# Date 2008-01-16 Time 05:06:30 PST -0800 (1200488790.25 s)
#phil __OFF__

Command line arguments: "../591.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25520
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 591

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.8686, 87.6859, 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: 3.25, 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: (69.8988, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99074
Completeness in resolution range: 0.944913
Completeness with d_max=infinity: 0.942005

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9985
                             d_min =   1.9907

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99074
Completeness in resolution range: 0.944913
Completeness with d_max=infinity: 0.942005

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9990 -  4.2592 [2188/2216]  1965   223  10.2%
  bin  2:  4.2592 -  3.3936 [2072/2095]  1869   203   9.8%
  bin  3:  3.3936 -  2.9684 [2071/2093]  1863   208  10.0%
  bin  4:  2.9684 -  2.6987 [2045/2064]  1841   204  10.0%
  bin  5:  2.6987 -  2.5062 [2024/2053]  1817   207  10.2%
  bin  6:  2.5062 -  2.3591 [2016/2058]  1818   198   9.8%
  bin  7:  2.3591 -  2.2413 [2007/2043]  1810   197   9.8%
  bin  8:  2.2413 -  2.1440 [2006/2043]  1802   204  10.2%
  bin  9:  2.1440 -  2.0617 [2015/2046]  1819   196   9.7%
  bin 10:  2.0617 -  1.9907 [1145/2020]  1026   119  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_591/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: 24
        2.42 -     3.04: 2156
        3.04 -     3.66: 4615
        3.66 -     4.28: 8854
        4.28 -     4.90: 12272
  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  42 " - " O   HOH Z 183 "  1.812 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.048 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.139 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.139 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27916 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_591/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_591/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.8686 87.68585 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: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4305   r_free= 0.4200   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.239867                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7503 0.99   1411  157 0.3368 0.3483      6.4817      6.4752|
|  2:  4.7503 -  3.7905 0.99   1369  152 0.3659 0.3802      6.7551      6.7757|
|  3:  3.7905 -  3.3173 0.99   1335  150 0.4017 0.3726      6.6218       6.552|
|  4:  3.3173 -  3.0167 0.99   1319  139 0.4197 0.4037      6.4614       6.403|
|  5:  3.0167 -  2.8019 0.99   1307  148 0.4523 0.3915      6.3236      6.3207|
|  6:  2.8019 -  2.6377 0.98   1310  149 0.4618 0.4673      6.2401      6.1201|
|  7:  2.6377 -  2.5062 0.99   1304  150 0.4492 0.4219      6.1919       6.126|
|  8:  2.5062 -  2.3976 0.99   1321  139 0.4753 0.4699      6.1477      6.1281|
|  9:  2.3976 -  2.3056 0.98   1285  145 0.4742 0.4281      6.0788      6.1075|
| 10:  2.3056 -  2.2263 0.98   1298  142 0.4916 0.4432      6.0847      6.0269|
| 11:  2.2263 -  2.1569 0.98   1287  145 0.4844 0.4783       6.002      6.0141|
| 12:  2.1569 -  2.0954 0.99   1281  143 0.4838 0.5282      5.9416      6.0108|
| 13:  2.0954 -  2.0404 0.97   1279  134 0.5026 0.4940       5.874      5.8147|
| 14:  2.0404 -  1.9907 0.41    524   66 0.4605 0.5283        5.84      5.7648|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7503  1411   157  0.73  31.66   0.84     0.75      61092.34|
|  2:  4.7503 -  3.7905  1369   152  0.75  30.89   0.92     0.83      84099.93|
|  3:  3.7905 -  3.3173  1335   150  0.68  36.98   0.91     0.83      85706.34|
|  4:  3.3173 -  3.0167  1319   139  0.62  42.21   0.92     0.78      73869.09|
|  5:  3.0167 -  2.8019  1307   148  0.56  46.97   0.90     0.72      58315.00|
|  6:  2.8019 -  2.6377  1310   149  0.53  50.07   0.90     0.69      52170.61|
|  7:  2.6377 -  2.5062  1304   150  0.52  50.17   0.95     0.67      47822.85|
|  8:  2.5062 -  2.3976  1321   139  0.51  51.41   0.92     0.68      44768.74|
|  9:  2.3976 -  2.3056  1285   145  0.51  51.73   0.92     0.71      41367.69|
| 10:  2.3056 -  2.2263  1298   142  0.50  51.89   0.93     0.71      38110.11|
| 11:  2.2263 -  2.1569  1287   145  0.46  55.67   0.93     0.67      38818.10|
| 12:  2.1569 -  2.0954  1281   143  0.39  60.94   0.94     0.58      40085.03|
| 13:  2.0954 -  2.0404  1279   134  0.31  66.71   0.91     0.47      37584.42|
| 14:  2.0404 -  1.9907   524    66  0.30  67.98   1.00     0.38      29550.07|
|alpha:            min =        0.38 max =            0.83 mean =         0.69|
|beta:             min =    29550.07 max =        85706.34 mean =     53700.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.98 mean =        48.60|
|phase err.(test): min =        0.00 max =           89.88 mean =        48.99|
|-----------------------------------------------------------------------------|

============================== 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 = 10.581073             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.103   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.434972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.164   (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:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      185 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1971 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1831 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2784 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4574 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4280 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5581 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6691 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.196 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    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: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4305   r_free= 0.4200   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.239867                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4193   r_free= 0.4085   ksol= 0.29   Bsol= 33.62   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.50,4.33,1.61,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.228057                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.279242              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.690   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.794261              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.910   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4193      final r-factor (work) = 0.2748          |
| start r-factor (free) = 0.4085      final r-factor (free) = 0.2991          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0559 = 9.28 * 0.50 * 6.2269 + 1.00 * 0.1654                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1289 = 9.28 * 0.50 * 6.0273 + 1.00 * 0.1647                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2748      final r-factor (work) = 0.2503          |
| start r-factor (free) = 0.2991      final r-factor (free) = 0.3104          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7933 = 0.79 * 1.00 * 6.0273 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6496 = 0.79 * 1.00 * 5.8361 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.52   17.66    None  None   None       |
|    all(noH): 2823   0      0.00    89.52   17.66    None  None   None       |
|    Sol.    : 438    0      3.55    89.52   39.64    None  None   None       |
|    Mac.    : 2385   0      0.00    73.25   13.63    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 -   8.952:  878   |   5:    44.758 -  53.709:   96        |
|      1:     8.952 -  17.903: 1024   |   6:    53.709 -  62.661:   70        |
|      2:    17.903 -  26.855:  379   |   7:    62.661 -  71.612:   31        |
|      3:    26.855 -  35.806:  200   |   8:    71.612 -  80.564:   13        |
|      4:    35.806 -  44.758:  128   |   9:    80.564 -  89.515:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2503 r_free = 0.3104             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2502 r_free = 0.3114             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2502   r_free= 0.3114   ksol= 0.29   Bsol= 33.62   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.50,4.33,1.61,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.847169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2472   r_free= 0.3074   ksol= 0.33   Bsol= 71.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,1.23,0.33,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.840865                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.153353              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.208   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.399452              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.080  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2472      final r-factor (work) = 0.1956          |
