# Date 2008-01-16 Time 06:41:52 PST -0800 (1200494512.52 s)
#phil __OFF__

Command line arguments: "../1248.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10441
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1248

-------------------------------------------------------------------------------
  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: (72.0062, 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: 3.24, per 1000 atoms: 1.15


================================== 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: (72.0062, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.98276
Completeness in resolution range: 0.946329
Completeness with d_max=infinity: 0.943593

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2644
                             d_min =   1.9828

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: (72.0062, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.98276
Completeness in resolution range: 0.946329
Completeness with d_max=infinity: 0.943593

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2649 -  4.2440 [2171/2198]  1956   215   9.9%
  bin  2:  4.2440 -  3.3806 [2086/2106]  1875   211  10.1%
  bin  3:  3.3806 -  2.9568 [2060/2079]  1855   205  10.0%
  bin  4:  2.9568 -  2.6881 [2039/2069]  1833   206  10.1%
  bin  5:  2.6881 -  2.4963 [2041/2060]  1846   195   9.6%
  bin  6:  2.4963 -  2.3497 [2009/2034]  1795   214  10.7%
  bin  7:  2.3497 -  2.2324 [2024/2052]  1823   201   9.9%
  bin  8:  2.2324 -  2.1355 [1982/2018]  1788   194   9.8%
  bin  9:  2.1355 -  2.0535 [1999/2041]  1802   197   9.9%
  bin 10:  2.0535 -  1.9828 [1178/2043]  1057   121  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1248/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2181
        3.04 -     3.66: 4669
        3.66 -     4.28: 9006
        4.28 -     4.90: 12279
  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 208 " - " O   HOH Z 342 "  1.911 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.019 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.125 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.125 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28148 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_1248/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1248/model_refine_001.geo

CPU time processing inputs: 9.02


============================ 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 = 72.00625 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 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3889   r_free= 0.3822   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.180077                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7342 0.99   1412  159 0.3200 0.3076      6.4294      6.3873|
|  2:  4.7342 -  3.7764 0.99   1352  148 0.3258 0.3239      6.6644      6.6362|
|  3:  3.7764 -  3.3046 0.99   1327  144 0.3419 0.3180      6.4924      6.5217|
|  4:  3.3046 -  3.0049 0.99   1334  155 0.3727 0.3838      6.3913      6.3775|
|  5:  3.0049 -  2.7909 0.99   1317  146 0.4014 0.4057      6.2545       6.292|
|  6:  2.7909 -  2.6273 0.99   1313  145 0.3943 0.4047      6.1634      6.1574|
|  7:  2.6273 -  2.4963 0.99   1310  135 0.4290 0.4003      6.1605      6.1415|
|  8:  2.4963 -  2.3881 0.98   1272  148 0.4324 0.4247      6.0932      6.0473|
|  9:  2.3881 -  2.2964 0.98   1281  151 0.4225 0.4435      6.0482      6.0769|
| 10:  2.2964 -  2.2174 1.00   1306  148 0.4406 0.4308      6.0128      6.0104|
| 11:  2.2174 -  2.1483 0.98   1302  136 0.4528 0.4263       5.998      5.9754|
| 12:  2.1483 -  2.0870 0.98   1260  142 0.4457 0.4478      5.9071      5.9661|
| 13:  2.0870 -  2.0322 0.96   1260  134 0.4620 0.4328      5.8307      5.7283|
| 14:  2.0322 -  1.9828 0.44    584   68 0.4467 0.4420      5.7786      5.7976|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7342  1412   159  0.77  27.77   0.84     0.80      48649.32|
|  2:  4.7342 -  3.7764  1352   148  0.80  26.40   0.94     0.88      63842.55|
|  3:  3.7764 -  3.3046  1327   144  0.72  33.29   0.96     0.88      69563.03|
|  4:  3.3046 -  3.0049  1334   155  0.67  38.08   0.95     0.85      64852.63|
|  5:  3.0049 -  2.7909  1317   146  0.59  44.94   0.93     0.77      55862.54|
|  6:  2.7909 -  2.6273  1313   145  0.58  45.69   0.96     0.77      48034.51|
|  7:  2.6273 -  2.4963  1310   135  0.58  46.09   0.96     0.75      43150.01|
|  8:  2.4963 -  2.3881  1272   148  0.58  45.37   0.93     0.78      38074.81|
|  9:  2.3881 -  2.2964  1281   151  0.57  46.68   0.99     0.76      35530.18|
| 10:  2.2964 -  2.2174  1306   148  0.55  48.29   0.98     0.76      34044.65|
| 11:  2.2174 -  2.1483  1302   136  0.53  50.22   0.99     0.74      33978.11|
| 12:  2.1483 -  2.0870  1260   142  0.52  50.77   0.97     0.73      30632.94|
| 13:  2.0870 -  2.0322  1260   134  0.51  51.85   0.96     0.74      26148.16|
| 14:  2.0322 -  1.9828   584    68  0.56  47.55   0.99     0.78      21002.22|
|alpha:            min =        0.73 max =            0.88 mean =         0.79|
|beta:             min =    21002.22 max =        69563.03 mean =     45005.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        42.68|
|phase err.(test): min =        0.00 max =           89.81 mean =        42.38|
|-----------------------------------------------------------------------------|

