# Date 2008-01-16 Time 05:41:52 PST -0800 (1200490912.35 s)
#phil __OFF__

Command line arguments: "../841.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26777
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 841

-------------------------------------------------------------------------------
  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: (70.6012, 48.1033, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, per 1000 atoms: 1.18


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00129
Completeness in resolution range: 0.959446
Completeness with d_max=infinity: 0.956447

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   2.0013

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: (70.6012, 48.1033, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00129
Completeness in resolution range: 0.959446
Completeness with d_max=infinity: 0.956447

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2817 [2148/2176]  1933   215  10.0%
  bin  2:  4.2817 -  3.4115 [2047/2070]  1843   204  10.0%
  bin  3:  3.4115 -  2.9841 [2035/2057]  1831   204  10.0%
  bin  4:  2.9841 -  2.7130 [2008/2027]  1812   196   9.8%
  bin  5:  2.7130 -  2.5195 [2014/2043]  1804   210  10.4%
  bin  6:  2.5195 -  2.3716 [1968/2009]  1779   189   9.6%
  bin  7:  2.3716 -  2.2532 [1986/2021]  1783   203  10.2%
  bin  8:  2.2532 -  2.1554 [1971/2009]  1772   199  10.1%
  bin  9:  2.1554 -  2.0726 [1956/1988]  1766   190   9.7%
  bin 10:  2.0726 -  2.0013 [1456/2017]  1307   149  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_841/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 10
        2.35 -     2.99: 1811
        2.99 -     3.62: 4519
        3.62 -     4.26: 8990
        4.26 -     4.90: 12588
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.710 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.713 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.815 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.829 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27913 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_841/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_841/model_refine_001.geo

CPU time processing inputs: 8.89


============================ 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 = 70.60125 48.10325 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4077   r_free= 0.3889   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.229720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7752 0.99   1388  155 0.3447 0.3656      6.5051      6.5121|
|  2:  4.7752 -  3.8105 0.99   1345  147 0.3572 0.3764       6.781      6.7563|
|  3:  3.8105 -  3.3348 0.99   1316  153 0.3808 0.3297      6.6256      6.5313|
|  4:  3.3348 -  3.0326 0.99   1311  137 0.3907 0.3559      6.4639      6.3671|
|  5:  3.0326 -  2.8168 0.99   1278  143 0.4281 0.3887      6.3421      6.3277|
|  6:  2.8168 -  2.6516 0.98   1293  144 0.4338 0.3918      6.2399       6.097|
|  7:  2.6516 -  2.5195 0.99   1292  150 0.4403 0.3714      6.2138      6.0614|
|  8:  2.5195 -  2.4103 0.99   1277  134 0.4365 0.4203      6.1151      6.1194|
|  9:  2.4103 -  2.3178 0.98   1291  145 0.4482 0.4371       6.073      6.1003|
| 10:  2.3178 -  2.2381 0.97   1251  143 0.4374 0.4079      6.0594      5.9864|
| 11:  2.2381 -  2.1683 0.98   1265  144 0.4465 0.3784      6.0114      5.9352|
| 12:  2.1683 -  2.1065 0.99   1270  133 0.4397 0.4737      5.9315      6.0034|
| 13:  2.1065 -  2.0512 0.97   1254  138 0.4398 0.4225      5.8313      5.8136|
| 14:  2.0512 -  2.0013 0.62    799   93 0.4166 0.4474      5.7647      5.7458|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7752  1388   155  0.71  33.74   0.83     0.74      69553.96|
|  2:  4.7752 -  3.8105  1345   147  0.76  30.37   0.91     0.83      81582.08|
|  3:  3.8105 -  3.3348  1316   153  0.70  35.54   0.92     0.85      81654.35|
|  4:  3.3348 -  3.0326  1311   137  0.66  39.31   0.92     0.82      68218.31|
|  5:  3.0326 -  2.8168  1278   143  0.61  43.42   0.91     0.79      54118.80|
|  6:  2.8168 -  2.6516  1293   144  0.61  43.09   0.91     0.77      42626.98|
|  7:  2.6516 -  2.5195  1292   150  0.61  43.54   0.94     0.77      38937.50|
|  8:  2.5195 -  2.4103  1277   134  0.58  45.95   0.94     0.76      38025.11|
|  9:  2.4103 -  2.3178  1291   145  0.56  47.42   0.93     0.76      36756.56|
| 10:  2.3178 -  2.2381  1251   143  0.57  46.51   0.97     0.77      33812.33|
| 11:  2.2381 -  2.1683  1265   144  0.57  46.91   0.96     0.79      31239.66|
| 12:  2.1683 -  2.1065  1270   133  0.54  48.79   0.98     0.76      30122.11|
| 13:  2.1065 -  2.0512  1254   138  0.50  52.42   0.95     0.71      27864.83|
| 14:  2.0512 -  2.0013   799    93  0.47  54.66   1.00     0.64      24839.31|