| start r-factor (free) = 0.3074      final r-factor (free) = 0.2379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3653 = 3.15 * 0.50 * 5.8355 + 1.00 * 0.1647                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1252 = 3.15 * 0.50 * 5.7496 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1956      final r-factor (work) = 0.1845          |
| start r-factor (free) = 0.2379      final r-factor (free) = 0.2265          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3109 = 0.40 * 1.00 * 5.7496 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2453 = 0.40 * 1.00 * 5.5931 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.27   17.45    None  None   None       |
|    all(noH): 2823   0      0.00    90.27   17.45    None  None   None       |
|    Sol.    : 438    0      5.17    90.27   40.77    None  None   None       |
|    Mac.    : 2385   0      0.00    80.51   13.17    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 -   9.027:  917   |   5:    45.134 -  54.161:  102        |
|      1:     9.027 -  18.054: 1077   |   6:    54.161 -  63.188:   69        |
|      2:    18.054 -  27.080:  324   |   7:    63.188 -  72.214:   39        |
|      3:    27.080 -  36.107:  161   |   8:    72.214 -  81.241:   11        |
|      4:    36.107 -  45.134:  119   |   9:    81.241 -  90.268:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1845 r_free = 0.2265             target_work(ml) = 5.575         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1843 r_free = 0.2265             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1843   r_free= 0.2265   ksol= 0.33   Bsol= 71.87   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,1.23,0.33,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.574019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1841   r_free= 0.2254   ksol= 0.33   Bsol= 71.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.04,-0.07,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.572430                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.652278              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.364   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.598965              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.577  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1841      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.2254      final r-factor (free) = 0.1848          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2739 = 3.65 * 0.50 * 5.5932 + 1.00 * 0.0599                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0313 = 3.65 * 0.50 * 5.4566 + 1.00 * 0.0668                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1426      final r-factor (work) = 0.1340          |
| start r-factor (free) = 0.1848      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2795 = 0.60 * 1.00 * 5.4566 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1939 = 0.60 * 1.00 * 5.3130 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.49   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    92.49   17.30    None  None   None       |
|    Sol.    : 438    0      5.24    92.49   42.60    None  None   None       |
|    Mac.    : 2385   0      0.00    87.76   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.249:  998   |   5:    46.246 -  55.495:   93        |
|      1:     9.249 -  18.498: 1103   |   6:    55.495 -  64.745:   75        |
|      2:    18.498 -  27.748:  250   |   7:    64.745 -  73.994:   47        |
|      3:    27.748 -  36.997:  128   |   8:    73.994 -  83.243:   16        |
|      4:    36.997 -  46.246:  107   |   9:    83.243 -  92.492:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1340 r_free = 0.1792             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1340 r_free = 0.1792             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1792   ksol= 0.33   Bsol= 71.87   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.04,-0.07,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.294231                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1794   ksol= 0.34   Bsol= 75.27   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-0.68,-0.11,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.295820                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.610525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.307  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514463              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.895  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1276          |
| start r-factor (free) = 0.1794      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3464 = 1.61 * 0.50 * 5.3146 + 1.00 * 0.0668                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2987 = 1.61 * 0.50 * 5.2734 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1276      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1724      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7245 = 0.51 * 1.00 * 5.2734 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7114 = 0.51 * 1.00 * 5.2479 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.38   16.95    None  None   None       |
|    all(noH): 2823   0      0.00    92.38   16.95    None  None   None       |
|    Sol.    : 438    0      0.00    92.38   42.26    None  None   None       |
|    Mac.    : 2385   0      0.00    90.32   12.30    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 -   9.239: 1052   |   5:    46.192 -  55.431:   91        |
|      1:     9.239 -  18.477: 1087   |   6:    55.431 -  64.669:   82        |
|      2:    18.477 -  27.715:  225   |   7:    64.669 -  73.908:   44        |
|      3:    27.715 -  36.954:  122   |   8:    73.908 -  83.146:   13        |
|      4:    36.954 -  46.192:  100   |   9:    83.146 -  92.385:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1259 r_free = 0.1710             target_work(ml) = 5.243         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1710             target_work(ml) = 5.243         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1710   ksol= 0.34   Bsol= 75.27   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-0.68,-0.11,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.242592                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1709   ksol= 0.33   Bsol= 72.20   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-0.73,0.05,-0.00,0.00,0.00); trace/3= -0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.242558                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.080216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.357  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.451444              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.690  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1347 = 3.08 * 0.50 * 5.2480 + 1.00 * 0.0522                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0933 = 3.08 * 0.50 * 5.2071 + 1.00 * 0.0738                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5692 = 1.45 * 1.00 * 5.2071 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5285 = 1.45 * 1.00 * 5.1786 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.98   16.74    None  None   None       |
|    all(noH): 2823   0      0.00    96.98   16.74    None  None   None       |
|    Sol.    : 438    0      0.45    93.74   42.13    None  None   None       |
|    Mac.    : 2385   0      0.00    96.98   12.08    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 -   9.699: 1185   |   5:    48.492 -  58.191:   88        |
|      1:     9.699 -  19.397:  995   |   6:    58.191 -  67.889:   63        |
|      2:    19.397 -  29.096:  214   |   7:    67.889 -  77.588:   40        |
|      3:    29.096 -  38.794:  118   |   8:    77.588 -  87.286:    9        |
|      4:    38.794 -  48.492:  102   |   9:    87.286 -  96.985:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1639             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1639             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1639   ksol= 0.33   Bsol= 72.20   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-0.73,0.05,-0.00,0.00,0.00); trace/3= -0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178623                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7503 0.99   1411  157 0.0973 0.1298      5.3838      5.5579|