============================== 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 = 7.596883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.700   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.306068              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.151   (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:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      198 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1983 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1846 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2823 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4638 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4368 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5623 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6656 |
|-----------------------------------------------------------------------------|
|-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 |   4.112    4.900  1.806 |       0.178 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.067)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3889   r_free= 0.3822   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.180077                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3775   r_free= 0.3703   ksol= 0.33   Bsol= 57.43   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,-0.91,-2.07,-0.00,-0.00,-0.00); trace/3= 0.00                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.165691                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.672550              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.988   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.628751              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.939   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3775      final r-factor (work) = 0.2222          |
| start r-factor (free) = 0.3703      final r-factor (free) = 0.2529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.7331 = 6.67 * 0.50 * 6.1655 + 1.00 * 0.1631                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8627 = 6.67 * 0.50 * 5.9223 + 1.00 * 0.1042                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2222      final r-factor (work) = 0.2045          |
| start r-factor (free) = 0.2529      final r-factor (free) = 0.2595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7301 = 0.63 * 1.00 * 5.9223 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5761 = 0.63 * 1.00 * 5.6559 + 1.00 * 0.0200                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.067)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.67   17.12    None  None   None       |
|    all(noH): 2823   0      0.00    65.67   17.12    None  None   None       |
|    Sol.    : 438    0      2.70    65.67   38.87    None  None   None       |
|    Mac.    : 2385   0      0.00    56.21   13.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.567:  391   |   5:    32.835 -  39.402:  105        |
|      1:     6.567 -  13.134: 1014   |   6:    39.402 -  45.969:  107        |
|      2:    13.134 -  19.701:  665   |   7:    45.969 -  52.535:   76        |
|      3:    19.701 -  26.268:  270   |   8:    52.535 -  59.102:   59        |
|      4:    26.268 -  32.835:  118   |   9:    59.102 -  65.669:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2045 r_free = 0.2595             target_work(ml) = 5.669         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2041 r_free = 0.2587             target_work(ml) = 5.667         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2041   r_free= 0.2587   ksol= 0.33   Bsol= 57.43   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,-0.91,-2.07,-0.00,-0.00,-0.00); trace/3= 0.00                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.666725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2018   r_free= 0.2562   ksol= 0.34   Bsol= 63.42   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-2.43,-1.85,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.660449                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.287504              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.116   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.273350              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.361   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2018      final r-factor (work) = 0.1573          |
| start r-factor (free) = 0.2562      final r-factor (free) = 0.2063          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5835 = 2.29 * 0.50 * 5.6649 + 1.00 * 0.1042                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4077 = 2.29 * 0.50 * 5.5575 + 1.00 * 0.0513                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1573      final r-factor (work) = 0.1497          |
| start r-factor (free) = 0.2063      final r-factor (free) = 0.1970          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5336 = 0.27 * 1.00 * 5.5575 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5437 = 0.27 * 1.00 * 5.4164 + 1.00 * 0.0631                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.067)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.92   17.05    None  None   None       |
|    all(noH): 2823   0      0.00    66.92   17.05    None  None   None       |
|    Sol.    : 438    0      4.96    66.92   38.80    None  None   None       |
|    Mac.    : 2385   0      0.00    63.82   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.692:  285   |   5:    33.462 -  40.154:  106        |
|      1:     6.692 -  13.385: 1268   |   6:    40.154 -  46.847:  102        |
|      2:    13.385 -  20.077:  594   |   7:    46.847 -  53.539:   78        |
|      3:    20.077 -  26.770:  205   |   8:    53.539 -  60.231:   58        |
|      4:    26.770 -  33.462:  114   |   9:    60.231 -  66.924:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1497 r_free = 0.1970             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1496 r_free = 0.1971             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1496   r_free= 0.1971   ksol= 0.34   Bsol= 63.42   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-2.43,-1.85,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.393994                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1496   r_free= 0.1970   ksol= 0.34   Bsol= 63.42   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-2.58,-1.47,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.393157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.795530              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.951  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.542616              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.085   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1496      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1970      final r-factor (free) = 0.1735          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6220 = 2.80 * 0.50 * 5.4161 + 1.00 * 0.0516                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4994 = 2.80 * 0.50 * 5.3208 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1263      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1735      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9479 = 0.54 * 1.00 * 5.3208 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8439 = 0.54 * 1.00 * 5.2237 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.067)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.98   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    86.98   17.44    None  None   None       |
|    Sol.    : 438    0      5.46    86.98   41.16    None  None   None       |
|    Mac.    : 2385   0      0.00    78.27   13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.698:  695   |   5:    43.488 -  52.185:   95        |
|      1:     8.698 -  17.395: 1320   |   6:    52.185 -  60.883:   86        |
|      2:    17.395 -  26.093:  320   |   7:    60.883 -  69.580:   42        |
|      3:    26.093 -  34.790:  137   |   8:    69.580 -  78.278:   14        |
|      4:    34.790 -  43.488:  110   |   9:    78.278 -  86.975:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1659             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1196 r_free = 0.1658             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1658   ksol= 0.34   Bsol= 63.42   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-2.58,-1.47,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199585                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1650   ksol= 0.33   Bsol= 60.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.78,-1.57,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198003                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.424780              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.629  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.050  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3961 = 2.42 * 0.50 * 5.2244 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3411 = 2.42 * 0.50 * 5.1780 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5062 = 0.48 * 1.00 * 5.1780 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5004 = 0.48 * 1.00 * 5.1660 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.067)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.16    91.89   17.29    None  None   None       |