|alpha:            min =        0.64 max =            0.85 mean =         0.77|
|beta:             min =    24839.31 max =        81654.35 mean =     48135.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.98 mean =        43.24|
|phase err.(test): min =        0.00 max =           89.97 mean =        43.36|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.703345              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.802   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.206197              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.841   (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 |  1.710 -  2.029:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.029 -  2.348:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.348 -  2.667:       70 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.667 -  2.986:     1741 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.986 -  3.305:     1870 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.305 -  3.624:     2649 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.624 -  3.943:     4659 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.943 -  4.262:     4331 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.262 -  4.581:     5718 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.581 -  4.900:     6870 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| 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  1.710 |       0.218 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4077   r_free= 0.3889   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.229720                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3924   r_free= 0.3726   ksol= 0.29   Bsol= 34.58   scale= 0.935   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,6.18,-2.02,0.00,-0.00,-0.00); trace/3= 0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.213915                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.278376              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.627298              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.751   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3924      final r-factor (work) = 0.3362          |
| start r-factor (free) = 0.3726      final r-factor (free) = 0.3611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5648 = 5.28 * 0.50 * 6.2132 + 1.00 * 0.1670                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1772 = 5.28 * 0.50 * 6.0909 + 1.00 * 0.1022                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3362      final r-factor (work) = 0.3120          |
| start r-factor (free) = 0.3611      final r-factor (free) = 0.3684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8268 = 0.63 * 1.00 * 6.0909 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8092 = 0.63 * 1.00 * 6.0363 + 1.00 * 0.0226                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.71   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    86.71   17.30    None  None   None       |
|    Sol.    : 438    0      2.75    86.71   34.14    None  None   None       |
|    Mac.    : 2385   0      0.00    79.72   14.20    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 -   8.671:  812   |   5:    43.355 -  52.026:   88        |
|      1:     8.671 -  17.342:  941   |   6:    52.026 -  60.697:   46        |
|      2:    17.342 -  26.013:  528   |   7:    60.697 -  69.368:   25        |
|      3:    26.013 -  34.684:  238   |   8:    69.368 -  78.039:    7        |
|      4:    34.684 -  43.355:  134   |   9:    78.039 -  86.710:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3120 r_free = 0.3684             target_work(ml) = 6.040         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3118 r_free = 0.3679             target_work(ml) = 6.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3118   r_free= 0.3679   ksol= 0.29   Bsol= 34.58   scale= 0.970   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,6.18,-2.02,0.00,-0.00,-0.00); trace/3= 0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.038592                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3105   r_free= 0.3665   ksol= 0.29   Bsol= 49.93   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,3.44,-0.70,0.00,-0.00,-0.00); trace/3= 0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.040283                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.045195              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.640  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.788031              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.076   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3105      final r-factor (work) = 0.2553          |
