0.9831     5888.346
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6301e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6301e-01
   1_xyz:   1.014  0.007  0.070 15.037  0.005  4.110   6.2025e-02
   1_adp:   1.014  0.007  0.070 15.037  0.005  4.110   6.2025e-02
   1_occ:   1.014  0.007  0.070 15.037  0.005  4.110   6.2025e-02
   2_bss:   1.014  0.007  0.070 15.037  0.005  4.110   6.2025e-02
   2_xyz:   0.958  0.006  0.071 14.757  0.004  4.114   5.4912e-02
   2_adp:   0.958  0.006  0.071 14.757  0.004  4.114   5.4912e-02
   2_occ:   0.958  0.006  0.071 14.757  0.004  4.114   5.4912e-02
   3_bss:   0.958  0.006  0.071 14.757  0.004  4.114   5.4912e-02
   3_xyz:   0.981  0.007  0.075 14.775  0.004  4.115   5.8556e-02
   3_adp:   0.981  0.007  0.075 14.775  0.004  4.115   5.8556e-02
   3_occ:   0.981  0.007  0.075 14.775  0.004  4.115   5.8556e-02
   4_bss:   0.981  0.007  0.075 14.775  0.004  4.115   5.8556e-02
   4_xyz:   0.999  0.007  0.076 14.766  0.004  4.115   5.9809e-02
   4_adp:   0.999  0.007  0.076 14.766  0.004  4.115   5.9809e-02
   4_occ:   0.999  0.007  0.076 14.766  0.004  4.115   5.9809e-02
   5_bss:   0.999  0.007  0.076 14.766  0.004  4.115   5.9809e-02
   5_xyz:   0.976  0.007  0.075 14.636  0.004  4.109   5.7608e-02
   5_adp:   0.976  0.007  0.075 14.636  0.004  4.109   5.7608e-02
   5_occ:   0.976  0.007  0.075 14.636  0.004  4.109   5.7608e-02
   5_bss:   0.976  0.007  0.075 14.636  0.004  4.109   5.7608e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3899e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3899e-01
   1_xyz:   6.926  0.042  0.235 85.268  0.040  2.232   5.5546e-02
   1_adp:   6.926  0.042  0.235 85.268  0.040  2.232   5.5546e-02
   1_occ:   6.926  0.042  0.235 85.268  0.040  2.232   5.5546e-02
   2_bss:   6.926  0.042  0.235 85.268  0.040  2.232   5.5546e-02
   2_xyz:   6.667  0.041  0.226 83.106  0.042  2.325   6.3260e-02
   2_adp:   6.667  0.041  0.226 83.106  0.042  2.325   6.3260e-02
   2_occ:   6.667  0.041  0.226 83.106  0.042  2.325   6.3260e-02
   3_bss:   6.667  0.041  0.226 83.106  0.042  2.325   6.3260e-02
   3_xyz:   6.516  0.040  0.245 84.562  0.037  2.290   5.2116e-02
   3_adp:   6.516  0.040  0.245 84.562  0.037  2.290   5.2116e-02
   3_occ:   6.516  0.040  0.245 84.562  0.037  2.290   5.2116e-02
   4_bss:   6.516  0.040  0.245 84.562  0.037  2.290   5.2116e-02
   4_xyz:   6.188  0.045  0.245 83.294  0.041  2.315   4.6269e-02
   4_adp:   6.188  0.045  0.245 83.294  0.041  2.315   4.6269e-02
   4_occ:   6.188  0.045  0.245 83.294  0.041  2.315   4.6269e-02
   5_bss:   6.188  0.045  0.245 83.294  0.041  2.315   4.6269e-02
   5_xyz:   6.305  0.044  0.249 83.737  0.038  2.298   4.2333e-02
   5_adp:   6.305  0.044  0.249 83.737  0.038  2.298   4.2333e-02
   5_occ:   6.305  0.044  0.249 83.737  0.038  2.298   4.2333e-02
   5_bss:   6.305  0.044  0.249 83.737  0.038  2.298   4.2333e-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:  67.07   0.51  17.02  66.73   0.51  13.04  67.07   8.07  38.70
   1_occ:  67.07   0.51  17.02  66.73   0.51  13.04  67.07   8.07  38.70
   2_bss:  67.07   0.51  17.02  66.73   0.51  13.04  67.07   8.07  38.70
   2_xyz:  67.07   0.51  17.02  66.73   0.51  13.04  67.07   8.07  38.70
   2_adp:  67.33   2.32  16.60  66.02   2.32  12.90  67.33   5.91  36.77
   2_occ:  67.33   2.32  16.60  66.02   2.32  12.90  67.33   5.91  36.77