|    all(noH): 2823   0      0.16    91.89   17.29    None  None   None       |
|    Sol.    : 438    0      5.98    91.89   40.61    None  None   None       |
|    Mac.    : 2385   0      0.16    84.60   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.164 -   9.336:  849   |   5:    46.025 -  55.198:  101        |
|      1:     9.336 -  18.508: 1255   |   6:    55.198 -  64.370:   61        |
|      2:    18.508 -  27.681:  257   |   7:    64.370 -  73.542:   28        |
|      3:    27.681 -  36.853:  140   |   8:    73.542 -  82.715:    9        |
|      4:    36.853 -  46.025:  119   |   9:    82.715 -  91.887:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1619             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1618             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1618   ksol= 0.33   Bsol= 60.85   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.78,-1.57,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163718                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1618   ksol= 0.33   Bsol= 60.85   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.67,-1.40,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163772                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.288096              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.494  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.401222              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.100  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9737 = 2.29 * 0.50 * 5.1662 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9651 = 2.29 * 0.50 * 5.1601 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0796 = 0.40 * 1.00 * 5.1601 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0790 = 0.40 * 1.00 * 5.1591 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.067)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.14    92.39   17.10    None  None   None       |
|    all(noH): 2823   0      0.14    92.39   17.10    None  None   None       |
|    Sol.    : 438    0      6.17    92.39   40.10    None  None   None       |
|    Mac.    : 2385   0      0.14    85.93   12.88    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:     0.139 -   9.364:  883   |   5:    46.266 -  55.491:  103        |
|      1:     9.364 -  18.590: 1234   |   6:    55.491 -  64.716:   55        |
|      2:    18.590 -  27.815:  249   |   7:    64.716 -  73.942:   28        |
|      3:    27.815 -  37.040:  146   |   8:    73.942 -  83.167:    7        |
|      4:    37.040 -  46.266:  114   |   9:    83.167 -  92.392:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1616             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1615             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1615   ksol= 0.33   Bsol= 60.85   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.67,-1.40,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158383                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7342 0.99   1412  159 0.0968 0.1316      5.3703      5.5669|
|  2:  4.7342 -  3.7764 0.99   1352  148 0.0849 0.1063      5.4399      5.6096|
|  3:  3.7764 -  3.3046 0.99   1327  144 0.1053 0.1588      5.4759       5.879|
|  4:  3.3046 -  3.0049 0.99   1334  155 0.1218 0.1724      5.4647       5.627|
|  5:  3.0049 -  2.7909 0.99   1317  146 0.1328 0.1775      5.3289      5.5723|
|  6:  2.7909 -  2.6273 0.99   1313  145 0.1223 0.1816      5.2192      5.4515|
|  7:  2.6273 -  2.4963 0.99   1310  135 0.1266 0.1680      5.1827      5.3574|
|  8:  2.4963 -  2.3881 0.98   1272  148 0.1172 0.1879      5.0645      5.3944|
|  9:  2.3881 -  2.2964 0.98   1281  151 0.1190 0.1874      5.0579      5.3357|
| 10:  2.2964 -  2.2174 1.00   1306  148 0.1143 0.1684      4.9589      5.2049|
| 11:  2.2174 -  2.1483 0.98   1302  136 0.1130 0.1881      4.9614      5.3364|
| 12:  2.1483 -  2.0870 0.98   1260  142 0.1121 0.1556      4.8745      5.0822|
| 13:  2.0870 -  2.0322 0.96   1260  134 0.1162 0.1799      4.8062      5.0841|
| 14:  2.0322 -  1.9828 0.44    584   68 0.1058 0.1688      4.6799      4.9494|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7342  1412   159  0.94   8.98   0.97     0.94       7028.40|
|  2:  4.7342 -  3.7764  1352   148  0.95   8.16   1.00     1.00       9225.59|
|  3:  3.7764 -  3.3046  1327   144  0.93  11.42   1.02     1.01      10598.49|
|  4:  3.3046 -  3.0049  1334   155  0.91  14.41   1.00     0.97      10764.64|
|  5:  3.0049 -  2.7909  1317   146  0.90  16.00   0.99     0.97       8515.89|
|  6:  2.7909 -  2.6273  1313   145  0.90  16.47   0.98     0.96       7324.75|
|  7:  2.6273 -  2.4963  1310   135  0.90  15.93   0.99     0.97       6599.67|
|  8:  2.4963 -  2.3881  1272   148  0.90  15.81   0.98     0.95       5357.07|
|  9:  2.3881 -  2.2964  1281   151  0.90  15.80   0.99     0.95       5192.66|
| 10:  2.2964 -  2.2174  1306   148  0.90  15.75   0.99     0.96       4435.11|
| 11:  2.2174 -  2.1483  1302   136  0.90  16.42   0.98     0.93       4549.25|
| 12:  2.1483 -  2.0870  1260   142  0.91  15.83   1.00     0.99       4048.90|
| 13:  2.0870 -  2.0322  1260   134  0.90  16.70   0.98     0.97       3529.14|
| 14:  2.0322 -  1.9828   584    68  0.91  15.21   0.96     0.92       2709.92|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2709.92 max =        10764.64 mean =      6614.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.40|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.90|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1615   ksol= 0.33   Bsol= 60.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.55,-1.26,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158466                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1615   ksol= 0.33   Bsol= 60.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.55,-1.26,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158466                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7342 0.99   1412  159 0.0968 0.1317      5.3707      5.5675|
|  2:  4.7342 -  3.7764 0.99   1352  148 0.0849 0.1063        5.44      5.6095|
|  3:  3.7764 -  3.3046 0.99   1327  144 0.1053 0.1587      5.4757      5.8787|
|  4:  3.3046 -  3.0049 0.99   1334  155 0.1217 0.1724      5.4646       5.627|
|  5:  3.0049 -  2.7909 0.99   1317  146 0.1329 0.1776       5.329      5.5724|
|  6:  2.7909 -  2.6273 0.99   1313  145 0.1223 0.1815      5.2191      5.4511|
|  7:  2.6273 -  2.4963 0.99   1310  135 0.1266 0.1679      5.1825      5.3572|
|  8:  2.4963 -  2.3881 0.98   1272  148 0.1171 0.1879      5.0645      5.3943|
|  9:  2.3881 -  2.2964 0.98   1281  151 0.1191 0.1874      5.0581      5.3355|
| 10:  2.2964 -  2.2174 1.00   1306  148 0.1143 0.1684       4.959      5.2051|
| 11:  2.2174 -  2.1483 0.98   1302  136 0.1130 0.1883      4.9617      5.3369|
| 12:  2.1483 -  2.0870 0.98   1260  142 0.1121 0.1557      4.8748      5.0827|
| 13:  2.0870 -  2.0322 0.96   1260  134 0.1162 0.1799      4.8063      5.0839|
| 14:  2.0322 -  1.9828 0.44    584   68 0.1058 0.1688      4.6799      4.9493|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7342  1412   159  0.94   8.98   0.97     0.94       7035.29|
|  2:  4.7342 -  3.7764  1352   148  0.95   8.17   1.01     1.00       9227.83|
|  3:  3.7764 -  3.3046  1327   144  0.93  11.42   1.02     1.02      10593.86|
|  4:  3.3046 -  3.0049  1334   155  0.91  14.41   1.00     0.97      10765.44|
|  5:  3.0049 -  2.7909  1317   146  0.90  16.00   0.99     0.97       8514.68|
|  6:  2.7909 -  2.6273  1313   145  0.90  16.47   0.99     0.96       7323.07|
|  7:  2.6273 -  2.4963  1310   135  0.90  15.93   1.00     0.97       6597.43|
|  8:  2.4963 -  2.3881  1272   148  0.90  15.81   0.98     0.96       5356.39|
|  9:  2.3881 -  2.2964  1281   151  0.90  15.80   1.00     0.96       5191.82|
| 10:  2.2964 -  2.2174  1306   148  0.90  15.75   0.99     0.96       4436.54|
| 11:  2.2174 -  2.1483  1302   136  0.90  16.42   0.99     0.94       4550.96|
| 12:  2.1483 -  2.0870  1260   142  0.91  15.84   1.00     0.99       4052.77|
| 13:  2.0870 -  2.0322  1260   134  0.90  16.71   0.99     0.98       3529.72|
| 14:  2.0322 -  1.9828   584    68  0.91  15.22   0.96     0.93       2709.79|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2709.79 max =        10765.44 mean =      6614.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.40|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.067)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.14    92.39   17.10    None  None   None       |
|    all(noH): 2823   0      0.14    92.39   17.10    None  None   None       |
|    Sol.    : 438    0      6.17    92.39   40.10    None  None   None       |
|    Mac.    : 2385   0      0.14    85.93   12.88    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:     0.137 -   9.362:  883   |   5:    46.263 -  55.489:  103        |
|      1:     9.362 -  18.588: 1234   |   6:    55.489 -  64.714:   55        |
|      2:    18.588 -  27.813:  249   |   7:    64.714 -  73.939:   28        |
|      3:    27.813 -  37.038:  146   |   8:    73.939 -  83.165:    7        |
|      4:    37.038 -  46.263:  114   |   9:    83.165 -  92.390:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.497 - 4.626
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 305
   mapped sites are within: 0.712 - 4.626