| start r-factor (free) = 0.3665      final r-factor (free) = 0.3057          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3546 = 6.05 * 0.50 * 6.0387 + 1.00 * 0.1022                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0806 = 6.05 * 0.50 * 5.9508 + 1.00 * 0.0938                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2553      final r-factor (work) = 0.2406          |
| start r-factor (free) = 0.3057      final r-factor (free) = 0.3021          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7102 = 0.79 * 1.00 * 5.9508 + 1.00 * 0.0208                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6118 = 0.79 * 1.00 * 5.8331 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.24   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    94.24   17.73    None  None   None       |
|    Sol.    : 438    0      0.95    92.65   37.76    None  None   None       |
|    Mac.    : 2385   0      0.00    94.24   14.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.424: 1002   |   5:    47.121 -  56.546:   91        |
|      1:     9.424 -  18.849:  918   |   6:    56.546 -  65.970:   56        |
|      2:    18.849 -  28.273:  377   |   7:    65.970 -  75.394:   24        |
|      3:    28.273 -  37.697:  215   |   8:    75.394 -  84.819:   15        |
|      4:    37.697 -  47.121:  121   |   9:    84.819 -  94.243:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2406 r_free = 0.3021             target_work(ml) = 5.831         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2404 r_free = 0.3020             target_work(ml) = 5.830         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2404   r_free= 0.3020   ksol= 0.29   Bsol= 49.93   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,3.44,-0.70,0.00,-0.00,-0.00); trace/3= 0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.830317                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2401   r_free= 0.3004   ksol= 0.31   Bsol= 63.75   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,2.23,0.06,0.00,0.00,0.00); trace/3= 0.42                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.830567                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.722341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.903   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.521605              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.476  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2401      final r-factor (work) = 0.1982          |
| start r-factor (free) = 0.3004      final r-factor (free) = 0.2516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9529 = 3.72 * 0.50 * 5.8345 + 1.00 * 0.0938                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7510 = 3.72 * 0.50 * 5.7446 + 1.00 * 0.0592                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1982      final r-factor (work) = 0.1853          |
| start r-factor (free) = 0.2516      final r-factor (free) = 0.2358          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0117 = 0.52 * 1.00 * 5.7446 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9510 = 0.52 * 1.00 * 5.6146 + 1.00 * 0.0223                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.52   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    98.52   17.18    None  None   None       |
|    Sol.    : 438    0      3.51    92.58   40.60    None  None   None       |
|    Mac.    : 2385   0      0.00    98.52   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.852: 1198   |   5:    49.259 -  59.111:   85        |
|      1:     9.852 -  19.704:  891   |   6:    59.111 -  68.963:   49        |
|      2:    19.704 -  29.555:  264   |   7:    68.963 -  78.814:   22        |
|      3:    29.555 -  39.407:  160   |   8:    78.814 -  88.666:   15        |
|      4:    39.407 -  49.259:  132   |   9:    88.666 -  98.518:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1853 r_free = 0.2358             target_work(ml) = 5.588         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1851 r_free = 0.2357             target_work(ml) = 5.588         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1851   r_free= 0.2357   ksol= 0.31   Bsol= 63.75   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,2.23,0.06,0.00,0.00,0.00); trace/3= 0.42                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.587663                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1853   r_free= 0.2355   ksol= 0.32   Bsol= 70.13   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,1.04,-0.00,0.00,-0.00,-0.00); trace/3= -0.02                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.588365                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.903949              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.736  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.972568              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.722   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1853      final r-factor (work) = 0.1469          |