   3_bss:  67.33   2.32  16.60  66.02   2.32  12.90  67.33   5.91  36.77
   3_xyz:  67.33   2.32  16.60  66.02   2.32  12.90  67.33   5.91  36.77
   3_adp:  78.83   0.72  17.09  78.83   0.72  12.96  75.55   4.36  39.57
   3_occ:  78.83   0.72  17.09  78.83   0.72  12.96  75.55   4.36  39.57
   4_bss:  78.83   0.72  17.09  78.83   0.72  12.96  75.55   4.36  39.57
   4_xyz:  78.83   0.72  17.09  78.83   0.72  12.96  75.55   4.36  39.57
   4_adp:  80.26   0.77  16.88  80.26   0.77  12.77  76.56   5.73  39.26
   4_occ:  80.26   0.77  16.88  80.26   0.77  12.77  76.56   5.73  39.26
   5_bss:  80.26   0.77  16.88  80.26   0.77  12.77  76.56   5.73  39.26
   5_xyz:  80.26   0.77  16.88  80.26   0.77  12.77  76.56   5.73  39.26
   5_adp:  81.78   1.03  16.47  81.78   1.03  12.53  78.08   6.22  37.91
   5_occ:  81.78   1.03  16.47  81.78   1.03  12.53  78.08   6.22  37.91
   5_bss:  81.74   0.99  16.43  81.74   0.99  12.49  78.05   6.18  37.88
------------------------------------------------------------------------
 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:    1.005    0.014    0.283
   1_adp:    1.005    0.014    0.283
   1_occ:    1.005    0.014    0.283
   2_bss:    1.005    0.014    0.283
   2_xyz:    0.731    0.028    0.340
   2_adp:    0.731    0.028    0.340
   2_occ:    0.731    0.028    0.340
   3_bss:    0.731    0.028    0.340
   3_xyz:    0.911    0.032    0.361
   3_adp:    0.911    0.032    0.361
   3_occ:    0.911    0.032    0.361
   4_bss:    0.911    0.032    0.361
   4_xyz:    1.030    0.029    0.370
   4_adp:    1.030    0.029    0.370
   4_occ:    1.030    0.029    0.370
   5_bss:    1.030    0.029    0.370
   5_xyz:    1.164    0.014    0.375
   5_adp:    1.164    0.014    0.375
   5_occ:    1.164    0.014    0.375
   5_bss:    1.164    0.014    0.375
------------------------------------------------------------------------

CPU time actual refinement: 325.66


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_401/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_401/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_401/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_401/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_401/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.51 
  Macro-tasks:
    bulk solvent and scale       = 36.93  
    individual site refinement   = 136.15 
    weights calculation          = 29.46  
    collect and process          = 6.62   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 209.28 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 103.50 
    alpha_beta                      = 8.25   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 113.15 
    fmodel                         = 6.31   
    r_factors                      = 0.18   
    phase_errors                   = 10.90  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 244.96 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.591 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    651 calls, 103.11 s
gradients_fft:          596 calls,  99.23 s

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

# Date 2008-01-16 Time 04:44:22 PST -0800 (1200487462.59 s)
Start R-work = 0.3038, R-free = 0.2985 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.2887, R-free = 0.2817
Final R-work = 0.1052, R-free = 0.1525