peak=    5.548 closest distance to " CB  GLN A 223 " =    1.473
peak=    5.543 closest distance to " NE2 GLN A  11 " =    1.220
peak=    5.420 closest distance to " O   HOH Z 111 " =    1.981
peak=    5.326 closest distance to " CG  PRO A  54 " =    1.289
peak=    5.190 closest distance to " O   HOH Z 232 " =    2.245
peak=    5.103 closest distance to " CG  PRO A 213 " =    1.259
peak=    5.035 closest distance to " CB  SER A  63 " =    1.286
peak=    4.995 closest distance to " O   HOH Z 126 " =    1.980
peak=    4.958 closest distance to " CB  PRO A  54 " =    0.968
peak=    4.829 closest distance to " O   HOH Z  78 " =    1.835
peak=    4.718 closest distance to " CB  LEU A 228 " =    1.096
peak=    4.699 closest distance to " O   HOH Z 298 " =    2.088
peak=    4.694 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.610 closest distance to " C   PRO A 198 " =    1.528
peak=    4.574 closest distance to " CG  PRO A 198 " =    1.266
peak=    4.509 closest distance to " O   HOH Z 369 " =    2.055
peak=    4.501 closest distance to " O   HOH Z 144 " =    1.702
peak=    4.442 closest distance to " CG  PRO A  90 " =    1.058
peak=    4.411 closest distance to " CA  TYR A  30 " =    0.981
peak=    4.404 closest distance to " CD  ARG A 159 " =    0.813
peak=    4.376 closest distance to " CB  ARG A 275 " =    0.960
peak=    4.367 closest distance to " CB  ASN A 148 " =    1.385
peak=    4.363 closest distance to " O   HOH Z 193 " =    1.828
peak=    4.361 closest distance to " O   HOH Z 236 " =    2.250
peak=    4.352 closest distance to " O   HOH Z  78 " =    2.180
peak=    4.346 closest distance to " CB  ARG A  79 " =    1.448
peak=    4.323 closest distance to " CB  GLU A 128 " =    1.042
peak=    4.314 closest distance to " ND2 ASN A 187 " =    1.472
peak=    4.311 closest distance to " O   HOH Z 423 " =    1.665
peak=    4.290 closest distance to " CD ALYS A 290 " =    1.027
peak=    4.253 closest distance to " CZ  PHE A 218 " =    1.040
peak=    4.233 closest distance to " CG  PRO A 280 " =    0.843
peak=    4.232 closest distance to " CG2 VAL A 257 " =    0.990
peak=    4.205 closest distance to " NH1AARG A 145 " =    1.204
peak=    4.193 closest distance to " O   HOH Z  15 " =    2.223
peak=    4.170 closest distance to " CB  ARG A 190 " =    1.528
peak=    4.161 closest distance to " CB  TRP A 266 " =    0.999
peak=    4.137 closest distance to " O   HOH Z 427 " =    2.913
peak=    4.112 closest distance to " CG  PRO A 243 " =    1.101
peak=    4.108 closest distance to " CE  LYS A  76 " =    0.861
peak=    4.083 closest distance to " O   HOH Z 132 " =    2.530
peak=    4.079 closest distance to " ND1 HIS A  86 " =    1.704
peak=    4.068 closest distance to " O   HOH Z 214 " =    2.009
peak=    4.064 closest distance to " O   HOH Z 133 " =    2.371
peak=    4.059 closest distance to " O   HOH Z 272 " =    1.884
peak=    4.058 closest distance to " CB  SER A 212 " =    1.138
peak=    4.047 closest distance to " OD1 ASN A  69 " =    2.622
peak=    4.026 closest distance to " O   HOH Z 303 " =    2.238
peak=    4.003 closest distance to " CD  ARG A  66 " =    2.123
peak=    3.998 closest distance to " CD1 LEU A 300 " =    1.277
peak=    3.996 closest distance to " O   HOH Z 234 " =    3.778
peak=    3.989 closest distance to " CB  GLU A 152 " =    1.279
peak=    3.972 closest distance to " O   HOH Z 261 " =    1.861
peak=    3.971 closest distance to " CG2 THR A 221 " =    1.006
peak=    3.960 closest distance to " CG  LEU A 167 " =    1.263
peak=    3.945 closest distance to " O   HOH Z  58 " =    1.702
peak=    3.890 closest distance to " CB  SER A   3 " =    1.420
peak=    3.885 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.874 closest distance to " CB  ASP A 124 " =    0.744
peak=    3.870 closest distance to " O   HOH Z 213 " =    1.941
peak=    3.863 closest distance to " CB  ASN A 187 " =    1.138
peak=    3.857 closest distance to " O   HOH Z 217 " =    3.117
peak=    3.855 closest distance to " O   HOH Z  88 " =    3.655
peak=    3.843 closest distance to " CB  SER A 216 " =    0.893
peak=    3.837 closest distance to " CG1 ILE A  33 " =    1.222
peak=    3.826 closest distance to " O   HOH Z 183 " =    1.505
peak=    3.824 closest distance to " O   HOH Z 193 " =    1.822
peak=    3.823 closest distance to " CB  VAL A 265 " =    1.292
peak=    3.819 closest distance to " O   HOH Z 425 " =    1.279
peak=    3.818 closest distance to " O   HOH Z 437 " =    1.496
peak=    3.818 closest distance to " O   HOH Z 368 " =    1.998
peak=    3.805 closest distance to " CA  THR A 264 " =    0.848
peak=    3.802 closest distance to " O   HOH Z   1 " =    1.878
peak=    3.801 closest distance to " OD2 ASP A 286 " =    2.914
peak=    3.796 closest distance to " O   HOH Z  10 " =    1.880
peak=    3.782 closest distance to " CA  MET A  40 " =    1.225
peak=    3.780 closest distance to " NH2 ARG A 156 " =    1.230
peak=    3.771 closest distance to " O   HOH Z 209 " =    2.331
peak=    3.759 closest distance to " O   HOH Z 316 " =    3.091
peak=    3.745 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.743 closest distance to " O   HOH Z 411 " =    3.745
peak=    3.743 closest distance to " O   HOH Z 135 " =    1.757
peak=    3.739 closest distance to " CA  ASN A 215 " =    1.260
peak=    3.738 closest distance to " CB  ASN A  39 " =    0.946
peak=    3.738 closest distance to " O   HOH Z 158 " =    2.891
peak=    3.731 closest distance to " CB  MET A  40 " =    0.766
peak=    3.713 closest distance to " O   HOH Z 180 " =    2.142
peak=    3.703 closest distance to " O   HOH Z 346 " =    1.667
peak=    3.681 closest distance to " O   HOH Z 265 " =    2.354
peak=    3.679 closest distance to " CB  ALA A 104 " =    0.747
peak=    3.678 closest distance to " N   PHE A 130 " =    1.202
peak=    3.666 closest distance to " CB  TYR A 169 " =    0.748
peak=    3.664 closest distance to " O   HOH Z 409 " =    2.531
peak=    3.663 closest distance to " CB  ALA A   1 " =    4.626
peak=    3.653 closest distance to " O   HOH Z 250 " =    1.441
peak=    3.652 closest distance to " O   TYR A 116 " =    1.295
peak=    3.635 closest distance to " O   HOH Z 426 " =    1.745
peak=    3.630 closest distance to " O   HOH Z   9 " =    2.022
peak=    3.629 closest distance to " CD  ARG A 269 " =    0.924
peak=    3.626 closest distance to " CB  VAL A 202 " =    1.641
peak=    3.626 closest distance to " O  BHOH Z 338 " =    2.362
peak=    3.621 closest distance to " O   HOH Z   2 " =    1.430
peak=    3.619 closest distance to " CB  ALA A 248 " =    0.936
peak=    3.616 closest distance to " O   MET A 105 " =    1.771
peak=    3.611 closest distance to " CD2 LEU A 255 " =    1.599
peak=    3.601 closest distance to " O   THR A 220 " =    1.443
peak=    3.597 closest distance to " CA  SER A  87 " =    1.010
peak=    3.592 closest distance to " CZ  PHE A 192 " =    0.919
peak=    3.587 closest distance to " O   HOH Z 391 " =    2.919
peak=    3.584 closest distance to " CG  MET A 113 " =    1.465
peak=    3.582 closest distance to " O   HOH Z 188 " =    2.274
peak=    3.581 closest distance to " O   HOH Z 133 " =    1.715
peak=    3.581 closest distance to " O   HOH Z 285 " =    2.800
peak=    3.575 closest distance to " N   ASN A 127 " =    1.278
peak=    3.572 closest distance to " CB  LEU A 143 " =    1.127
peak=    3.568 closest distance to " CB  ASP A 140 " =    0.873
peak=    3.567 closest distance to " O   HOH Z  20 " =    1.926
peak=    3.564 closest distance to " O   HOH Z 193 " =    2.168
peak=    3.558 closest distance to " O   HOH Z   1 " =    1.777
peak=    3.553 closest distance to " CG  ARG A 159 " =    0.907
peak=    3.547 closest distance to " CB  ASN A 110 " =    1.189
peak=    3.544 closest distance to " CB  GLU A 277 " =    3.706
peak=    3.540 closest distance to " CG BARG A 275 " =    1.505
peak=    3.536 closest distance to " CA  ARG A 195 " =    1.340
peak=    3.536 closest distance to " CB  ALA A  34 " =    1.130
peak=    3.535 closest distance to " CA  ALA A 158 " =    1.144
peak=    3.533 closest distance to " CA  ALA A 154 " =    1.025
peak=    3.526 closest distance to " O   HOH Z 189 " =    2.656
peak=    3.508 closest distance to " O   HOH Z 109 " =    2.645
peak=    3.506 closest distance to " O   HOH Z 108 " =    2.476
peak=    3.503 closest distance to " CA  TYR A 116 " =    1.397
peak=    3.500 closest distance to " CD  LYS A 166 " =    1.309
peak=    3.491 closest distance to " CB  MET A  47 " =    1.020
peak=    3.482 closest distance to " CA  ASP A 124 " =    0.712
peak=    3.482 closest distance to " O   THR A 251 " =    1.276
peak=    3.481 closest distance to " CD  ARG A 219 " =    1.120
peak=    3.479 closest distance to " O   HOH Z 238 " =    3.671
peak=    3.478 closest distance to " O   HOH Z 368 " =    3.639
peak=    3.476 closest distance to " O   HOH Z 126 " =    1.511
peak=    3.475 closest distance to " O   HOH Z  88 " =    2.870
peak=    3.473 closest distance to " O   HOH Z 148 " =    3.406
peak=    3.472 closest distance to " O   HOH Z 371 " =    1.868
peak=    3.471 closest distance to " O   HOH Z 371 " =    2.902
peak=    3.471 closest distance to " O   HOH Z 327 " =    1.793
peak=    3.469 closest distance to " O   HOH Z 280 " =    3.078
peak=    3.467 closest distance to " O   ASN A 209 " =    1.352
peak=    3.466 closest distance to " CA  ILE A 234 " =    1.020
peak=    3.466 closest distance to " CB  SER A 210 " =    0.790
peak=    3.464 closest distance to " O   HOH Z 419 " =    1.965
peak=    3.464 closest distance to " O   HOH Z  44 " =    2.965
peak=    3.463 closest distance to " N   ASN A  39 " =    1.330