| start r-factor (free) = 0.2355      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0216 = 3.90 * 0.50 * 5.6161 + 1.00 * 0.0592                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7834 = 3.90 * 0.50 * 5.4873 + 1.00 * 0.0723                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1469      final r-factor (work) = 0.1356          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1832          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3505 = 0.97 * 1.00 * 5.4873 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2003 = 0.97 * 1.00 * 5.3329 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.94  17.07    None  None   None       |
|    all(noH): 2823   0      0.00    110.94  17.07    None  None   None       |
|    Sol.    : 438    0      1.48    103.55  43.56    None  None   None       |
|    Mac.    : 2385   0      0.00    110.94  12.20    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 -  11.094: 1476   |   5:    55.471 -  66.565:   79        |
|      1:    11.094 -  22.188:  779   |   6:    66.565 -  77.659:   47        |
|      2:    22.188 -  33.282:  176   |   7:    77.659 -  88.753:   21        |
|      3:    33.282 -  44.376:  126   |   8:    88.753 -  99.847:    9        |
|      4:    44.376 -  55.471:  106   |   9:    99.847 - 110.941:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1356 r_free = 0.1832             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1356 r_free = 0.1833             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1833   ksol= 0.32   Bsol= 70.13   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,1.04,-0.00,0.00,-0.00,-0.00); trace/3= -0.02                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.306772                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1833   ksol= 0.33   Bsol= 73.32   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,0.36,0.10,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.308157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.881389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.352  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.210883              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.780  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1358      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1833      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4238 = 3.88 * 0.50 * 5.3339 + 1.00 * 0.0723                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2870 = 3.88 * 0.50 * 5.2592 + 1.00 * 0.0805                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1207      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1226 = 0.21 * 1.00 * 5.2592 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1112 = 0.21 * 1.00 * 5.2196 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    105.94  16.31    None  None   None       |
|    all(noH): 2823   0      0.83    105.94  16.31    None  None   None       |
|    Sol.    : 438    0      4.12    103.17  41.32    None  None   None       |
|    Mac.    : 2385   0      0.83    105.94  11.72    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:     0.832 -  11.343: 1596   |   5:    53.384 -  63.894:   68        |
|      1:    11.343 -  21.853:  694   |   6:    63.894 -  74.404:   45        |
|      2:    21.853 -  32.363:  160   |   7:    74.404 -  84.915:   18        |
|      3:    32.363 -  42.874:  120   |   8:    84.915 -  95.425:    7        |
|      4:    42.874 -  53.384:  109   |   9:    95.425 - 105.935:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1667             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1189 r_free = 0.1666             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1666   ksol= 0.33   Bsol= 73.32   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,0.36,0.10,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201524                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7752 0.99   1388  155 0.0980 0.1330      5.3983      5.5867|
|  2:  4.7752 -  3.8105 0.99   1345  147 0.0861 0.1127      5.4491      5.6526|
|  3:  3.8105 -  3.3348 0.99   1316  153 0.1077 0.1576      5.5055      5.8745|
|  4:  3.3348 -  3.0326 0.99   1311  137 0.1315 0.1705      5.5079      5.6657|
|  5:  3.0326 -  2.8168 0.99   1278  143 0.1417 0.1789      5.4006      5.5687|