|  2:  4.7503 -  3.7905 0.99   1369  152 0.0823 0.1045       5.408      5.6009|
|  3:  3.7905 -  3.3173 0.99   1335  150 0.1049 0.1500      5.4637      5.8426|
|  4:  3.3173 -  3.0167 0.99   1319  139 0.1255 0.1713      5.4687      5.6383|
|  5:  3.0167 -  2.8019 0.99   1307  148 0.1405 0.1770      5.3798      5.5518|
|  6:  2.8019 -  2.6377 0.98   1310  149 0.1360 0.2169      5.2867      5.5416|
|  7:  2.6377 -  2.5062 0.99   1304  150 0.1329 0.1674      5.2172      5.3853|
|  8:  2.5062 -  2.3976 0.99   1321  139 0.1210 0.1753      5.1237      5.3367|
|  9:  2.3976 -  2.3056 0.98   1285  145 0.1232 0.1961      5.0578      5.3922|
| 10:  2.3056 -  2.2263 0.98   1298  142 0.1171 0.1763      5.0051      5.1879|
| 11:  2.2263 -  2.1569 0.98   1287  145 0.1190 0.1878      4.9541      5.2789|
| 12:  2.1569 -  2.0954 0.99   1281  143 0.1121 0.1807      4.8814      5.2105|
| 13:  2.0954 -  2.0404 0.97   1279  134 0.1149 0.1693      4.8107      5.0179|
| 14:  2.0404 -  1.9907 0.41    524   66 0.1097 0.1921      4.7429       5.001|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7503  1411   157  0.94   9.38   0.96     0.93       7399.34|
|  2:  4.7503 -  3.7905  1369   152  0.95   7.97   1.00     0.99       8811.12|
|  3:  3.7905 -  3.3173  1335   150  0.94  11.13   1.02     1.01      10175.10|
|  4:  3.3173 -  3.0167  1319   139  0.92  14.18   1.00     0.98      10673.18|
|  5:  3.0167 -  2.8019  1307   148  0.89  17.04   0.99     0.97       9287.57|
|  6:  2.8019 -  2.6377  1310   149  0.88  17.77   0.97     0.95       8161.90|
|  7:  2.6377 -  2.5062  1304   150  0.90  16.49   0.98     0.96       6899.57|
|  8:  2.5062 -  2.3976  1321   139  0.90  16.18   0.98     0.94       6013.17|
|  9:  2.3976 -  2.3056  1285   145  0.90  16.50   0.98     0.93       5208.48|
| 10:  2.3056 -  2.2263  1298   142  0.89  16.78   0.97     0.93       4921.14|
| 11:  2.2263 -  2.1569  1287   145  0.90  16.68   0.97     0.93       4516.37|
| 12:  2.1569 -  2.0954  1281   143  0.90  15.95   0.99     0.98       4066.26|
| 13:  2.0954 -  2.0404  1279   134  0.90  16.57   0.97     0.95       3547.07|
| 14:  2.0404 -  1.9907   524    66  0.89  16.69   0.94     0.89       3067.57|
|alpha:            min =        0.89 max =            1.01 mean =         0.96|
|beta:             min =     3067.57 max =        10673.18 mean =      6816.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.80|
|phase err.(test): min =        0.00 max =           89.13 mean =        14.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1637   ksol= 0.33   Bsol= 69.84   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.57,0.32,-0.00,0.00,0.00); trace/3= -0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1637   ksol= 0.33   Bsol= 69.84   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.57,0.32,-0.00,0.00,0.00); trace/3= -0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7503 0.99   1411  157 0.0972 0.1298      5.3826      5.5583|
|  2:  4.7503 -  3.7905 0.99   1369  152 0.0823 0.1045      5.4079      5.6002|
|  3:  3.7905 -  3.3173 0.99   1335  150 0.1050 0.1501      5.4637      5.8436|
|  4:  3.3173 -  3.0167 0.99   1319  139 0.1256 0.1716      5.4692      5.6388|
|  5:  3.0167 -  2.8019 0.99   1307  148 0.1406 0.1771      5.3802      5.5516|
|  6:  2.8019 -  2.6377 0.98   1310  149 0.1359 0.2168      5.2866      5.5414|
|  7:  2.6377 -  2.5062 0.99   1304  150 0.1329 0.1676      5.2174      5.3856|
|  8:  2.5062 -  2.3976 0.99   1321  139 0.1209 0.1753      5.1242       5.337|
|  9:  2.3976 -  2.3056 0.98   1285  145 0.1232 0.1961      5.0583      5.3925|
| 10:  2.3056 -  2.2263 0.98   1298  142 0.1172 0.1765      5.0054      5.1893|
| 11:  2.2263 -  2.1569 0.98   1287  145 0.1189 0.1877      4.9539      5.2782|
| 12:  2.1569 -  2.0954 0.99   1281  143 0.1121 0.1808      4.8812      5.2106|
| 13:  2.0954 -  2.0404 0.97   1279  134 0.1149 0.1691      4.8107       5.017|
| 14:  2.0404 -  1.9907 0.41    524   66 0.1096 0.1921      4.7434       5.001|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7503  1411   157  0.94   9.38   0.96     0.94       7386.07|
|  2:  4.7503 -  3.7905  1369   152  0.95   7.98   1.01     0.99       8803.28|
|  3:  3.7905 -  3.3173  1335   150  0.94  11.13   1.02     1.02      10175.58|
|  4:  3.3173 -  3.0167  1319   139  0.92  14.19   1.01     0.99      10682.88|
|  5:  3.0167 -  2.8019  1307   148  0.89  17.04   1.00     0.97       9289.21|
|  6:  2.8019 -  2.6377  1310   149  0.89  17.78   0.98     0.96       8159.93|
|  7:  2.6377 -  2.5062  1304   150  0.90  16.49   0.99     0.97       6900.55|
|  8:  2.5062 -  2.3976  1321   139  0.90  16.19   0.99     0.95       6019.18|
|  9:  2.3976 -  2.3056  1285   145  0.90  16.51   0.99     0.94       5214.11|
| 10:  2.3056 -  2.2263  1298   142  0.89  16.79   0.98     0.94       4923.31|
| 11:  2.2263 -  2.1569  1287   145  0.90  16.68   0.98     0.94       4516.23|
| 12:  2.1569 -  2.0954  1281   143  0.90  15.94   1.00     0.99       4066.27|
| 13:  2.0954 -  2.0404  1279   134  0.90  16.57   0.98     0.97       3545.19|
| 14:  2.0404 -  1.9907   524    66  0.89  16.67   0.95     0.91       3064.03|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3064.03 max =        10682.88 mean =      6816.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.80|
|phase err.(test): min =        0.00 max =           89.11 mean =        14.27|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.99   16.75    None  None   None       |
|    all(noH): 2823   0      0.00    96.99   16.75    None  None   None       |
|    Sol.    : 438    0      0.45    93.75   42.13    None  None   None       |
|    Mac.    : 2385   0      0.00    96.99   12.08    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:     0.003 -   9.702: 1185   |   5:    48.495 -  58.194:   88        |
|      1:     9.702 -  19.400:  995   |   6:    58.194 -  67.892:   63        |
|      2:    19.400 -  29.098:  214   |   7:    67.892 -  77.591:   40        |
|      3:    29.098 -  38.797:  118   |   8:    77.591 -  87.289:    9        |
|      4:    38.797 -  48.495:  102   |   9:    87.289 -  96.988:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.688 - 5.634
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 324
   mapped sites are within: 0.740 - 5.634

peak=    6.042 closest distance to " O   HOH Z 210 " =    1.251
peak=    5.655 closest distance to " O   HOH Z 113 " =    2.146
peak=    5.156 closest distance to " CB  GLN A 223 " =    1.409
peak=    4.959 closest distance to " CG  PRO A  54 " =    1.294
peak=    4.956 closest distance to " CB  ARG A 190 " =    1.740
peak=    4.948 closest distance to " CB  GLN A 183 " =    1.292
peak=    4.947 closest distance to " CB  SER A  63 " =    1.125
peak=    4.903 closest distance to " O   HOH Z 403 " =    1.759
peak=    4.544 closest distance to " CD2 TRP A 179 " =    1.322
peak=    4.530 closest distance to " O   HOH Z 369 " =    2.211
peak=    4.525 closest distance to " O   HOH Z  43 " =    2.065
peak=    4.504 closest distance to " O   PRO A 198 " =    1.530
peak=    4.495 closest distance to " CA  TYR A  30 " =    0.913
peak=    4.458 closest distance to " O   HOH Z 232 " =    2.378
peak=    4.415 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.407 closest distance to " O   HOH Z 433 " =    1.615
peak=    4.336 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.332 closest distance to " O   HOH Z  49 " =    1.090
peak=    4.294 closest distance to " CG  PRO A  90 " =    1.207
peak=    4.269 closest distance to " O   HOH Z 298 " =    1.932
peak=    4.243 closest distance to " O   HOH Z 234 " =    3.758
peak=    4.231 closest distance to " O   SER A  87 " =    2.223
peak=    4.227 closest distance to " O   HOH Z 209 " =    2.359
peak=    4.208 closest distance to " O   HOH Z 402 " =    1.549
peak=    4.173 closest distance to " CD  ARG A 269 " =    0.946
peak=    4.160 closest distance to " CA  ARG A  36 " =    1.088
peak=    4.147 closest distance to " CB  GLU A 277 " =    3.777
peak=    4.144 closest distance to " CA  ALA A  51 " =    0.954
peak=    4.142 closest distance to " CG  PRO A 280 " =    0.775
peak=    4.125 closest distance to " CZ  PHE A 218 " =    1.129
peak=    4.098 closest distance to " CA  ARG A 195 " =    1.240
peak=    4.081 closest distance to " CB  ARG A  79 " =    1.405
peak=    4.072 closest distance to " CB  GLU A 152 " =    1.091
peak=    4.069 closest distance to " CB  GLU A 128 " =    1.139