peak=    3.461 closest distance to " CB  LEU A 237 " =    0.801
peak=    3.451 closest distance to " CG  GLN A  88 " =    1.063
peak=    3.451 closest distance to " CB  ASN A 142 " =    0.932
peak=    3.449 closest distance to " CZ  PHE A 208 " =    1.148
peak=    3.445 closest distance to " O   HOH Z 344 " =    3.334
peak=    3.444 closest distance to " CB  TYR A 116 " =    0.846
peak=    3.435 closest distance to " O   HOH Z  61 " =    1.507
peak=    3.434 closest distance to " O   HOH Z 332 " =    1.614
peak=    3.432 closest distance to " O   HOH Z 359 " =    4.007
peak=    3.429 closest distance to " CB  GLU A 236 " =    1.178
peak=    3.428 closest distance to " CA  LYS A 290 " =    1.327
peak=    3.424 closest distance to " CB  ALA A 233 " =    1.322
peak=    3.423 closest distance to " N   ALA A   1 " =    2.147
peak=    3.423 closest distance to " O   HOH Z 365 " =    2.889
peak=    3.419 closest distance to " NE2 HIS A 207 " =    1.353
peak=    3.417 closest distance to " O   HOH Z 219 " =    2.032
peak=    3.417 closest distance to " O   HOH Z 185 " =    1.907
peak=    3.403 closest distance to " O   HOH Z 166 " =    3.806
peak=    3.402 closest distance to " CB  SER A  62 " =    1.172
peak=    3.395 closest distance to " CA  ALA A 160 " =    0.914
peak=    3.393 closest distance to " CD2 TRP A 179 " =    1.303
peak=    3.392 closest distance to " OG  SER A  62 " =    3.088
peak=    3.386 closest distance to " O   HOH Z 286 " =    2.244
peak=    3.384 closest distance to " ND2 ASN A 110 " =    1.762
peak=    3.384 closest distance to " CG1 ILE A 151 " =    1.033
peak=    3.383 closest distance to " CG  GLN A 144 " =    0.866
peak=    3.376 closest distance to " O   HOH Z 218 " =    4.558
peak=    3.375 closest distance to " O   HOH Z 175 " =    2.194
peak=    3.373 closest distance to " O   HOH Z  40 " =    1.981
peak=    3.371 closest distance to " O   HOH Z  68 " =    2.007
peak=    3.370 closest distance to " O   HOH Z 227 " =    1.706
peak=    3.368 closest distance to " N   TYR A  15 " =    0.771
peak=    3.367 closest distance to " CA  ALA A 291 " =    0.920
peak=    3.363 closest distance to " O   HOH Z 345 " =    3.593
peak=    3.362 closest distance to " CB  ARG A 138 " =    1.017
peak=    3.362 closest distance to " O   HOH Z  64 " =    2.086
peak=    3.360 closest distance to " CB  ALA A   9 " =    1.603
peak=    3.359 closest distance to " CG1 VAL A 153 " =    0.964
peak=    3.352 closest distance to " O   HOH Z  53 " =    2.535
peak=    3.351 closest distance to " CD  GLN A 240 " =    1.669
peak=    3.338 closest distance to " CA  THR A 221 " =    1.010
peak=    3.336 closest distance to " CD1 ILE A 106 " =    0.795
peak=    3.332 closest distance to " CB  THR A  82 " =    1.441
peak=    3.328 closest distance to " CB  TRP A 179 " =    1.504
peak=    3.327 closest distance to " CE2 TYR A 186 " =    0.890
peak=    3.326 closest distance to " O   HOH Z 329 " =    3.902
peak=    3.323 closest distance to " NH2BARG A 145 " =    2.095
peak=    3.323 closest distance to " O   HOH Z 128 " =    2.275
peak=    3.320 closest distance to " CA  ALA A 233 " =    1.391
peak=    3.320 closest distance to " CA  ALA A  21 " =    1.199
peak=    3.319 closest distance to " CB  TYR A 169 " =    0.838
peak=    3.312 closest distance to " OD1 ASN A 217 " =    1.569
peak=    3.311 closest distance to " O   HOH Z 423 " =    2.620
peak=    3.306 closest distance to " OH  TYR A 186 " =    1.095
peak=    3.305 closest distance to " CA  GLU A  46 " =    0.796
peak=    3.302 closest distance to " CB  ALA A 291 " =    1.359
peak=    3.300 closest distance to " CA  ARG A 102 " =    1.205
peak=    3.298 closest distance to " OG  SER A  22 " =    2.847
peak=    3.297 closest distance to " CG1 VAL A 189 " =    2.015
peak=    3.296 closest distance to " CB  SER A 276 " =    1.126
peak=    3.296 closest distance to " ND2 ASN A 249 " =    1.919
peak=    3.296 closest distance to " CA  ASN A 217 " =    1.219
peak=    3.296 closest distance to " O   HOH Z 116 " =    1.775
peak=    3.292 closest distance to " OD1BASN A 224 " =    2.301
peak=    3.282 closest distance to " O   HOH Z 184 " =    1.505
peak=    3.282 closest distance to " CB  HIS A 108 " =    0.793
peak=    3.281 closest distance to " CZ3 TRP A 123 " =    1.276
peak=    3.278 closest distance to " O   HOH Z 147 " =    1.804
peak=    3.276 closest distance to " CB  LYS A 117 " =    1.177
peak=    3.275 closest distance to " O   HOH Z 302 " =    1.829
peak=    3.273 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.273 closest distance to " CG1BVAL A  72 " =    1.608
peak=    3.272 closest distance to " O   ALA A 158 " =    1.327
peak=    3.271 closest distance to " O   HOH Z 386 " =    2.949
peak=    3.271 closest distance to " CB  ILE A 120 " =    1.245
peak=    3.270 closest distance to " O   HOH Z 386 " =    3.161
peak=    3.260 closest distance to " CA  ARG A  36 " =    1.166
peak=    3.255 closest distance to " O   HOH Z 291 " =    1.948
peak=    3.255 closest distance to " N   ARG A 156 " =    1.387
peak=    3.253 closest distance to " CB  TRP A 150 " =    1.272
peak=    3.251 closest distance to " O   HOH Z 425 " =    2.057
peak=    3.248 closest distance to " O   HOH Z 305 " =    3.655
peak=    3.241 closest distance to " O   ALA A 291 " =    1.484
peak=    3.241 closest distance to " CA  GLY A 267 " =    1.169
peak=    3.240 closest distance to " CB  ILE A 234 " =    1.148
peak=    3.237 closest distance to " NH2AARG A 190 " =    1.722
peak=    3.231 closest distance to " O   HOH Z 352 " =    1.817
peak=    3.224 closest distance to " OG  SER A  62 " =    3.118
peak=    3.222 closest distance to " CD1AILE A 234 " =    1.005
peak=    3.222 closest distance to " O   HOH Z 407 " =    2.055
peak=    3.221 closest distance to " O   HOH Z 368 " =    4.266
peak=    3.220 closest distance to " CG  GLN A 278 " =    1.361
peak=    3.219 closest distance to " O   HOH Z   3 " =    1.907
peak=    3.219 closest distance to " CG  LYS A  76 " =    0.965
peak=    3.219 closest distance to " CB  GLN A 103 " =    0.884
peak=    3.218 closest distance to " CB  GLU A 152 " =    1.406
peak=    3.217 closest distance to " CA  ALA A 299 " =    0.911
peak=    3.204 closest distance to " O   HOH Z 130 " =    3.875
peak=    3.202 closest distance to " CD  ARG A  14 " =    1.235
peak=    3.200 closest distance to " O   HOH Z 273 " =    2.774
peak=    3.199 closest distance to " ND2 ASN A 249 " =    0.842
peak=    3.198 closest distance to " CA  MET A 105 " =    0.962
peak=    3.198 closest distance to " CG2 ILE A 151 " =    0.873
peak=    3.196 closest distance to " CA  TYR A 186 " =    1.599
peak=    3.193 closest distance to " O   HOH Z 362 " =    2.704
peak=    3.191 closest distance to " C   TYR A 214 " =    1.621
peak=    3.187 closest distance to " O   THR A 294 " =    1.085
peak=    3.186 closest distance to " O   HOH Z 145 " =    2.141
peak=    3.185 closest distance to " O   HOH Z 345 " =    1.714
peak=    3.179 closest distance to " CD  PRO A 243 " =    1.721
peak=    3.179 closest distance to " O   HOH Z  64 " =    2.342
peak=    3.175 closest distance to " O   HOH Z 213 " =    3.034
peak=    3.173 closest distance to " O   HOH Z 327 " =    2.642
peak=    3.171 closest distance to " O   HOH Z  59 " =    1.832
peak=    3.169 closest distance to " O   HOH Z 258 " =    2.223
peak=    3.169 closest distance to " CA  ASP A 140 " =    1.240
peak=    3.167 closest distance to " CA  LYS A 117 " =    1.147
peak=    3.166 closest distance to " O   HOH Z 112 " =    1.523
peak=    3.161 closest distance to " O   HOH Z 172 " =    3.285
peak=    3.160 closest distance to " NH1BARG A 145 " =    1.189
peak=    3.151 closest distance to " O   HOH Z 392 " =    2.020
peak=    3.147 closest distance to " CA  GLN A 223 " =    0.920
peak=    3.146 closest distance to " CB  ARG A 139 " =    0.968
peak=    3.144 closest distance to " OG BSER A 134 " =    2.835
peak=    3.143 closest distance to " OG  SER A  97 " =    3.453
peak=    3.141 closest distance to " ND1 HIS A  81 " =    1.619
peak=    3.141 closest distance to " NH2 ARG A 219 " =    1.781
peak=    3.140 closest distance to " OG  SER A 206 " =    1.210
peak=    3.137 closest distance to " CG  GLU A 277 " =    3.310
peak=    3.134 closest distance to " O   HOH Z 406 " =    1.631
peak=    3.130 closest distance to " O   HOH Z 213 " =    2.160
peak=    3.128 closest distance to " NZ ALYS A 290 " =    1.086
peak=    3.126 closest distance to " NH2AARG A 190 " =    1.201
peak=    3.120 closest distance to " CB  PHE A  16 " =    1.024
peak=    3.117 closest distance to " CB  PHE A 283 " =    0.822
peak=    3.116 closest distance to " CB  ALA A 100 " =    1.311
peak=    3.115 closest distance to " CE2 TYR A 293 " =    1.049
peak=    3.114 closest distance to " OG BSER A 164 " =    2.451
peak=    3.112 closest distance to " O   HOH Z 295 " =    1.474
peak=    3.112 closest distance to " O   SER A  87 " =    2.389
peak=    3.104 closest distance to " NE2 GLN A  58 " =    3.540
peak=    3.102 closest distance to " CB  ALA A 248 " =    1.253
peak=    3.101 closest distance to " O   HOH Z 128 " =    2.251
peak=    3.101 closest distance to " CB  PRO A 243 " =    1.182
peak=    3.099 closest distance to " O   HOH Z 124 " =    1.870
peak=    3.084 closest distance to " CE1 TYR A 214 " =    1.019
peak=    3.079 closest distance to " O   HOH Z 403 " =    1.660
peak=    3.075 closest distance to " CB  ALA A 184 " =    0.974
peak=    3.063 closest distance to " CB  ASP A 171 " =    0.829
peak=    3.039 closest distance to " O   LEU A 300 " =    1.400
peak=    3.023 closest distance to " O   HOH Z 359 " =    1.420