|  6:  2.8168 -  2.6516 0.98   1293  144 0.1392 0.2097      5.3038      5.5268|
|  7:  2.6516 -  2.5195 0.99   1292  150 0.1314 0.1838      5.2231      5.4724|
|  8:  2.5195 -  2.4103 0.99   1277  134 0.1283 0.1826      5.1527      5.3797|
|  9:  2.4103 -  2.3178 0.98   1291  145 0.1273 0.1854      5.0922      5.3743|
| 10:  2.3178 -  2.2381 0.97   1251  143 0.1257 0.1839      5.0513      5.2431|
| 11:  2.2381 -  2.1683 0.98   1265  144 0.1265 0.1913      4.9948      5.3252|
| 12:  2.1683 -  2.1065 0.99   1270  133 0.1198 0.1712      4.9242      5.1572|
| 13:  2.1065 -  2.0512 0.97   1254  138 0.1233 0.1790       4.842      5.0849|
| 14:  2.0512 -  2.0013 0.62    799   93 0.1193 0.1849      4.7429      4.9827|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7752  1388   155  0.94   9.73   0.96     0.93       7954.31|
|  2:  4.7752 -  3.8105  1345   147  0.95   8.68   1.00     0.99       9761.76|
|  3:  3.8105 -  3.3348  1316   153  0.93  11.78   1.02     1.01      11236.59|
|  4:  3.3348 -  3.0326  1311   137  0.91  14.70   1.00     0.98      11293.46|
|  5:  3.0326 -  2.8168  1278   143  0.89  17.19   1.00     0.98       9618.14|
|  6:  2.8168 -  2.6516  1293   144  0.89  17.45   0.98     0.95       8172.38|
|  7:  2.6516 -  2.5195  1292   150  0.89  16.79   0.99     0.96       7015.54|
|  8:  2.5195 -  2.4103  1277   134  0.90  16.69   1.00     0.96       6345.57|
|  9:  2.4103 -  2.3178  1291   145  0.89  17.14   0.99     0.95       5577.12|
| 10:  2.3178 -  2.2381  1251   143  0.89  17.08   0.99     0.96       5253.98|
| 11:  2.2381 -  2.1683  1265   144  0.89  17.07   0.99     0.94       4637.02|
| 12:  2.1683 -  2.1065  1270   133  0.90  16.05   1.00     0.98       4215.62|
| 13:  2.1065 -  2.0512  1254   138  0.90  16.73   0.98     0.98       3600.46|
| 14:  2.0512 -  2.0013   799    93  0.90  16.29   0.97     0.94       2949.07|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2949.07 max =        11293.46 mean =      7127.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.14|
|phase err.(test): min =        0.00 max =           88.80 mean =        14.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1666   ksol= 0.32   Bsol= 66.88   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,0.05,0.19,0.00,0.00,0.00); trace/3= -0.28                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1666   ksol= 0.32   Bsol= 66.88   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,0.05,0.19,0.00,0.00,0.00); trace/3= -0.28                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201340                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7752 0.99   1388  155 0.0978 0.1328      5.3971      5.5849|
|  2:  4.7752 -  3.8105 0.99   1345  147 0.0858 0.1124      5.4461      5.6489|
|  3:  3.8105 -  3.3348 0.99   1316  153 0.1077 0.1575      5.5045      5.8756|
|  4:  3.3348 -  3.0326 0.99   1311  137 0.1316 0.1706      5.5088      5.6651|
|  5:  3.0326 -  2.8168 0.99   1278  143 0.1419 0.1793      5.4015      5.5707|
|  6:  2.8168 -  2.6516 0.98   1293  144 0.1392 0.2088      5.3039      5.5241|
|  7:  2.6516 -  2.5195 0.99   1292  150 0.1314 0.1839      5.2231      5.4727|
|  8:  2.5195 -  2.4103 0.99   1277  134 0.1282 0.1830      5.1535      5.3814|
|  9:  2.4103 -  2.3178 0.98   1291  145 0.1269 0.1851      5.0921      5.3744|
| 10:  2.3178 -  2.2381 0.97   1251  143 0.1257 0.1845       5.052      5.2452|
| 11:  2.2381 -  2.1683 0.98   1265  144 0.1264 0.1911      4.9945      5.3248|
| 12:  2.1683 -  2.1065 0.99   1270  133 0.1196 0.1720      4.9244      5.1599|
| 13:  2.1065 -  2.0512 0.97   1254  138 0.1233 0.1790      4.8425      5.0858|
| 14:  2.0512 -  2.0013 0.62    799   93 0.1194 0.1841      4.7416      4.9789|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7752  1388   155  0.94   9.72   0.96     0.93       7938.78|
|  2:  4.7752 -  3.8105  1345   147  0.95   8.65   1.00     0.99       9710.18|
|  3:  3.8105 -  3.3348  1316   153  0.93  11.74   1.02     1.01      11190.08|
|  4:  3.3348 -  3.0326  1311   137  0.91  14.72   1.00     0.98      11318.74|
|  5:  3.0326 -  2.8168  1278   143  0.89  17.17   1.00     0.98       9608.57|
|  6:  2.8168 -  2.6516  1293   144  0.89  17.44   0.98     0.95       8171.51|
|  7:  2.6516 -  2.5195  1292   150  0.89  16.78   0.99     0.96       7014.59|
|  8:  2.5195 -  2.4103  1277   134  0.90  16.72   0.99     0.95       6364.76|
|  9:  2.4103 -  2.3178  1291   145  0.89  17.16   0.99     0.94       5591.72|
| 10:  2.3178 -  2.2381  1251   143  0.89  17.11   0.99     0.95       5265.06|
| 11:  2.2381 -  2.1683  1265   144  0.89  17.08   0.98     0.94       4640.74|
| 12:  2.1683 -  2.1065  1270   133  0.90  16.06   0.99     0.98       4225.34|