peak=    4.065 closest distance to " O   HOH Z  15 " =    2.188
peak=    4.062 closest distance to " O   HOH Z 134 " =    1.560
peak=    4.061 closest distance to " CG  PRO A 198 " =    1.166
peak=    4.058 closest distance to " O   HOH Z  40 " =    1.909
peak=    4.003 closest distance to " CG  ARG A  66 " =    2.677
peak=    3.994 closest distance to " O   HOH Z 132 " =    2.725
peak=    3.988 closest distance to " O   HOH Z 423 " =    1.856
peak=    3.974 closest distance to " O   HOH Z 412 " =    3.742
peak=    3.973 closest distance to " CB  TYR A 169 " =    0.826
peak=    3.964 closest distance to " O   HOH Z 368 " =    2.166
peak=    3.940 closest distance to " CB  SER A 141 " =    1.051
peak=    3.937 closest distance to " CB  TRP A 266 " =    1.029
peak=    3.936 closest distance to " CZ3 TRP A 266 " =    1.079
peak=    3.918 closest distance to " O   HOH Z 284 " =    2.951
peak=    3.917 closest distance to " O   HOH Z 189 " =    2.801
peak=    3.910 closest distance to " CB  PRO A  54 " =    0.913
peak=    3.901 closest distance to " O   HOH Z  63 " =    1.968
peak=    3.898 closest distance to " O   HOH Z 336 " =    1.913
peak=    3.897 closest distance to " O   HOH Z 265 " =    1.990
peak=    3.884 closest distance to " O   HOH Z 346 " =    1.526
peak=    3.863 closest distance to " CD  LYS A 166 " =    1.397
peak=    3.837 closest distance to " O   HOH Z 261 " =    2.070
peak=    3.837 closest distance to " O   HOH Z 258 " =    2.080
peak=    3.830 closest distance to " O   HOH Z 406 " =    1.600
peak=    3.829 closest distance to " O   HOH Z  97 " =    2.032
peak=    3.829 closest distance to " NE2 GLN A  77 " =    3.234
peak=    3.827 closest distance to " CB  VAL A 202 " =    1.529
peak=    3.826 closest distance to " NE2 GLN A  11 " =    1.113
peak=    3.821 closest distance to " O   HOH Z  44 " =    1.896
peak=    3.820 closest distance to " O   HOH Z 203 " =    1.794
peak=    3.820 closest distance to " O   HOH Z  80 " =    1.815
peak=    3.809 closest distance to " O   HOH Z 345 " =    1.658
peak=    3.808 closest distance to " NH2 ARG A 156 " =    1.204
peak=    3.802 closest distance to " O   HOH Z 285 " =    2.667
peak=    3.798 closest distance to " CG1 ILE A  33 " =    1.187
peak=    3.797 closest distance to " O   HOH Z 361 " =    3.490
peak=    3.794 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.787 closest distance to " NZ  LYS A  48 " =    1.224
peak=    3.777 closest distance to " O   HOH Z 425 " =    1.405
peak=    3.775 closest distance to " O   HOH Z  20 " =    1.453
peak=    3.768 closest distance to " O   HOH Z  59 " =    2.480
peak=    3.766 closest distance to " NH2BARG A 145 " =    2.145
peak=    3.763 closest distance to " NH1AARG A 145 " =    1.324
peak=    3.758 closest distance to " O   HOH Z 214 " =    1.356
peak=    3.753 closest distance to " O   ASN A  74 " =    1.703
peak=    3.751 closest distance to " CB  ASN A 148 " =    1.429
peak=    3.747 closest distance to " CG  PRO A 243 " =    1.096
peak=    3.732 closest distance to " CA  ALA A 295 " =    1.102
peak=    3.727 closest distance to " N   CYS A 260 " =    0.817
peak=    3.718 closest distance to " CA  VAL A 125 " =    1.315
peak=    3.717 closest distance to " O   HOH Z 299 " =    4.360
peak=    3.716 closest distance to " O   HOH Z  61 " =    1.566
peak=    3.711 closest distance to " CA  ASN A 176 " =    1.740
peak=    3.711 closest distance to " CD2 LEU A 297 " =    1.031
peak=    3.710 closest distance to " O   HOH Z 102 " =    1.330
peak=    3.707 closest distance to " O   HOH Z 142 " =    1.489
peak=    3.706 closest distance to " O   HOH Z 316 " =    3.056
peak=    3.706 closest distance to " N   HIS A 108 " =    1.863
peak=    3.701 closest distance to " O   HOH Z 248 " =    1.543
peak=    3.700 closest distance to " O   HOH Z 418 " =    1.334
peak=    3.698 closest distance to " NZ  LYS A 117 " =    3.020
peak=    3.691 closest distance to " OG BSER A 164 " =    2.280
peak=    3.689 closest distance to " OH  TYR A 116 " =    1.156
peak=    3.689 closest distance to " O   ALA A 165 " =    1.377
peak=    3.687 closest distance to " O   HOH Z 403 " =    1.549
peak=    3.687 closest distance to " O   HOH Z 214 " =    2.332
peak=    3.685 closest distance to " CB  ASP A 140 " =    1.035
peak=    3.673 closest distance to " CB  TRP A 179 " =    1.342
peak=    3.644 closest distance to " O   HOH Z 128 " =    2.077
peak=    3.638 closest distance to " CB  GLU A  46 " =    1.029
peak=    3.632 closest distance to " O   HOH Z 287 " =    1.841
peak=    3.631 closest distance to " O   HOH Z 389 " =    1.978
peak=    3.628 closest distance to " CA  ALA A 160 " =    0.912
peak=    3.628 closest distance to " O   TYR A 116 " =    1.431
peak=    3.627 closest distance to " O   HOH Z 383 " =    2.241
peak=    3.616 closest distance to " O   HOH Z 279 " =    2.168
peak=    3.610 closest distance to " O   HOH Z 427 " =    3.048
peak=    3.606 closest distance to " O   HOH Z 303 " =    2.328
peak=    3.594 closest distance to " O   HOH Z 365 " =    2.698
peak=    3.592 closest distance to " ND2 ASN A 187 " =    1.543
peak=    3.588 closest distance to " CA  TYR A 116 " =    1.306
peak=    3.573 closest distance to " O   HOH Z 271 " =    2.720
peak=    3.567 closest distance to " O   ASP A 124 " =    1.432
peak=    3.567 closest distance to " CB  ASN A 142 " =    1.173
peak=    3.556 closest distance to " O   HOH Z 180 " =    2.300
peak=    3.555 closest distance to " O   HOH Z 126 " =    1.583
peak=    3.554 closest distance to " CD1 LEU A  96 " =    0.802
peak=    3.553 closest distance to " O   HOH Z 193 " =    2.165
peak=    3.550 closest distance to " O   HOH Z  21 " =    1.845
peak=    3.548 closest distance to " O   HOH Z 435 " =    2.950
peak=    3.547 closest distance to " CG2AVAL A  72 " =    1.922
peak=    3.545 closest distance to " CZ  PHE A  38 " =    1.224
peak=    3.545 closest distance to " CG  MET A 185 " =    1.134
peak=    3.544 closest distance to " CA  ALA A  21 " =    1.370
peak=    3.537 closest distance to " O   HOH Z 393 " =    3.270
peak=    3.534 closest distance to " O   HOH Z 251 " =    1.555
peak=    3.530 closest distance to " O   HOH Z  19 " =    1.599
peak=    3.528 closest distance to " O   HOH Z 366 " =    2.650
peak=    3.526 closest distance to " O   HOH Z 327 " =    1.607
peak=    3.521 closest distance to " N   ASN A  39 " =    1.321
peak=    3.520 closest distance to " CB  LEU A  83 " =    0.892
peak=    3.517 closest distance to " O   HOH Z  35 " =    2.328
peak=    3.516 closest distance to " CB  LEU A 228 " =    1.136
peak=    3.514 closest distance to " CB  ALA A 291 " =    1.260
peak=    3.512 closest distance to " CB  ASN A 285 " =    0.963
peak=    3.509 closest distance to " O   HOH Z 250 " =    1.322
peak=    3.507 closest distance to " OD1 ASN A  69 " =    2.537
peak=    3.506 closest distance to " O   HOH Z 357 " =    2.183
peak=    3.504 closest distance to " O   HOH Z 132 " =    2.832
peak=    3.502 closest distance to " CB  SER A  62 " =    0.862
peak=    3.502 closest distance to " CA  GLU A  46 " =    0.942
peak=    3.493 closest distance to " CB  THR A  52 " =    0.823
peak=    3.493 closest distance to " O   HOH Z  30 " =    1.027
peak=    3.492 closest distance to " O   HOH Z 126 " =    2.143
peak=    3.492 closest distance to " O   HOH Z 417 " =    2.991
peak=    3.490 closest distance to " CB  ALA A 248 " =    1.320
peak=    3.488 closest distance to " O   HOH Z  78 " =    1.621
peak=    3.484 closest distance to " CG2BVAL A  41 " =    0.912
peak=    3.483 closest distance to " O   HOH Z 353 " =    2.846
peak=    3.480 closest distance to " O   HOH Z 246 " =    1.450
peak=    3.479 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.471 closest distance to " CG2 ILE A  20 " =    1.328
peak=    3.470 closest distance to " O   HOH Z 361 " =    2.584
peak=    3.468 closest distance to " O   HOH Z 158 " =    3.072
peak=    3.465 closest distance to " O   HOH Z   1 " =    2.645
peak=    3.463 closest distance to " O   HOH Z 176 " =    1.526
peak=    3.461 closest distance to " CE  LYS A  76 " =    0.798
peak=    3.459 closest distance to " OG  SER A  22 " =    2.765
peak=    3.459 closest distance to " O   HOH Z 185 " =    1.704
peak=    3.458 closest distance to " O   HOH Z 285 " =    1.681
peak=    3.449 closest distance to " O   HOH Z 422 " =    2.580
peak=    3.446 closest distance to " CG2 ILE A 120 " =    1.062
peak=    3.441 closest distance to " CG2 THR A 221 " =    1.241
peak=    3.438 closest distance to " O   HOH Z  68 " =    2.032
peak=    3.436 closest distance to " CG AARG A 275 " =    1.220
peak=    3.425 closest distance to " CB  SER A   3 " =    1.387