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.730 - 5.684
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.730 - 5.684

peak=   -4.663 closest distance to " CB  PRO A 243 " =    2.590
peak=   -4.579 closest distance to " O   HOH Z 377 " =    1.878
peak=   -4.267 closest distance to " O   PRO A 198 " =    1.261
peak=   -4.183 closest distance to " CD  ARG A  14 " =    3.402
peak=   -4.168 closest distance to " O   HOH Z 266 " =    5.122
peak=   -4.117 closest distance to " O   HOH Z 231 " =    2.046
peak=   -4.037 closest distance to " CD  ARG A 156 " =    2.097
peak=   -4.031 closest distance to " CD  GLN A 223 " =    2.041
peak=   -4.020 closest distance to " O   HOH Z 389 " =    2.030
peak=   -3.969 closest distance to " O   HOH Z  38 " =    1.304
peak=   -3.949 closest distance to " O   HOH Z 290 " =    1.351
peak=   -3.923 closest distance to " N   ALA A  43 " =    2.428
peak=   -3.902 closest distance to " CZ3 TRP A 179 " =    1.125
peak=   -3.896 closest distance to " CE2 TYR A  30 " =    2.798
peak=   -3.867 closest distance to " CD2 LEU A 143 " =    2.620
peak=   -3.867 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.831 closest distance to " O   VAL A  67 " =    2.684
peak=   -3.813 closest distance to " O   HOH Z 435 " =    2.780
peak=   -3.795 closest distance to " OG BSER A 134 " =    1.257
peak=   -3.789 closest distance to " O   HOH Z 407 " =    3.402
peak=   -3.780 closest distance to " ND2 ASN A  45 " =    1.096
peak=   -3.774 closest distance to " O   VAL A 189 " =    2.515
peak=   -3.761 closest distance to " NH2AARG A 275 " =    5.635
peak=   -3.738 closest distance to " O   HOH Z  52 " =    1.333
peak=   -3.727 closest distance to " O   GLY A 211 " =    1.396
peak=   -3.727 closest distance to " CB  ALA A  43 " =    2.532
peak=   -3.727 closest distance to " CD1 PHE A  59 " =    1.832
peak=   -3.721 closest distance to " C   LEU A 222 " =    0.730
peak=   -3.713 closest distance to " O   TYR A 247 " =    2.874
peak=   -3.703 closest distance to " O   HOH Z  73 " =    1.991
peak=   -3.694 closest distance to " O   HOH Z 351 " =    1.499
peak=   -3.680 closest distance to " CB  CYS A 254 " =    2.170
peak=   -3.679 closest distance to " O   HOH Z 185 " =    2.299
peak=   -3.677 closest distance to " OD1 ASN A 148 " =    1.577
peak=   -3.671 closest distance to " CB  ALA A   9 " =    2.509
peak=   -3.667 closest distance to " CG  ARG A 269 " =    2.636
peak=   -3.661 closest distance to " ND2 ASN A  45 " =    1.513
peak=   -3.655 closest distance to " CA  ASP A  27 " =    2.542
peak=   -3.654 closest distance to " O   HOH Z  43 " =    1.530
peak=   -3.652 closest distance to " CD  ARG A 195 " =    5.143
peak=   -3.652 closest distance to " CZ BARG A 275 " =    1.762
peak=   -3.640 closest distance to " C   ASN A 285 " =    2.513
peak=   -3.632 closest distance to " OD1 ASN A 187 " =    1.603
peak=   -3.628 closest distance to " CG  GLN A  88 " =    0.862
peak=   -3.628 closest distance to " CD1 LEU A 228 " =    2.434
peak=   -3.609 closest distance to " CB  ALA A 291 " =    2.239
peak=   -3.607 closest distance to " O   HOH Z 426 " =    1.670
peak=   -3.607 closest distance to " CB  TRP A  85 " =    2.440
peak=   -3.605 closest distance to " CA  GLY A 203 " =    2.355
peak=   -3.600 closest distance to " O   HOH Z 313 " =    1.938
peak=   -3.596 closest distance to " CG1 VAL A 112 " =    2.996
peak=   -3.590 closest distance to " OG BSER A 134 " =    1.669
peak=   -3.590 closest distance to " O   HOH Z  65 " =    1.174
peak=   -3.587 closest distance to " CA  GLY A  98 " =    1.938
peak=   -3.581 closest distance to " O   HOH Z 353 " =    2.106
peak=   -3.572 closest distance to " OG  SER A  87 " =    1.399
peak=   -3.567 closest distance to " O   HOH Z 372 " =    2.476
peak=   -3.564 closest distance to " CE  MET A 105 " =    2.185
peak=   -3.561 closest distance to " C   ALA A 158 " =    1.454
peak=   -3.560 closest distance to " CB  PRO A  54 " =    2.505
peak=   -3.556 closest distance to " O   HOH Z 198 " =    2.172
peak=   -3.544 closest distance to " O   GLY A 203 " =    2.436
peak=   -3.538 closest distance to " O   HOH Z 198 " =    1.500
peak=   -3.529 closest distance to " CG1 VAL A 197 " =    2.239
peak=   -3.515 closest distance to " O   HOH Z 111 " =    1.909
peak=   -3.509 closest distance to " O   HOH Z  10 " =    1.544
peak=   -3.508 closest distance to " C   HIS A 108 " =    1.160
peak=   -3.507 closest distance to " CG  ASP A 231 " =    0.787
peak=   -3.506 closest distance to " CD1 LEU A 101 " =    2.359
peak=   -3.503 closest distance to " CG1 VAL A 250 " =    2.622
peak=   -3.503 closest distance to " CG  PRO A 163 " =    2.406
peak=   -3.502 closest distance to " C   ASN A 187 " =    1.862
peak=   -3.489 closest distance to " OD1 ASP A 191 " =    1.751
peak=   -3.480 closest distance to " CE3 TRP A 150 " =    2.038
peak=   -3.477 closest distance to " CA  GLY A 241 " =    2.286
peak=   -3.472 closest distance to " O   ILE A 109 " =    2.643
peak=   -3.470 closest distance to " CD2 TYR A 293 " =    2.007
peak=   -3.467 closest distance to " CE BMET A  47 " =    1.765
peak=   -3.463 closest distance to " ND2 ASN A 249 " =    2.076
peak=   -3.463 closest distance to " O   HOH Z 176 " =    0.819
peak=   -3.462 closest distance to " CA  GLY A 241 " =    3.083
peak=   -3.456 closest distance to " CB  ASN A  39 " =    2.213
peak=   -3.453 closest distance to " O   HOH Z 211 " =    1.492
peak=   -3.445 closest distance to " O   HOH Z 168 " =    1.881
peak=   -3.438 closest distance to " O   HOH Z 281 " =    2.672
peak=   -3.435 closest distance to " O   ALA A 180 " =    1.349
peak=   -3.434 closest distance to " CD2 LEU A 300 " =    2.856
peak=   -3.426 closest distance to " O   GLY A  80 " =    2.489
peak=   -3.420 closest distance to " O   HOH Z 377 " =    0.936
peak=   -3.419 closest distance to " O   HOH Z 207 " =    2.177
peak=   -3.393 closest distance to " O   HOH Z 118 " =    3.185
peak=   -3.391 closest distance to " CD  GLN A  58 " =    0.940
peak=   -3.387 closest distance to " O   HOH Z 114 " =    0.757
peak=   -3.386 closest distance to " C   GLY A  17 " =    1.305
peak=   -3.377 closest distance to " OG  SER A  97 " =    2.153
peak=   -3.377 closest distance to " CG  PHE A 283 " =    2.824
peak=   -3.377 closest distance to " CB  ALA A 291 " =    2.258
peak=   -3.374 closest distance to " O   HOH Z 345 " =    2.289
peak=   -3.366 closest distance to " OXT GLY A 302 " =    2.989
peak=   -3.365 closest distance to " O   HOH Z 394 " =    1.480
peak=   -3.363 closest distance to " C   LEU A 143 " =    1.472