| 13:  2.1065 -  2.0512  1254   138  0.90  16.72   0.98     0.98       3597.13|
| 14:  2.0512 -  2.0013   799    93  0.90  16.24   0.97     0.94       2932.86|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2932.86 max =        11318.74 mean =      7122.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.14|
|phase err.(test): min =        0.00 max =           88.76 mean =        14.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.80    105.91  16.28    None  None   None       |
|    all(noH): 2823   0      0.80    105.91  16.28    None  None   None       |
|    Sol.    : 438    0      4.09    103.14  41.29    None  None   None       |
|    Mac.    : 2385   0      0.80    105.91  11.69    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:     0.804 -  11.314: 1596   |   5:    53.356 -  63.866:   68        |
|      1:    11.314 -  21.825:  694   |   6:    63.866 -  74.376:   45        |
|      2:    21.825 -  32.335:  160   |   7:    74.376 -  84.886:   18        |
|      3:    32.335 -  42.845:  120   |   8:    84.886 -  95.397:    7        |
|      4:    42.845 -  53.356:  109   |   9:    95.397 - 105.907:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.494 - 5.067
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 332
   mapped sites are within: 0.738 - 5.067

peak=    6.199 closest distance to " O   HOH Z 210 " =    1.402
peak=    5.842 closest distance to " O   HOH Z 111 " =    2.334
peak=    5.412 closest distance to " CB  SER A  63 " =    1.203
peak=    5.329 closest distance to " O   HOH Z 433 " =    1.790
peak=    5.127 closest distance to " O   PRO A 198 " =    1.574
peak=    4.871 closest distance to " CB  GLN A 223 " =    1.383
peak=    4.826 closest distance to " O   HOH Z 134 " =    1.865
peak=    4.735 closest distance to " CG  PRO A  54 " =    1.317
peak=    4.604 closest distance to " O   HOH Z 209 " =    2.312
peak=    4.596 closest distance to " O   HOH Z 422 " =    0.895
peak=    4.545 closest distance to " CA  TYR A  30 " =    0.935
peak=    4.487 closest distance to " CB  GLN A 183 " =    1.285
peak=    4.400 closest distance to " O   HOH Z  15 " =    2.098
peak=    4.374 closest distance to " O   HOH Z 357 " =    2.157
peak=    4.347 closest distance to " NE2 GLN A  11 " =    1.088
peak=    4.345 closest distance to " CG  PRO A 280 " =    0.820
peak=    4.342 closest distance to " O   HOH Z 418 " =    1.935
peak=    4.332 closest distance to " O   HOH Z  80 " =    1.989
peak=    4.326 closest distance to " CB  ARG A 190 " =    1.757
peak=    4.308 closest distance to " O   HOH Z 234 " =    3.828
peak=    4.294 closest distance to " O   ALA A 165 " =    1.298
peak=    4.284 closest distance to " O   HOH Z 403 " =    1.831
peak=    4.238 closest distance to " CA  ALA A  51 " =    0.981
peak=    4.236 closest distance to " CB  ARG A 275 " =    0.790
peak=    4.230 closest distance to " O   HOH Z 133 " =    2.367
peak=    4.194 closest distance to " O   HOH Z 369 " =    2.180
peak=    4.186 closest distance to " O   HOH Z 176 " =    2.299
peak=    4.144 closest distance to " O   HOH Z 412 " =    3.351
peak=    4.140 closest distance to " O   HOH Z 189 " =    2.494
peak=    4.135 closest distance to " O   HOH Z 154 " =    1.496
peak=    4.134 closest distance to " O   HOH Z 258 " =    2.234
peak=    4.133 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.127 closest distance to " CB  GLU A 128 " =    1.136
peak=    4.126 closest distance to " O   HOH Z  20 " =    1.820
peak=    4.119 closest distance to " CB  PRO A  54 " =    0.820
peak=    4.107 closest distance to " O   HOH Z   7 " =    0.830
peak=    4.104 closest distance to " O   HOH Z 406 " =    1.619
peak=    4.074 closest distance to " O   HOH Z  40 " =    1.898
peak=    4.071 closest distance to " CD  LYS A 166 " =    1.387
peak=    4.070 closest distance to " O   HOH Z  97 " =    1.976
peak=    4.051 closest distance to " CG1 ILE A  33 " =    1.244
peak=    4.051 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.049 closest distance to " O   HOH Z  63 " =    2.119
peak=    4.040 closest distance to " CG  ARG A  66 " =    2.762
peak=    4.031 closest distance to " CG  PRO A  90 " =    1.231
peak=    4.018 closest distance to " CB  GLU A 277 " =    3.795
peak=    4.012 closest distance to " O   HOH Z 196 " =    1.645
peak=    4.011 closest distance to " O   HOH Z  49 " =    0.872
peak=    3.996 closest distance to " CB  VAL A 202 " =    1.500
peak=    3.995 closest distance to " O   HOH Z 232 " =    2.415
peak=    3.993 closest distance to " O   SER A  87 " =    2.256
peak=    3.977 closest distance to " O   HOH Z 425 " =    1.533
peak=    3.975 closest distance to " CB  TRP A 266 " =    0.995
peak=    3.955 closest distance to " CA  ASP A 191 " =    0.875