peak=    3.424 closest distance to " O   HOH Z  47 " =    2.506
peak=    3.418 closest distance to " CA  MET A 188 " =    0.994
peak=    3.418 closest distance to " O   HOH Z 371 " =    3.005
peak=    3.415 closest distance to " CA  ALA A 233 " =    1.793
peak=    3.415 closest distance to " O   HOH Z 291 " =    1.468
peak=    3.414 closest distance to " CA  GLU A 152 " =    0.868
peak=    3.410 closest distance to " CB  SER A  26 " =    1.745
peak=    3.409 closest distance to " CB  PRO A  90 " =    1.130
peak=    3.404 closest distance to " CB  PHE A 204 " =    0.863
peak=    3.403 closest distance to " O   HOH Z 196 " =    1.281
peak=    3.403 closest distance to " O   ALA A 158 " =    1.148
peak=    3.400 closest distance to " OG BSER A 134 " =    2.823
peak=    3.399 closest distance to " O   HOH Z 227 " =    1.634
peak=    3.398 closest distance to " CG  ARG A 219 " =    1.204
peak=    3.397 closest distance to " O   HOH Z 325 " =    2.060
peak=    3.387 closest distance to " O   HOH Z 359 " =    1.554
peak=    3.386 closest distance to " CD  ARG A 195 " =    0.950
peak=    3.384 closest distance to " CA  SER A  32 " =    1.641
peak=    3.384 closest distance to " O   HOH Z 163 " =    1.555
peak=    3.383 closest distance to " CA  ASP A 162 " =    1.166
peak=    3.382 closest distance to " CB  GLN A  89 " =    1.316
peak=    3.380 closest distance to " O   HOH Z 154 " =    1.336
peak=    3.378 closest distance to " O   THR A 251 " =    1.180
peak=    3.374 closest distance to " CD1 LEU A 300 " =    1.140
peak=    3.372 closest distance to " CD  PRO A  54 " =    1.023
peak=    3.372 closest distance to " CB  ASN A 148 " =    1.742
peak=    3.364 closest distance to " O  BHOH Z 338 " =    2.163
peak=    3.363 closest distance to " CA  MET A 105 " =    1.068
peak=    3.359 closest distance to " O   HOH Z 109 " =    2.414
peak=    3.358 closest distance to " CZ3 TRP A  85 " =    0.931
peak=    3.356 closest distance to " OD2 ASP A 298 " =    3.982
peak=    3.354 closest distance to " CA  ASP A 191 " =    0.959
peak=    3.353 closest distance to " O   HOH Z 374 " =    2.789
peak=    3.351 closest distance to " CB  MET A 105 " =    1.084
peak=    3.351 closest distance to " OG  SER A  62 " =    2.865
peak=    3.349 closest distance to " CA  GLY A 241 " =    0.943
peak=    3.349 closest distance to " O   HOH Z 193 " =    1.742
peak=    3.329 closest distance to " CB  VAL A 265 " =    1.225
peak=    3.323 closest distance to " CG  GLN A  11 " =    1.360
peak=    3.317 closest distance to " CG2 ILE A 234 " =    1.028
peak=    3.315 closest distance to " OE1 GLN A  11 " =    2.036
peak=    3.315 closest distance to " CE1 TYR A 186 " =    1.231
peak=    3.313 closest distance to " CA  LEU A 101 " =    1.762
peak=    3.312 closest distance to " O   HOH Z 199 " =    1.664
peak=    3.304 closest distance to " CD  ARG A 159 " =    0.837
peak=    3.303 closest distance to " CG2 THR A  29 " =    1.403
peak=    3.296 closest distance to " O   HOH Z 305 " =    3.732
peak=    3.295 closest distance to " CA  ALA A 100 " =    1.021
peak=    3.294 closest distance to " O   HOH Z 245 " =    1.331
peak=    3.291 closest distance to " O   HOH Z 427 " =    3.145
peak=    3.287 closest distance to " CB  TYR A 116 " =    0.966
peak=    3.282 closest distance to " N   TYR A 116 " =    1.603
peak=    3.280 closest distance to " CA  ASN A 217 " =    1.279
peak=    3.279 closest distance to " O   HOH Z  78 " =    2.126
peak=    3.278 closest distance to " O   HOH Z 216 " =    5.224
peak=    3.278 closest distance to " O   HOH Z 380 " =    1.811
peak=    3.277 closest distance to " O   HOH Z 313 " =    1.648
peak=    3.276 closest distance to " CB  ALA A 100 " =    1.273
peak=    3.274 closest distance to " CG2 VAL A 197 " =    1.180
peak=    3.272 closest distance to " O   THR A 220 " =    1.154
peak=    3.272 closest distance to " O   HOH Z 408 " =    3.133
peak=    3.270 closest distance to " O   HOH Z 294 " =    1.492
peak=    3.269 closest distance to " CB  MET A  40 " =    1.072
peak=    3.267 closest distance to " OE1 GLN A  58 " =    3.599
peak=    3.266 closest distance to " CB  GLN A  88 " =    1.169
peak=    3.265 closest distance to " CA  ILE A 106 " =    0.818
peak=    3.262 closest distance to " CB  HIS A 108 " =    0.740
peak=    3.257 closest distance to " O   HOH Z 281 " =    4.972
peak=    3.257 closest distance to " O   HOH Z 313 " =    1.845
peak=    3.255 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.254 closest distance to " O   HOH Z 420 " =    5.634
peak=    3.254 closest distance to " CG1 VAL A 153 " =    1.105
peak=    3.252 closest distance to " O   HOH Z 189 " =    2.653
peak=    3.251 closest distance to " N   ASP A 132 " =    1.106
peak=    3.250 closest distance to " CA  ARG A 275 " =    1.838
peak=    3.250 closest distance to " C   TYR A 214 " =    1.552
peak=    3.249 closest distance to " O   HOH Z 421 " =    1.842
peak=    3.249 closest distance to " O   HOH Z 298 " =    2.394
peak=    3.247 closest distance to " O   ASP A 191 " =    1.504
peak=    3.245 closest distance to " ND2 ASN A 249 " =    0.893
peak=    3.243 closest distance to " NH2AARG A 275 " =    3.450
peak=    3.241 closest distance to " CG  GLU A  37 " =    0.938
peak=    3.238 closest distance to " CG  LEU A 167 " =    1.136
peak=    3.235 closest distance to " O   HOH Z 240 " =    2.239
peak=    3.226 closest distance to " O   HOH Z 250 " =    1.559
peak=    3.221 closest distance to " O   HOH Z 392 " =    2.471
peak=    3.220 closest distance to " O   HOH Z 125 " =    3.960
peak=    3.220 closest distance to " O   HOH Z  97 " =    2.303
peak=    3.218 closest distance to " O   HOH Z  48 " =    1.667
peak=    3.217 closest distance to " CB  MET A  47 " =    0.958
peak=    3.216 closest distance to " CG  ARG A 138 " =    1.194
peak=    3.211 closest distance to " N   ILE A  33 " =    1.050
peak=    3.209 closest distance to " CB  ASP A 298 " =    1.226
peak=    3.203 closest distance to " O   HOH Z 394 " =    3.786
peak=    3.202 closest distance to " O   HOH Z 130 " =    2.207
peak=    3.202 closest distance to " O   HOH Z 394 " =    1.493
peak=    3.201 closest distance to " CB  THR A  31 " =    1.689
peak=    3.199 closest distance to " CA  SER A  12 " =    1.556
peak=    3.194 closest distance to " CB  ALA A  43 " =    0.805
peak=    3.194 closest distance to " O   HOH Z  88 " =    3.318
peak=    3.194 closest distance to " CB  ALA A   9 " =    1.624
peak=    3.193 closest distance to " CG  GLN A  58 " =    2.706
peak=    3.177 closest distance to " CA  SER A  87 " =    1.065
peak=    3.173 closest distance to " CA  GLN A  73 " =    1.070
peak=    3.173 closest distance to " O   HOH Z 298 " =    4.170
peak=    3.171 closest distance to " CB  PRO A 198 " =    1.173
peak=    3.170 closest distance to " CE3 TRP A 150 " =    1.072
peak=    3.167 closest distance to " O   HOH Z 411 " =    1.709
peak=    3.167 closest distance to " ND1 HIS A  81 " =    1.615
peak=    3.166 closest distance to " CB  PRO A 243 " =    1.730
peak=    3.165 closest distance to " O   HOH Z 162 " =    1.632
peak=    3.165 closest distance to " NE2 HIS A 115 " =    1.038
peak=    3.161 closest distance to " O   HOH Z 141 " =    1.659
peak=    3.157 closest distance to " CA  LYS A 117 " =    1.224
peak=    3.152 closest distance to " CB  SER A  97 " =    0.808
peak=    3.148 closest distance to " CB  ASN A 187 " =    1.190
peak=    3.143 closest distance to " OG  SER A 245 " =    1.620
peak=    3.143 closest distance to " CB  ASN A 110 " =    1.162
peak=    3.141 closest distance to " CD1 LEU A 228 " =    1.575
peak=    3.140 closest distance to " CA  LEU A  83 " =    1.253
peak=    3.139 closest distance to " CG  GLN A  58 " =    0.882
peak=    3.139 closest distance to " O   HOH Z  63 " =    2.125
peak=    3.130 closest distance to " CD1 ILE A 199 " =    1.177
peak=    3.126 closest distance to " O   HOH Z 150 " =    1.495
peak=    3.126 closest distance to " OG  SER A 135 " =    1.328
peak=    3.123 closest distance to " ND2 ASN A 110 " =    1.540
peak=    3.119 closest distance to " O   HOH Z 286 " =    2.207
peak=    3.112 closest distance to " O   HOH Z 244 " =    1.682
peak=    3.108 closest distance to " O   HOH Z 173 " =    2.147
peak=    3.103 closest distance to " CA  ALA A 291 " =    0.755
peak=    3.099 closest distance to " O   HOH Z 344 " =    3.183
peak=    3.094 closest distance to " O   HOH Z 345 " =    2.947
peak=    3.092 closest distance to " CB  ASN A 215 " =    1.184
peak=    3.091 closest distance to " CA  ALA A 248 " =    1.180
peak=    3.087 closest distance to " CA  ALA A 299 " =    0.988
peak=    3.081 closest distance to " CA  ALA A  84 " =    1.206
peak=    3.080 closest distance to " O   HOH Z  88 " =    1.712