peak=   -3.362 closest distance to " C   GLY A  13 " =    1.015
peak=   -3.362 closest distance to " O   SER A  62 " =    2.318
peak=   -3.361 closest distance to " N   THR A 157 " =    1.534
peak=   -3.361 closest distance to " O   HOH Z 231 " =    1.161
peak=   -3.359 closest distance to " O   HOH Z 292 " =    1.703
peak=   -3.357 closest distance to " O   PRO A 198 " =    1.382
peak=   -3.356 closest distance to " CB  PHE A 192 " =    1.919
peak=   -3.341 closest distance to " O   HOH Z  22 " =    2.390
peak=   -3.340 closest distance to " O   VAL A  67 " =    2.768
peak=   -3.340 closest distance to " O   PHE A 218 " =    1.448
peak=   -3.338 closest distance to " CA  SER A 135 " =    1.328
peak=   -3.337 closest distance to " O   HOH Z  51 " =    1.818
peak=   -3.324 closest distance to " SG  CYS A 168 " =    1.063
peak=   -3.324 closest distance to " O   PRO A 163 " =    2.029
peak=   -3.323 closest distance to " O   ALA A  10 " =    1.684
peak=   -3.318 closest distance to " O   HOH Z 243 " =    2.037
peak=   -3.317 closest distance to " O   HOH Z 102 " =    1.651
peak=   -3.315 closest distance to " CG  TRP A 266 " =    1.682
peak=   -3.311 closest distance to " NE  ARG A  36 " =    1.988
peak=   -3.307 closest distance to " N   SER A 212 " =    1.958
peak=   -3.306 closest distance to " O   HOH Z   6 " =    1.642
peak=   -3.302 closest distance to " OH  TYR A 172 " =    1.767
peak=   -3.299 closest distance to " CE2 PHE A 218 " =    2.432
peak=   -3.298 closest distance to " CE3 TRP A 123 " =    1.328
peak=   -3.293 closest distance to " O   HOH Z 275 " =    1.557
peak=   -3.292 closest distance to " ND2BASN A 224 " =    1.692
peak=   -3.287 closest distance to " CD  LYS A 289 " =    2.397
peak=   -3.285 closest distance to " O   HOH Z 252 " =    4.248
peak=   -3.281 closest distance to " O   ASN A 301 " =    1.440
peak=   -3.280 closest distance to " O   HOH Z 359 " =    3.274
peak=   -3.278 closest distance to " CD1 LEU A 297 " =    2.610
peak=   -3.272 closest distance to " CD  ARG A 139 " =    1.623
peak=   -3.269 closest distance to " O   HOH Z  51 " =    1.199
peak=   -3.269 closest distance to " O   HOH Z  90 " =    3.066
peak=   -3.264 closest distance to " C   MET A 188 " =    1.391
peak=   -3.262 closest distance to " CB  ALA A 248 " =    2.453
peak=   -3.258 closest distance to " OE1 GLN A  88 " =    1.145
peak=   -3.252 closest distance to " O   HOH Z 184 " =    2.208
peak=   -3.251 closest distance to " O   HOH Z 298 " =    2.439
peak=   -3.251 closest distance to " CB  PRO A 163 " =    2.584
peak=   -3.249 closest distance to " O   HOH Z 417 " =    2.740
peak=   -3.248 closest distance to " CD2 PHE A  61 " =    1.988
peak=   -3.243 closest distance to " CD2 PHE A 225 " =    1.095
peak=   -3.243 closest distance to " OD2 ASP A 171 " =    1.861
peak=   -3.235 closest distance to " CE2 PHE A  61 " =    2.681
peak=   -3.235 closest distance to " CG2 ILE A  20 " =    2.755
peak=   -3.232 closest distance to " N   THR A  52 " =    1.744
peak=   -3.230 closest distance to " O   HOH Z 385 " =    2.075
peak=   -3.227 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.220 closest distance to " O   HOH Z  11 " =    1.914
peak=   -3.219 closest distance to " O   HOH Z 191 " =    5.684
peak=   -3.218 closest distance to " CD1 LEU A   5 " =    2.663
peak=   -3.217 closest distance to " NH1AARG A 275 " =    1.869
peak=   -3.216 closest distance to " O   HOH Z 189 " =    2.062
peak=   -3.210 closest distance to " NH2 ARG A  79 " =    1.880
peak=   -3.208 closest distance to " O   HOH Z 409 " =    4.478
peak=   -3.202 closest distance to " O   HOH Z 282 " =    4.894
peak=   -3.200 closest distance to " O   TRP A  70 " =    1.409
peak=   -3.194 closest distance to " SG ACYS A 201 " =    1.907
peak=   -3.194 closest distance to " O   HOH Z 390 " =    2.282
peak=   -3.186 closest distance to " O   HOH Z 350 " =    1.471
peak=   -3.186 closest distance to " O   ALA A 161 " =    1.529
peak=   -3.186 closest distance to " CB  ASP A 286 " =    2.275
peak=   -3.182 closest distance to " OH  TYR A 169 " =    1.084
peak=   -3.178 closest distance to " O   VAL A 125 " =    2.294
peak=   -3.175 closest distance to " CE  MET A  93 " =    1.210
peak=   -3.163 closest distance to " O   HOH Z 337 " =    1.661
peak=   -3.162 closest distance to " CZ  PHE A  59 " =    1.649
peak=   -3.161 closest distance to " NE2 GLN A  88 " =    2.002
peak=   -3.156 closest distance to " OD1 ASP A 171 " =    1.619
peak=   -3.154 closest distance to " O   HOH Z  90 " =    1.580
peak=   -3.153 closest distance to " N   ALA A 226 " =    2.229
peak=   -3.152 closest distance to " O   ALA A  34 " =    2.653
peak=   -3.150 closest distance to " N   SER A 276 " =    1.282
peak=   -3.149 closest distance to " CA  ASP A 298 " =    1.046
peak=   -3.149 closest distance to " O   VAL A 197 " =    1.552
peak=   -3.142 closest distance to " OD1 ASP A 191 " =    1.570
peak=   -3.141 closest distance to " NZ  LYS A 166 " =    1.205
peak=   -3.139 closest distance to " ND2 ASN A  60 " =    1.678
peak=   -3.138 closest distance to " CG1 VAL A 125 " =    1.882
peak=   -3.132 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.127 closest distance to " CD2 PHE A 192 " =    2.295
peak=   -3.118 closest distance to " CG2 THR A 178 " =    2.255
peak=   -3.118 closest distance to " CG2 VAL A 189 " =    1.931
peak=   -3.117 closest distance to " O   HOH Z 174 " =    2.658
peak=   -3.116 closest distance to " CG2 THR A  18 " =    2.864
peak=   -3.115 closest distance to " CZ  TYR A 169 " =    1.632
peak=   -3.114 closest distance to " CH2 TRP A 177 " =    2.245
peak=   -3.109 closest distance to " CD1 LEU A 228 " =    2.302
peak=   -3.105 closest distance to " CE3 TRP A 274 " =    2.482
peak=   -3.099 closest distance to " CE1 TYR A 169 " =    2.534
peak=   -3.098 closest distance to " CD1 ILE A 239 " =    2.039
peak=   -3.091 closest distance to " CB  ASP A 132 " =    2.339
peak=   -3.071 closest distance to " O   HOH Z 114 " =    1.669
peak=   -3.069 closest distance to " O   HOH Z  25 " =    2.329
peak=   -3.068 closest distance to " SG  CYS A 254 " =    2.906
peak=   -3.045 closest distance to " O   HOH Z 323 " =    1.518
peak=   -3.038 closest distance to " OD1 ASN A 301 " =    1.893
peak=   -3.025 closest distance to " O   HOH Z 166 " =    1.889
peak=   -3.025 closest distance to " O   HOH Z  63 " =    1.492
peak=   -3.022 closest distance to " CG1 VAL A 197 " =    2.164
peak=   -3.022 closest distance to " CD  GLN A  58 " =    0.967
peak=   -3.016 closest distance to " CA  GLY A 241 " =    2.843