peak=    3.945 closest distance to " O   HOH Z  30 " =    1.678
peak=    3.939 closest distance to " CB  LEU A 228 " =    1.111
peak=    3.927 closest distance to " O   HOH Z 163 " =    1.682
peak=    3.922 closest distance to " O   HOH Z 431 " =    1.150
peak=    3.914 closest distance to " CB  TRP A 179 " =    1.371
peak=    3.912 closest distance to " O   HOH Z 132 " =    2.737
peak=    3.910 closest distance to " O   HOH Z 128 " =    2.129
peak=    3.909 closest distance to " O   HOH Z 298 " =    1.970
peak=    3.907 closest distance to " O   HOH Z 423 " =    1.864
peak=    3.888 closest distance to " CB  ARG A  79 " =    1.402
peak=    3.888 closest distance to " O   HOH Z 271 " =    2.758
peak=    3.878 closest distance to " O   HOH Z  61 " =    1.553
peak=    3.868 closest distance to " CB  SER A 141 " =    1.003
peak=    3.858 closest distance to " CD2 TRP A 179 " =    1.309
peak=    3.858 closest distance to " CB  TYR A 169 " =    0.739
peak=    3.846 closest distance to " O   HOH Z 126 " =    1.621
peak=    3.821 closest distance to " CZ3 TRP A  85 " =    1.028
peak=    3.809 closest distance to " CG2BVAL A  41 " =    0.896
peak=    3.799 closest distance to " O   HOH Z 265 " =    2.001
peak=    3.794 closest distance to " O   HOH Z 437 " =    1.738
peak=    3.788 closest distance to " O   HOH Z 374 " =    2.746
peak=    3.780 closest distance to " O   HOH Z 389 " =    2.082
peak=    3.780 closest distance to " NH2BARG A 145 " =    1.981
peak=    3.779 closest distance to " CB  GLU A 152 " =    1.158
peak=    3.763 closest distance to " O   HOH Z  67 " =    2.085
peak=    3.761 closest distance to " CG2 VAL A 197 " =    1.192
peak=    3.759 closest distance to " O   HOH Z  48 " =    1.956
peak=    3.754 closest distance to " O   HOH Z 284 " =    2.979
peak=    3.751 closest distance to " CA  GLY A 196 " =    0.985
peak=    3.747 closest distance to " O   HOH Z 346 " =    1.495
peak=    3.743 closest distance to " O   HOH Z 150 " =    1.894
peak=    3.742 closest distance to " NH2 ARG A 156 " =    1.226
peak=    3.731 closest distance to " CD  ARG A 269 " =    0.999
peak=    3.730 closest distance to " CD  PRO A  54 " =    0.992
peak=    3.727 closest distance to " OD1 ASN A 217 " =    1.767
peak=    3.725 closest distance to " O   HOH Z 247 " =    1.459
peak=    3.725 closest distance to " CB  ASN A  39 " =    0.845
peak=    3.721 closest distance to " O   HOH Z 174 " =    2.118
peak=    3.716 closest distance to " CB  ASN A 142 " =    1.167
peak=    3.715 closest distance to " O   HOH Z 352 " =    1.922
peak=    3.709 closest distance to " CA  ARG A 195 " =    1.099
peak=    3.708 closest distance to " CD1 LEU A 300 " =    1.217
peak=    3.702 closest distance to " OG BSER A 164 " =    2.348
peak=    3.701 closest distance to " O   HOH Z  44 " =    1.909
peak=    3.694 closest distance to " O   HOH Z 362 " =    3.462
peak=    3.692 closest distance to " CG2 THR A 221 " =    1.046
peak=    3.685 closest distance to " O   ASN A  74 " =    1.710
peak=    3.672 closest distance to " O   HOH Z 214 " =    1.370
peak=    3.671 closest distance to " O   HOH Z  95 " =    1.777
peak=    3.671 closest distance to " O   HOH Z 281 " =    4.778
peak=    3.669 closest distance to " CB  PRO A  54 " =    1.269
peak=    3.667 closest distance to " O   HOH Z 394 " =    1.733
peak=    3.666 closest distance to " O   THR A 251 " =    1.268
peak=    3.663 closest distance to " O   HOH Z  47 " =    1.340
peak=    3.657 closest distance to " O   HOH Z 402 " =    1.690
peak=    3.656 closest distance to " O   HOH Z  78 " =    2.040
peak=    3.652 closest distance to " CZ  PHE A 218 " =    1.190
peak=    3.650 closest distance to " CG2 ILE A  20 " =    1.421
peak=    3.649 closest distance to " CA  ALA A  21 " =    1.355
peak=    3.646 closest distance to " O   HOH Z 428 " =    1.091
peak=    3.642 closest distance to " O   HOH Z 245 " =    1.358
peak=    3.639 closest distance to " CB  ASN A 148 " =    1.362
peak=    3.638 closest distance to " CB  SER A   3 " =    1.386
peak=    3.635 closest distance to " O   HOH Z  21 " =    1.888
peak=    3.635 closest distance to " O   HOH Z 126 " =    2.162
peak=    3.633 closest distance to " O   HOH Z 147 " =    1.761
peak=    3.631 closest distance to " CA  ILE A 106 " =    0.761
peak=    3.630 closest distance to " NZ  LYS A 117 " =    1.900
peak=    3.619 closest distance to " CB  SER A  62 " =    0.797
peak=    3.614 closest distance to " O   HOH Z 336 " =    1.602
peak=    3.612 closest distance to " O   HOH Z 118 " =    1.222
peak=    3.601 closest distance to " O   HOH Z 109 " =    2.077
peak=    3.594 closest distance to " O   ALA A 158 " =    1.215
peak=    3.587 closest distance to " CZ  PHE A  38 " =    1.400