peak=    3.078 closest distance to " O   HOH Z 124 " =    1.744
peak=    3.076 closest distance to " O   ASP A 200 " =    1.720
peak=    3.075 closest distance to " O   HOH Z 130 " =    2.587
peak=    3.074 closest distance to " CB  ASN A 127 " =    0.864
peak=    3.073 closest distance to " O   HOH Z 116 " =    3.059
peak=    3.063 closest distance to " O   HOH Z 426 " =    1.344
peak=    3.059 closest distance to " CD  ARG A  66 " =    2.542
peak=    3.057 closest distance to " CD  LYS A 119 " =    1.772
peak=    3.047 closest distance to " O   GLU A   2 " =    1.600
peak=    3.046 closest distance to " CB  PHE A 283 " =    0.772
peak=    3.026 closest distance to " O   HOH Z  83 " =    1.540
peak=    3.025 closest distance to " CE1 PHE A 218 " =    1.135
peak=    3.015 closest distance to " O   HOH Z 264 " =    2.303
peak=    3.002 closest distance to " O   HOH Z   6 " =    2.427
peak=    2.991 closest distance to " O   THR A 251 " =    1.599

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.922 - 5.990
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 224 from: 225
   mapped sites are within: 0.922 - 5.990

peak=   -4.634 closest distance to " CD  GLN A  58 " =    0.971
peak=   -4.607 closest distance to " O   HOH Z 266 " =    5.352
peak=   -4.367 closest distance to " O   HOH Z  10 " =    1.618
peak=   -4.355 closest distance to " CB  PRO A 243 " =    2.710
peak=   -4.265 closest distance to " CG1 VAL A 250 " =    2.708
peak=   -4.260 closest distance to " CD  ARG A  14 " =    3.463
peak=   -4.212 closest distance to " CA  ASP A 298 " =    1.053
peak=   -4.198 closest distance to " CD1 LEU A 101 " =    2.438
peak=   -4.115 closest distance to " OXT GLY A 302 " =    2.975
peak=   -4.101 closest distance to " O   HOH Z 196 " =    2.337
peak=   -4.058 closest distance to " CG1 VAL A 112 " =    2.593
peak=   -4.045 closest distance to " O   PRO A 198 " =    1.349
peak=   -4.042 closest distance to " CD1 PHE A  59 " =    2.081
peak=   -4.034 closest distance to " O   HOH Z 150 " =    1.067
peak=   -4.019 closest distance to " CD  ARG A 156 " =    2.101
peak=   -3.993 closest distance to " CD2 TYR A 293 " =    1.903
peak=   -3.984 closest distance to " O   HOH Z 231 " =    2.348
peak=   -3.981 closest distance to " O   VAL A  67 " =    2.755
peak=   -3.971 closest distance to " O   HOH Z  13 " =    1.792
peak=   -3.962 closest distance to " O   HOH Z 166 " =    1.638
peak=   -3.941 closest distance to " CG2 ILE A  49 " =    2.741
peak=   -3.936 closest distance to " CD1 LEU A  25 " =    2.480
peak=   -3.928 closest distance to " N   ALA A  43 " =    2.765
peak=   -3.914 closest distance to " O   HOH Z 283 " =    2.240
peak=   -3.896 closest distance to " CE2 PHE A  61 " =    2.631
peak=   -3.884 closest distance to " OG  SER A  97 " =    2.217
peak=   -3.881 closest distance to " O   HOH Z 348 " =    2.334
peak=   -3.879 closest distance to " C   HIS A 108 " =    1.095
peak=   -3.866 closest distance to " O   ALA A  34 " =    2.395
peak=   -3.865 closest distance to " O   HOH Z 377 " =    2.093
peak=   -3.861 closest distance to " O   HOH Z 374 " =    1.911
peak=   -3.846 closest distance to " CG2 ILE A  20 " =    2.982
peak=   -3.838 closest distance to " CZ  TYR A 169 " =    1.847
peak=   -3.826 closest distance to " CG  GLN A  58 " =    1.159
peak=   -3.820 closest distance to " O   SER A 210 " =    1.874
peak=   -3.816 closest distance to " CD  GLN A 223 " =    1.334
peak=   -3.814 closest distance to " CG2 ILE A 263 " =    2.299
peak=   -3.812 closest distance to " CH2 TRP A 179 " =    1.254
peak=   -3.794 closest distance to " ND2 ASN A  45 " =    1.958
peak=   -3.778 closest distance to " CB  ASP A 132 " =    2.403
peak=   -3.778 closest distance to " CB  ALA A 291 " =    2.413
peak=   -3.770 closest distance to " CD1 ILE A 151 " =    2.458
peak=   -3.751 closest distance to " ND2BASN A 224 " =    1.861
peak=   -3.747 closest distance to " O   PHE A 218 " =    1.511
peak=   -3.736 closest distance to " O   HOH Z 185 " =    2.484
peak=   -3.714 closest distance to " CG  GLU A  53 " =    1.547
peak=   -3.710 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.703 closest distance to " CB  ALA A 161 " =    2.600
peak=   -3.693 closest distance to " CB  ALA A  10 " =    2.189
peak=   -3.686 closest distance to " OE1 GLN A 223 " =    2.230
peak=   -3.680 closest distance to " O   PRO A 163 " =    2.104
peak=   -3.672 closest distance to " CE2 TYR A  30 " =    2.716
peak=   -3.659 closest distance to " O   HOH Z 234 " =    4.233
peak=   -3.657 closest distance to " ND2 ASN A 187 " =    1.641
peak=   -3.652 closest distance to " OD1 ASN A 148 " =    1.465
peak=   -3.641 closest distance to " OG BSER A 134 " =    1.313
peak=   -3.636 closest distance to " N   SER A 276 " =    1.553
peak=   -3.624 closest distance to " O   HOH Z 264 " =    1.819
peak=   -3.621 closest distance to " O   SER A 276 " =    1.618
peak=   -3.615 closest distance to " NE2 GLN A 223 " =    1.161
peak=   -3.613 closest distance to " CG2 VAL A 189 " =    2.221
peak=   -3.601 closest distance to " O   HOH Z  71 " =    2.273
peak=   -3.597 closest distance to " C   ASN A 285 " =    2.393
peak=   -3.592 closest distance to " O   HOH Z 301 " =    2.461
peak=   -3.579 closest distance to " O   HOH Z 394 " =    1.581
peak=   -3.575 closest distance to " CE3 TRP A 150 " =    2.281
peak=   -3.562 closest distance to " CB  PHE A 192 " =    1.976
peak=   -3.561 closest distance to " CB  ALA A 291 " =    2.241
peak=   -3.559 closest distance to " O   HOH Z 128 " =    2.689
peak=   -3.544 closest distance to " NE  ARG A  66 " =    4.436
peak=   -3.539 closest distance to " O   HOH Z 210 " =    0.922
peak=   -3.525 closest distance to " O   HOH Z 200 " =    1.348
peak=   -3.519 closest distance to " O   HOH Z 197 " =    1.990
peak=   -3.515 closest distance to " ND2 ASN A 249 " =    2.273
peak=   -3.513 closest distance to " NE2 GLN A  11 " =    1.684
peak=   -3.503 closest distance to " O   HOH Z 290 " =    1.085
peak=   -3.503 closest distance to " O   HOH Z 171 " =    2.286
peak=   -3.502 closest distance to " O   HOH Z 372 " =    2.454
peak=   -3.496 closest distance to " CD2 PHE A  61 " =    2.100
peak=   -3.486 closest distance to " O   HOH Z 351 " =    1.573
peak=   -3.484 closest distance to " O   TRP A  92 " =    1.876
peak=   -3.480 closest distance to " O   HOH Z 240 " =    3.915
peak=   -3.475 closest distance to " CA  GLY A 241 " =    2.367
peak=   -3.474 closest distance to " CD  LYS A 289 " =    2.381
peak=   -3.473 closest distance to " CB  ALA A  43 " =    2.603
peak=   -3.472 closest distance to " O   VAL A 189 " =    2.607
peak=   -3.467 closest distance to " O   HOH Z 102 " =    1.630
peak=   -3.463 closest distance to " O   HOH Z 292 " =    4.609
peak=   -3.457 closest distance to " CG  ARG A 269 " =    2.303
peak=   -3.454 closest distance to " C   SER A 206 " =    1.464
peak=   -3.450 closest distance to " OG BSER A 210 " =    1.327
peak=   -3.446 closest distance to " O   HOH Z 366 " =    1.842
peak=   -3.446 closest distance to " OD1 ASP A 191 " =    1.646
peak=   -3.446 closest distance to " CD  ARG A 139 " =    1.609
peak=   -3.444 closest distance to " O   HOH Z 111 " =    1.928
peak=   -3.436 closest distance to " O   HOH Z 418 " =    1.257
peak=   -3.436 closest distance to " O   HOH Z 154 " =    1.514
peak=   -3.434 closest distance to " CB  PHE A  16 " =    2.510
peak=   -3.433 closest distance to " O   ALA A   1 " =    1.946
peak=   -3.430 closest distance to " CG1 VAL A  78 " =    2.632
peak=   -3.429 closest distance to " O   ALA A  10 " =    1.812
peak=   -3.422 closest distance to " NE2 GLN A  88 " =    1.901
peak=   -3.419 closest distance to " CE BMET A  47 " =    1.705
peak=   -3.418 closest distance to " N   THR A  52 " =    1.711
peak=   -3.411 closest distance to " O   TYR A 186 " =    1.768
peak=   -3.409 closest distance to " O   HOH Z 378 " =    1.276
peak=   -3.408 closest distance to " CA  GLY A 241 " =    3.019
peak=   -3.408 closest distance to " O   HOH Z 136 " =    2.187
peak=   -3.399 closest distance to " O   HOH Z 252 " =    3.805
peak=   -3.396 closest distance to " CA  GLY A 133 " =    2.390
peak=   -3.394 closest distance to " NH2 ARG A  79 " =    2.177
peak=   -3.387 closest distance to " O   HOH Z   6 " =    1.499
peak=   -3.386 closest distance to " CA  GLY A 203 " =    2.361
peak=   -3.385 closest distance to " O   HOH Z 285 " =    1.367
peak=   -3.380 closest distance to " CD2 PHE A 225 " =    1.263
peak=   -3.379 closest distance to " O   HOH Z 198 " =    1.888
peak=   -3.372 closest distance to " CG  PRO A 243 " =    1.725
peak=   -3.371 closest distance to " O   HOH Z 196 " =    1.906