================= 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    :  0.3889 0.3822   6.180077e+00   6.171380e+00
   1_bss:  0.3775 0.3703   6.165691e+00   6.154822e+00
   1_xyz:  0.2222 0.2529   5.713486e+00   5.807894e+00
   1_adp:  0.2045 0.2595   5.668662e+00   5.837200e+00
   1_occ:  0.2041 0.2587   5.666725e+00   5.835501e+00
   2_bss:  0.2018 0.2562   5.660449e+00   5.827051e+00
   2_xyz:  0.1573 0.2063   5.437776e+00   5.638972e+00
   2_adp:  0.1497 0.1970   5.394234e+00   5.599443e+00
   2_occ:  0.1496 0.1971   5.393994e+00   5.599667e+00
   3_bss:  0.1496 0.1970   5.393157e+00   5.598308e+00
   3_xyz:  0.1263 0.1735   5.248689e+00   5.478012e+00
   3_adp:  0.1197 0.1659   5.199900e+00   5.437679e+00
   3_occ:  0.1196 0.1658   5.199585e+00   5.437366e+00
   4_bss:  0.1197 0.1650   5.198003e+00   5.433784e+00
   4_xyz:  0.1141 0.1628   5.169728e+00   5.416419e+00
   4_adp:  0.1130 0.1619   5.164013e+00   5.412188e+00
   4_occ:  0.1130 0.1618   5.163718e+00   5.411989e+00
   5_bss:  0.1130 0.1618   5.163772e+00   5.411942e+00
   5_xyz:  0.1120 0.1618   5.159807e+00   5.412696e+00
   5_adp:  0.1119 0.1616   5.158635e+00   5.411636e+00
   5_occ:  0.1119 0.1615   5.158383e+00   5.411442e+00
   5_bss:  0.1118 0.1615   5.158466e+00   5.411465e+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:  0.329  57.425   2.979  -0.907  -2.068  -0.000  -0.000  -0.000
   1_xyz:  0.329  57.425   2.979  -0.907  -2.068  -0.000  -0.000  -0.000
   1_adp:  0.329  57.425   2.979  -0.907  -2.068  -0.000  -0.000  -0.000
   1_occ:  0.329  57.425   2.979  -0.907  -2.068  -0.000  -0.000  -0.000
   2_bss:  0.339  63.418  -0.483  -2.425  -1.848  -0.000  -0.000  -0.000
   2_xyz:  0.339  63.418  -0.483  -2.425  -1.848  -0.000  -0.000  -0.000
   2_adp:  0.339  63.418  -0.483  -2.425  -1.848  -0.000  -0.000  -0.000
   2_occ:  0.339  63.418  -0.483  -2.425  -1.848  -0.000  -0.000  -0.000
   3_bss:  0.339  63.418  -1.448  -2.585  -1.471  -0.000  -0.000  -0.000
   3_xyz:  0.339  63.418  -1.448  -2.585  -1.471  -0.000  -0.000  -0.000
   3_adp:  0.339  63.418  -1.448  -2.585  -1.471  -0.000  -0.000  -0.000
   3_occ:  0.339  63.418  -1.448  -2.585  -1.471  -0.000  -0.000  -0.000
   4_bss:  0.327  60.854  -1.940  -2.783  -1.565  -0.000  -0.000  -0.000
   4_xyz:  0.327  60.854  -1.940  -2.783  -1.565  -0.000  -0.000  -0.000
   4_adp:  0.327  60.854  -1.940  -2.783  -1.565  -0.000  -0.000  -0.000
   4_occ:  0.327  60.854  -1.940  -2.783  -1.565  -0.000  -0.000  -0.000
   5_bss:  0.327  60.854  -1.916  -2.669  -1.403  -0.000  -0.000  -0.000
   5_xyz:  0.327  60.854  -1.916  -2.669  -1.403  -0.000  -0.000  -0.000
   5_adp:  0.327  60.854  -1.916  -2.669  -1.403  -0.000  -0.000  -0.000
   5_occ:  0.327  60.854  -1.916  -2.669  -1.403  -0.000  -0.000  -0.000
   5_bss:  0.327  60.852  -1.839  -2.552  -1.256  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.650 0.6131  0.7875    45004.641
   1_bss:  41.613 0.6243  0.8035    42278.512
   1_xyz:  24.881 0.8138  0.9873    16586.154
   1_adp:  25.994 0.8013  0.9767    17587.171
   1_occ:  25.946 0.8016  0.9764    17487.054
   2_bss:  25.572 0.8057  0.9291    17154.460
   2_xyz:  19.847 0.8630  0.9696    10853.225
   2_adp:  18.601 0.8754  0.9754     9974.014
   2_occ:  18.608 0.8754  0.9752     9978.941
   3_bss:  18.581 0.8757  0.9665     9951.383
   3_xyz:  15.827 0.8998  0.9803     7650.567
   3_adp:  14.927 0.9075  0.9801     7010.610
   3_occ:  14.917 0.9076  0.9800     7005.112
   4_bss:  14.870 0.9079  0.9711     6921.410
   4_xyz:  14.510 0.9109  0.9714     6664.171
   4_adp:  14.391 0.9121  0.9672     6622.624
   4_occ:  14.386 0.9121  0.9672     6615.206
   5_bss:  14.387 0.9121  0.9706     6614.581
   5_xyz:  14.389 0.9121  0.9706     6633.529
   5_adp:  14.352 0.9124  0.9657     6620.945
   5_occ:  14.347 0.9125  0.9657     6614.434
   5_bss:  14.350 0.9124  0.9695     6614.924
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6313e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6313e-01
   1_xyz:   1.319  0.012  0.089 15.434  0.006  4.117   1.0421e-01
   1_adp:   1.319  0.012  0.089 15.434  0.006  4.117   1.0421e-01
   1_occ:   1.319  0.012  0.089 15.434  0.006  4.117   1.0421e-01
   2_bss:   1.319  0.012  0.089 15.434  0.006  4.117   1.0421e-01
   2_xyz:   0.948  0.006  0.068 14.021  0.003  4.129   5.1304e-02
   2_adp:   0.948  0.006  0.068 14.021  0.003  4.129   5.1304e-02
   2_occ:   0.948  0.006  0.068 14.021  0.003  4.129   5.1304e-02
   3_bss:   0.948  0.006  0.068 14.021  0.003  4.129   5.1304e-02
   3_xyz:   1.028  0.008  0.078 14.372  0.004  4.126   6.2136e-02
   3_adp:   1.028  0.008  0.078 14.372  0.004  4.126   6.2136e-02
   3_occ:   1.028  0.008  0.078 14.372  0.004  4.126   6.2136e-02
   4_bss:   1.028  0.008  0.078 14.372  0.004  4.126   6.2136e-02
   4_xyz:   1.031  0.008  0.076 14.428  0.004  4.113   6.3362e-02
   4_adp:   1.031  0.008  0.076 14.428  0.004  4.113   6.3362e-02
   4_occ:   1.031  0.008  0.076 14.428  0.004  4.113   6.3362e-02
   5_bss:   1.031  0.008  0.076 14.428  0.004  4.113   6.3362e-02
   5_xyz:   1.022  0.008  0.076 14.370  0.004  4.114   6.1773e-02
   5_adp:   1.022  0.008  0.076 14.370  0.004  4.114   6.1773e-02
   5_occ:   1.022  0.008  0.076 14.370  0.004  4.114   6.1773e-02
   5_bss:   1.022  0.008  0.076 14.370  0.004  4.114   6.1773e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4189e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4189e-01
   1_xyz:  10.611  0.118  0.270 88.300  0.052  2.215   1.8319e-01
   1_adp:  10.611  0.118  0.270 88.300  0.052  2.215   1.8319e-01
   1_occ:  10.611  0.118  0.270 88.300  0.052  2.215   1.8319e-01
   2_bss:  10.611  0.118  0.270 88.300  0.052  2.215   1.8319e-01
   2_xyz:   8.299  0.053  0.243 83.537  0.020  2.369   3.5738e-02
   2_adp:   8.299  0.053  0.243 83.537  0.020  2.369   3.5738e-02
   2_occ:   8.299  0.053  0.243 83.537  0.020  2.369   3.5738e-02
   3_bss:   8.299  0.053  0.243 83.537  0.020  2.369   3.5738e-02
   3_xyz:   9.157  0.050  0.212 84.041  0.033  2.336   7.7767e-02
   3_adp:   9.157  0.050  0.212 84.041  0.033  2.336   7.7767e-02
   3_occ:   9.157  0.050  0.212 84.041  0.033  2.336   7.7767e-02
   4_bss:   9.157  0.050  0.212 84.041  0.033  2.336   7.7767e-02
   4_xyz:   8.416  0.045  0.236 83.666  0.033  2.317   4.5426e-02
   4_adp:   8.416  0.045  0.236 83.666  0.033  2.317   4.5426e-02
   4_occ:   8.416  0.045  0.236 83.666  0.033  2.317   4.5426e-02
   5_bss:   8.416  0.045  0.236 83.666  0.033  2.317   4.5426e-02
   5_xyz:   8.345  0.045  0.227 84.003  0.030  2.360   4.2825e-02
   5_adp:   8.345  0.045  0.227 84.003  0.030  2.360   4.2825e-02
   5_occ:   8.345  0.045  0.227 84.003  0.030  2.360   4.2825e-02
   5_bss:   8.345  0.045  0.227 84.003  0.030  2.360   4.2825e-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:  65.67   0.00  17.12  56.21   0.00  13.12  65.67   2.70  38.87
   1_occ:  65.67   0.00  17.12  56.21   0.00  13.12  65.67   2.70  38.87
   2_bss:  65.67   0.00  17.12  56.21   0.00  13.12  65.67   2.70  38.87
   2_xyz:  65.67   0.00  17.12  56.21   0.00  13.12  65.67   2.70  38.87
   2_adp:  66.92   0.00  17.05  63.82   0.00  13.05  66.92   4.96  38.80
   2_occ:  66.92   0.00  17.05  63.82   0.00  13.05  66.92   4.96  38.80
   3_bss:  66.92   0.00  17.05  63.82   0.00  13.05  66.92   4.96  38.80
   3_xyz:  66.92   0.00  17.05  63.82   0.00  13.05  66.92   4.96  38.80
   3_adp:  86.98   0.00  17.44  78.27   0.00  13.09  86.98   5.46  41.16
   3_occ:  86.98   0.00  17.44  78.27   0.00  13.09  86.98   5.46  41.16
   4_bss:  86.98   0.00  17.44  78.27   0.00  13.09  86.98   5.46  41.16
   4_xyz:  86.98   0.00  17.44  78.27   0.00  13.09  86.98   5.46  41.16
   4_adp:  91.89   0.16  17.29  84.60   0.16  13.01  91.89   5.98  40.61
   4_occ:  91.89   0.16  17.29  84.60   0.16  13.01  91.89   5.98  40.61
   5_bss:  91.89   0.16  17.29  84.60   0.16  13.01  91.89   5.98  40.61
   5_xyz:  91.89   0.16  17.29  84.60   0.16  13.01  91.89   5.98  40.61
   5_adp:  92.39   0.14  17.10  85.93   0.14  12.88  92.39   6.17  40.10
   5_occ:  92.39   0.14  17.10  85.93   0.14  12.88  92.39   6.17  40.10
   5_bss:  92.39   0.14  17.10  85.93   0.14  12.88  92.39   6.17  40.10
------------------------------------------------------------------------
 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:    1.338    0.032    0.399
   1_adp:    1.338    0.032    0.399
   1_occ:    1.338    0.032    0.399
   2_bss:    1.338    0.032    0.399
   2_xyz:    1.097    0.028    0.457
   2_adp:    1.097    0.028    0.457
   2_occ:    1.097    0.028    0.457
   3_bss:    1.097    0.028    0.457
   3_xyz:    1.041    0.032    0.528
   3_adp:    1.041    0.032    0.528
   3_occ:    1.041    0.032    0.528
   4_bss:    1.041    0.032    0.528
   4_xyz:    1.132    0.035    0.543
   4_adp:    1.132    0.035    0.543
   4_occ:    1.132    0.035    0.543
   5_bss:    1.132    0.035    0.543
   5_xyz:    1.181    0.055    0.553
   5_adp:    1.181    0.055    0.553
   5_occ:    1.181    0.055    0.553
   5_bss:    1.181    0.055    0.553
------------------------------------------------------------------------

CPU time actual refinement: 339.29


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1248/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_1248/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1248/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1248/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1248/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.13 
  Macro-tasks:
    bulk solvent and scale       = 36.83  
    individual site refinement   = 143.91 
    weights calculation          = 29.50  
    collect and process          = 6.48   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 216.82 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 111.52 
    alpha_beta                      = 8.07   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 120.22 
    fmodel                         = 6.41   
    r_factors                      = 0.23   
    phase_errors                   = 11.01  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 260.63 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.782 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    649 calls, 111.15 s
gradients_fft:          594 calls, 106.45 s

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

# Date 2008-01-16 Time 06:47:43 PST -0800 (1200494863.73 s)
Start R-work = 0.3889, R-free = 0.3822 (no bulk solvent and anisotropic scale)
Final R-work = 0.1355, R-free = 0.1807 (no bulk solvent and anisotropic scale)

Start R-work = 0.3775, R-free = 0.3703
Final R-work = 0.1118, R-free = 0.1615