peak=   -3.369 closest distance to " CG  GLN A 103 " =    2.522
peak=   -3.366 closest distance to " CA  GLY A 241 " =    3.239
peak=   -3.361 closest distance to " CG  GLU A 277 " =    1.220
peak=   -3.355 closest distance to " O   HOH Z  37 " =    1.897
peak=   -3.354 closest distance to " CG  MET A 105 " =    1.006
peak=   -3.353 closest distance to " C   THR A 279 " =    1.190
peak=   -3.349 closest distance to " CD2 LEU A 300 " =    2.755
peak=   -3.345 closest distance to " O   HOH Z 407 " =    3.333
peak=   -3.343 closest distance to " NH2 ARG A 159 " =    2.417
peak=   -3.343 closest distance to " O   HOH Z   6 " =    1.909
peak=   -3.339 closest distance to " O   HOH Z 149 " =    2.085
peak=   -3.335 closest distance to " O   ALA A  34 " =    2.148
peak=   -3.331 closest distance to " ND2 ASN A  45 " =    1.243
peak=   -3.330 closest distance to " O   HOH Z 106 " =    1.954
peak=   -3.329 closest distance to " O   HOH Z  56 " =    1.624
peak=   -3.320 closest distance to " O   HOH Z 145 " =    2.769
peak=   -3.317 closest distance to " CG1AVAL A  41 " =    2.648
peak=   -3.313 closest distance to " O   HOH Z 407 " =    1.413
peak=   -3.311 closest distance to " OD1 ASP A 171 " =    1.528
peak=   -3.311 closest distance to " O   HOH Z 109 " =    3.485
peak=   -3.308 closest distance to " O   HOH Z 422 " =    1.507
peak=   -3.304 closest distance to " CZ  PHE A  38 " =    2.381
peak=   -3.298 closest distance to " CG  LEU A  83 " =    2.037
peak=   -3.292 closest distance to " O   HOH Z 150 " =    2.132
peak=   -3.289 closest distance to " CE3 TRP A 274 " =    2.462
peak=   -3.280 closest distance to " O   GLY A  80 " =    2.700
peak=   -3.280 closest distance to " O   HOH Z 252 " =    4.023
peak=   -3.277 closest distance to " O   HOH Z 191 " =    5.990
peak=   -3.273 closest distance to " O   HOH Z 275 " =    1.513
peak=   -3.273 closest distance to " O   HOH Z  78 " =    1.892
peak=   -3.269 closest distance to " CD  ARG A 195 " =    5.103
peak=   -3.262 closest distance to " CD  GLN A  88 " =    0.927
peak=   -3.261 closest distance to " O   HOH Z 426 " =    1.687
peak=   -3.258 closest distance to " O   HOH Z  63 " =    1.195
peak=   -3.258 closest distance to " NH2 ARG A  66 " =    2.060
peak=   -3.252 closest distance to " CG1 VAL A 112 " =    2.807
peak=   -3.252 closest distance to " NE2 GLN A 103 " =    1.711
peak=   -3.249 closest distance to " O   SER A 271 " =    2.045
peak=   -3.246 closest distance to " CB  ALA A 248 " =    2.228
peak=   -3.245 closest distance to " CA  VAL A 197 " =    0.991
peak=   -3.241 closest distance to " O   HOH Z 311 " =    3.759
peak=   -3.240 closest distance to " O   HOH Z 396 " =    1.937
peak=   -3.236 closest distance to " O   GLY A 196 " =    1.094
peak=   -3.234 closest distance to " O   SER A 135 " =    1.573
peak=   -3.234 closest distance to " CD2 HIS A 207 " =    2.337
peak=   -3.233 closest distance to " OD1 ASN A 301 " =    1.926
peak=   -3.231 closest distance to " CH2 TRP A 150 " =    1.168
peak=   -3.231 closest distance to " O   HOH Z 211 " =    1.506
peak=   -3.229 closest distance to " O   HOH Z 377 " =    1.294
peak=   -3.227 closest distance to " CB  TRP A  85 " =    2.456
peak=   -3.220 closest distance to " N   ALA A 248 " =    2.012
peak=   -3.219 closest distance to " O   HOH Z 193 " =    1.446
peak=   -3.215 closest distance to " OD2 ASP A 171 " =    1.836
peak=   -3.214 closest distance to " O   HOH Z 177 " =    1.913
peak=   -3.212 closest distance to " NH2 ARG A  79 " =    1.654
peak=   -3.211 closest distance to " O   HOH Z 150 " =    1.755
peak=   -3.211 closest distance to " CB  ARG A 219 " =    2.294
peak=   -3.210 closest distance to " OH  TYR A 172 " =    1.816
peak=   -3.209 closest distance to " CZ  PHE A 155 " =    1.271
peak=   -3.207 closest distance to " O   HOH Z 236 " =    1.679
peak=   -3.205 closest distance to " OD2 ASP A 171 " =    2.485
peak=   -3.204 closest distance to " N   THR A 157 " =    1.661
peak=   -3.196 closest distance to " CG2AVAL A  41 " =    2.884
peak=   -3.186 closest distance to " CG1 VAL A 112 " =    2.755
peak=   -3.181 closest distance to " O   GLN A 240 " =    2.640
peak=   -3.180 closest distance to " O   HOH Z 174 " =    3.740
peak=   -3.179 closest distance to " CE  MET A  93 " =    1.762
peak=   -3.176 closest distance to " O   ASN A 187 " =    1.595
peak=   -3.173 closest distance to " O   ASN A 301 " =    1.282
peak=   -3.170 closest distance to " O   HOH Z 174 " =    2.201
peak=   -3.166 closest distance to " O   GLY A  75 " =    2.041
peak=   -3.163 closest distance to " O   HOH Z  52 " =    1.696
peak=   -3.157 closest distance to " CD1 TRP A 179 " =    1.192
peak=   -3.157 closest distance to " CB  PRO A 213 " =    1.912
peak=   -3.155 closest distance to " OG BSER A 134 " =    1.972
peak=   -3.154 closest distance to " O   HOH Z 287 " =    2.016
peak=   -3.148 closest distance to " CG2BVAL A  41 " =    1.589
peak=   -3.144 closest distance to " O   HOH Z 357 " =    2.129
peak=   -3.144 closest distance to " OE1 GLN A  88 " =    0.958
peak=   -3.141 closest distance to " NE2 GLN A  94 " =    1.844
peak=   -3.139 closest distance to " CB  ALA A   9 " =    2.554
peak=   -3.126 closest distance to " CB  SER A 210 " =    1.152
peak=   -3.126 closest distance to " O   HOH Z  40 " =    2.490
peak=   -3.124 closest distance to " OH  TYR A 169 " =    0.994
peak=   -3.124 closest distance to " CD1 LEU A 222 " =    2.528
peak=   -3.123 closest distance to " O   HOH Z 166 " =    1.666
peak=   -3.109 closest distance to " CG  PHE A 283 " =    2.578
peak=   -3.106 closest distance to " O   GLY A  17 " =    1.100
peak=   -3.100 closest distance to " CG  TRP A 266 " =    1.918
peak=   -3.099 closest distance to " O   HOH Z 193 " =    2.158
peak=   -3.098 closest distance to " O   HOH Z 134 " =    2.641
peak=   -3.098 closest distance to " OD1 ASN A  39 " =    2.264
peak=   -3.097 closest distance to " CG  PRO A 163 " =    2.644
peak=   -3.097 closest distance to " OD1 ASN A 187 " =    1.669
peak=   -3.095 closest distance to " O   HOH Z 126 " =    1.936
peak=   -3.094 closest distance to " CE  MET A 105 " =    2.941
peak=   -3.092 closest distance to " C   LEU A 143 " =    1.151
peak=   -3.084 closest distance to " OE2 GLU A   2 " =    1.673
peak=   -3.070 closest distance to " O   HOH Z  11 " =    1.797
peak=   -3.070 closest distance to " N   GLN A  58 " =    1.485
peak=   -3.069 closest distance to " O   HOH Z 156 " =    3.573
peak=   -3.068 closest distance to " O   HOH Z  40 " =    3.048
peak=   -3.066 closest distance to " CG  PRO A 280 " =    2.266
peak=   -3.061 closest distance to " CD2 TYR A 247 " =    2.383
peak=   -3.058 closest distance to " NE2 GLN A  88 " =    1.083
peak=   -3.051 closest distance to " CB  ASP A 286 " =    1.891

================= 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    :  0.4305 0.4200   6.239867e+00   6.212365e+00
   1_bss:  0.4193 0.4085   6.228057e+00   6.196412e+00
   1_xyz:  0.2748 0.2991   5.896185e+00   5.966690e+00
   1_adp:  0.2503 0.3104   5.846984e+00   5.992365e+00
   1_occ:  0.2502 0.3114   5.847169e+00   5.993075e+00
   2_bss:  0.2472 0.3074   5.840865e+00   5.987204e+00
   2_xyz:  0.1956 0.2379   5.619917e+00   5.783094e+00
   2_adp:  0.1845 0.2265   5.574545e+00   5.741409e+00
   2_occ:  0.1843 0.2265   5.574019e+00   5.741379e+00
   3_bss:  0.1841 0.2254   5.572430e+00   5.739661e+00
   3_xyz:  0.1426 0.1848   5.343421e+00   5.546335e+00
   3_adp:  0.1340 0.1792   5.294490e+00   5.507817e+00
   3_occ:  0.1340 0.1792   5.294231e+00   5.507452e+00
   4_bss:  0.1344 0.1794   5.295820e+00   5.507158e+00
   4_xyz:  0.1276 0.1724   5.255448e+00   5.470558e+00
   4_adp:  0.1259 0.1710   5.242633e+00   5.458550e+00
   4_occ:  0.1259 0.1710   5.242592e+00   5.458560e+00
   5_bss:  0.1258 0.1709   5.242558e+00   5.458585e+00
   5_xyz:  0.1162 0.1640   5.183569e+00   5.419338e+00
   5_adp:  0.1152 0.1639   5.178526e+00   5.417067e+00
   5_occ:  0.1151 0.1639   5.178623e+00   5.417340e+00
   5_bss:  0.1150 0.1637   5.178681e+00   5.417459e+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:  0.286  33.619  -3.496   4.332   1.607   0.000   0.000   0.000
   1_xyz:  0.286  33.619  -3.496   4.332   1.607   0.000   0.000   0.000
   1_adp:  0.286  33.619  -3.496   4.332   1.607   0.000   0.000   0.000
   1_occ:  0.286  33.619  -3.496   4.332   1.607   0.000   0.000   0.000
   2_bss:  0.326  71.868  -2.430   1.229   0.325   0.000   0.000   0.000
   2_xyz:  0.326  71.868  -2.430   1.229   0.325   0.000   0.000   0.000
   2_adp:  0.326  71.868  -2.430   1.229   0.325   0.000   0.000   0.000
   2_occ:  0.326  71.868  -2.430   1.229   0.325   0.000   0.000   0.000
   3_bss:  0.326  71.868  -2.367  -0.038  -0.066  -0.000  -0.000  -0.000
   3_xyz:  0.326  71.868  -2.367  -0.038  -0.066  -0.000  -0.000  -0.000
   3_adp:  0.326  71.868  -2.367  -0.038  -0.066  -0.000  -0.000  -0.000
   3_occ:  0.326  71.868  -2.367  -0.038  -0.066  -0.000  -0.000  -0.000
   4_bss:  0.335  75.270  -2.244  -0.676  -0.112  -0.000  -0.000  -0.000
   4_xyz:  0.335  75.270  -2.244  -0.676  -0.112  -0.000  -0.000  -0.000
   4_adp:  0.335  75.270  -2.244  -0.676  -0.112  -0.000  -0.000  -0.000
   4_occ:  0.335  75.270  -2.244  -0.676  -0.112  -0.000  -0.000  -0.000
   5_bss:  0.331  72.204  -1.985  -0.732   0.052  -0.000   0.000   0.000
   5_xyz:  0.331  72.204  -1.985  -0.732   0.052  -0.000   0.000   0.000
   5_adp:  0.331  72.204  -1.985  -0.732   0.052  -0.000   0.000   0.000
   5_occ:  0.331  72.204  -1.985  -0.732   0.052  -0.000   0.000   0.000
   5_bss:  0.326  69.841  -1.655  -0.565   0.318  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.639 0.5385  0.6919    53692.896
   1_bss:  47.519 0.5508  0.7281    50445.678
   1_xyz:  32.019 0.7356  0.9281    24862.819
   1_adp:  33.275 0.7206  0.9058    26589.953
   1_occ:  33.351 0.7197  0.9045    26665.478
   2_bss:  32.712 0.7272  0.8837    26011.710
   2_xyz:  24.266 0.8184  0.9596    15029.896
   2_adp:  22.702 0.8352  0.9579    13605.466
   2_occ:  22.697 0.8352  0.9578    13599.256
   3_bss:  22.590 0.8363  0.9419    13506.640
   3_xyz:  17.663 0.8830  0.9720     8702.864
   3_adp:  16.697 0.8920  0.9669     8129.915
   3_occ:  16.689 0.8921  0.9668     8125.796
   4_bss:  16.671 0.8923  0.9611     8118.544
   4_xyz:  15.815 0.9001  0.9632     7533.072
   4_adp:  15.551 0.9026  0.9543     7425.698
   4_occ:  15.551 0.9026  0.9541     7426.303
   5_bss:  15.551 0.9026  0.9585     7425.924
   5_xyz:  14.825 0.9083  0.9642     6861.007
   5_adp:  14.748 0.9091  0.9560     6814.543
   5_occ:  14.749 0.9091  0.9558     6816.196
   5_bss:  14.751 0.9091  0.9645     6816.098
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6543e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6543e-01
   1_xyz:   1.624  0.014  0.091 15.368  0.006  4.117   1.6467e-01
   1_adp:   1.624  0.014  0.091 15.368  0.006  4.117   1.6467e-01
   1_occ:   1.624  0.014  0.091 15.368  0.006  4.117   1.6467e-01
   2_bss:   1.624  0.014  0.091 15.368  0.006  4.117   1.6467e-01
   2_xyz:   1.026  0.007  0.072 14.283  0.004  4.132   5.9948e-02
   2_adp:   1.026  0.007  0.072 14.283  0.004  4.132   5.9948e-02
   2_occ:   1.026  0.007  0.072 14.283  0.004  4.132   5.9948e-02
   3_bss:   1.026  0.007  0.072 14.283  0.004  4.132   5.9948e-02
   3_xyz:   1.074  0.008  0.074 14.511  0.004  4.113   6.6784e-02
   3_adp:   1.074  0.008  0.074 14.511  0.004  4.113   6.6784e-02
   3_occ:   1.074  0.008  0.074 14.511  0.004  4.113   6.6784e-02
   4_bss:   1.074  0.008  0.074 14.511  0.004  4.113   6.6784e-02
   4_xyz:   0.941  0.006  0.071 14.197  0.003  4.119   5.2213e-02
   4_adp:   0.941  0.006  0.071 14.197  0.003  4.119   5.2213e-02
   4_occ:   0.941  0.006  0.071 14.197  0.003  4.119   5.2213e-02
   5_bss:   0.941  0.006  0.071 14.197  0.003  4.119   5.2213e-02
   5_xyz:   1.117  0.010  0.083 14.573  0.004  4.115   7.3828e-02
   5_adp:   1.117  0.010  0.083 14.573  0.004  4.115   7.3828e-02
   5_occ:   1.117  0.010  0.083 14.573  0.004  4.115   7.3828e-02
   5_bss:   1.117  0.010  0.083 14.573  0.004  4.115   7.3828e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4352e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4352e-01
   1_xyz:  10.087  0.123  0.286 85.984  0.030  2.051   4.0836e-01
   1_adp:  10.087  0.123  0.286 85.984  0.030  2.051   4.0836e-01
   1_occ:  10.087  0.123  0.286 85.984  0.030  2.051   4.0836e-01
   2_bss:  10.087  0.123  0.286 85.984  0.030  2.051   4.0836e-01
   2_xyz:   7.191  0.034  0.233 82.757  0.054  2.349   1.0578e-01
   2_adp:   7.191  0.034  0.233 82.757  0.054  2.349   1.0578e-01
   2_occ:   7.191  0.034  0.233 82.757  0.054  2.349   1.0578e-01
   3_bss:   7.191  0.034  0.233 82.757  0.054  2.349   1.0578e-01
   3_xyz:   8.181  0.048  0.237 81.968  0.029  2.288   4.7494e-02
   3_adp:   8.181  0.048  0.237 81.968  0.029  2.288   4.7494e-02
   3_occ:   8.181  0.048  0.237 81.968  0.029  2.288   4.7494e-02
   4_bss:   8.181  0.048  0.237 81.968  0.029  2.288   4.7494e-02
   4_xyz:   6.645  0.043  0.230 81.824  0.034  2.428   3.1997e-02
   4_adp:   6.645  0.043  0.230 81.824  0.034  2.428   3.1997e-02
   4_occ:   6.645  0.043  0.230 81.824  0.034  2.428   3.1997e-02
   5_bss:   6.645  0.043  0.230 81.824  0.034  2.428   3.1997e-02
   5_xyz:   8.662  0.046  0.304 82.061  0.031  2.317   5.3882e-02
   5_adp:   8.662  0.046  0.304 82.061  0.031  2.317   5.3882e-02
   5_occ:   8.662  0.046  0.304 82.061  0.031  2.317   5.3882e-02
   5_bss:   8.662  0.046  0.304 82.061  0.031  2.317   5.3882e-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:  89.52   0.00  17.66  73.25   0.00  13.63  89.52   3.55  39.64
   1_occ:  89.52   0.00  17.66  73.25   0.00  13.63  89.52   3.55  39.64
   2_bss:  89.52   0.00  17.66  73.25   0.00  13.63  89.52   3.55  39.64
   2_xyz:  89.52   0.00  17.66  73.25   0.00  13.63  89.52   3.55  39.64
   2_adp:  90.27   0.00  17.45  80.51   0.00  13.17  90.27   5.17  40.77
   2_occ:  90.27   0.00  17.45  80.51   0.00  13.17  90.27   5.17  40.77
   3_bss:  90.27   0.00  17.45  80.51   0.00  13.17  90.27   5.17  40.77
   3_xyz:  90.27   0.00  17.45  80.51   0.00  13.17  90.27   5.17  40.77
   3_adp:  92.49   0.00  17.30  87.76   0.00  12.66  92.49   5.24  42.60
   3_occ:  92.49   0.00  17.30  87.76   0.00  12.66  92.49   5.24  42.60
   4_bss:  92.49   0.00  17.30  87.76   0.00  12.66  92.49   5.24  42.60
   4_xyz:  92.49   0.00  17.30  87.76   0.00  12.66  92.49   5.24  42.60
   4_adp:  92.38   0.00  16.95  90.32   0.00  12.30  92.38   0.00  42.26
   4_occ:  92.38   0.00  16.95  90.32   0.00  12.30  92.38   0.00  42.26
   5_bss:  92.38   0.00  16.95  90.32   0.00  12.30  92.38   0.00  42.26
   5_xyz:  92.38   0.00  16.95  90.32   0.00  12.30  92.38   0.00  42.26
   5_adp:  96.98   0.00  16.74  96.98   0.00  12.08  93.74   0.45  42.13
   5_occ:  96.98   0.00  16.74  96.98   0.00  12.08  93.74   0.45  42.13
   5_bss:  96.99   0.00  16.75  96.99   0.00  12.08  93.75   0.45  42.13
------------------------------------------------------------------------
 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:    1.435    0.038    0.465
   1_adp:    1.435    0.038    0.465
   1_occ:    1.435    0.038    0.465
   2_bss:    1.435    0.038    0.465
   2_xyz:    1.208    0.044    0.529
   2_adp:    1.208    0.044    0.529
   2_occ:    1.208    0.044    0.529
   3_bss:    1.208    0.044    0.529
   3_xyz:    1.235    0.059    0.637
   3_adp:    1.235    0.059    0.637
   3_occ:    1.235    0.059    0.637
   4_bss:    1.235    0.059    0.637
   4_xyz:    1.296    0.025    0.669
   4_adp:    1.296    0.025    0.669
   4_occ:    1.296    0.025    0.669
   5_bss:    1.296    0.025    0.669
   5_xyz:    1.295    0.053    0.690
   5_adp:    1.295    0.053    0.690
   5_occ:    1.295    0.053    0.690
   5_bss:    1.295    0.053    0.690
------------------------------------------------------------------------

CPU time actual refinement: 337.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_591/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_591/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_591/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_591/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_591/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.88 
  Macro-tasks:
    bulk solvent and scale       = 45.87  
    individual site refinement   = 139.40 
    weights calculation          = 29.56  
    collect and process          = 6.66   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.60 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 104.18 
    alpha_beta                      = 8.21   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 113.72 
    fmodel                         = 7.55   
    r_factors                      = 0.34   
    phase_errors                   = 10.96  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 248.12 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.764 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    629 calls, 103.89 s
gradients_fft:          574 calls, 100.30 s

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

# Date 2008-01-16 Time 05:12:19 PST -0800 (1200489139.97 s)
Start R-work = 0.4305, R-free = 0.4200 (no bulk solvent and anisotropic scale)
Final R-work = 0.1332, R-free = 0.1783 (no bulk solvent and anisotropic scale)

Start R-work = 0.4193, R-free = 0.4085
Final R-work = 0.1150, R-free = 0.1637