peak=    3.580 closest distance to " C   ILE A 106 " =    1.910
peak=    3.577 closest distance to " O   ASP A 124 " =    1.586
peak=    3.575 closest distance to " O   HOH Z 128 " =    2.170
peak=    3.574 closest distance to " O   HOH Z   6 " =    1.006
peak=    3.573 closest distance to " CD2 LEU A 297 " =    0.832
peak=    3.573 closest distance to " N   ASN A  39 " =    1.283
peak=    3.567 closest distance to " OD1 ASN A  69 " =    2.486
peak=    3.566 closest distance to " OE1 GLN A  11 " =    2.071
peak=    3.565 closest distance to " CA  ALA A 295 " =    1.109
peak=    3.558 closest distance to " CD  ARG A 159 " =    0.863
peak=    3.548 closest distance to " O   HOH Z 316 " =    3.091
peak=    3.543 closest distance to " OG  SER A  62 " =    3.002
peak=    3.540 closest distance to " O   HOH Z 193 " =    1.978
peak=    3.512 closest distance to " ND2 ASN A 187 " =    1.563
peak=    3.512 closest distance to " OG  SER A 245 " =    1.640
peak=    3.510 closest distance to " O   HOH Z  90 " =    3.478
peak=    3.510 closest distance to " CB  MET A 105 " =    1.168
peak=    3.509 closest distance to " O   HOH Z 303 " =    2.374
peak=    3.508 closest distance to " O   HOH Z  40 " =    2.143
peak=    3.496 closest distance to " O   HOH Z 386 " =    2.256
peak=    3.494 closest distance to " O   HOH Z 154 " =    2.549
peak=    3.483 closest distance to " CB  ASN A 285 " =    0.811
peak=    3.476 closest distance to " CA  SER A  12 " =    1.670
peak=    3.476 closest distance to " O   HOH Z 291 " =    1.488
peak=    3.473 closest distance to " O   HOH Z 279 " =    2.165
peak=    3.472 closest distance to " CB  PHE A 283 " =    0.742
peak=    3.470 closest distance to " CB  ALA A 100 " =    1.450
peak=    3.468 closest distance to " O   HOH Z  66 " =    2.116
peak=    3.467 closest distance to " NZ  LYS A 166 " =    3.084
peak=    3.465 closest distance to " CG1BVAL A  72 " =    1.708
peak=    3.463 closest distance to " CA  TYR A 116 " =    1.449
peak=    3.463 closest distance to " CA  ASP A 162 " =    1.159
peak=    3.462 closest distance to " O  BHOH Z 338 " =    2.224
peak=    3.455 closest distance to " O   HOH Z 130 " =    1.162
peak=    3.453 closest distance to " CB  LEU A  83 " =    0.828
peak=    3.452 closest distance to " O   HOH Z 146 " =    1.536
peak=    3.446 closest distance to " O   HOH Z  11 " =    1.286
peak=    3.445 closest distance to " CA  GLN A  88 " =    1.256
peak=    3.445 closest distance to " CD  ARG A 195 " =    0.987
peak=    3.444 closest distance to " O   HOH Z 395 " =    1.494
peak=    3.441 closest distance to " CB  ARG A  79 " =    0.904
peak=    3.431 closest distance to " CA  LEU A  83 " =    1.444
peak=    3.430 closest distance to " O   HOH Z 421 " =    1.877
peak=    3.429 closest distance to " O   HOH Z 327 " =    1.613
peak=    3.429 closest distance to " O   HOH Z 368 " =    4.368
peak=    3.429 closest distance to " NE2 GLN A  77 " =    3.292
peak=    3.426 closest distance to " O   HOH Z 339 " =    1.341
peak=    3.425 closest distance to " CB  ALA A   9 " =    1.653
peak=    3.422 closest distance to " O   HOH Z  48 " =    1.609
peak=    3.419 closest distance to " O   HOH Z 371 " =    3.166
peak=    3.413 closest distance to " O   HOH Z 417 " =    3.071
peak=    3.410 closest distance to " O   HOH Z  43 " =    1.244
peak=    3.408 closest distance to " O   HOH Z 345 " =    1.675
peak=    3.404 closest distance to " CB  ASP A 140 " =    0.738
peak=    3.403 closest distance to " NZ  LYS A 117 " =    3.122
peak=    3.401 closest distance to " O   HOH Z  22 " =    2.580
peak=    3.401 closest distance to " O   HOH Z 120 " =    0.926
peak=    3.401 closest distance to " O   HOH Z 368 " =    2.072
peak=    3.400 closest distance to " N   CYS A 260 " =    0.806
peak=    3.392 closest distance to " O   HOH Z 214 " =    2.693
peak=    3.391 closest distance to " O   HOH Z 380 " =    1.888
peak=    3.390 closest distance to " O   HOH Z  88 " =    1.655
peak=    3.389 closest distance to " OG1 THR A 294 " =    2.451
peak=    3.388 closest distance to " O   HOH Z 180 " =    2.344
peak=    3.387 closest distance to " OG  SER A 276 " =    1.569
peak=    3.385 closest distance to " CB  ALA A  71 " =    1.287
peak=    3.384 closest distance to " CG2 THR A 220 " =    0.744
peak=    3.381 closest distance to " CA  ALA A 160 " =    1.000
peak=    3.380 closest distance to " O   HOH Z 414 " =    1.703
peak=    3.378 closest distance to " CG AARG A 275 " =    1.113
peak=    3.376 closest distance to " CD2 LEU A 255 " =    1.296
peak=    3.376 closest distance to " ND1 HIS A  81 " =    1.539
peak=    3.372 closest distance to " CA  GLU A 152 " =    0.988
peak=    3.372 closest distance to " CE1 TYR A 186 " =    1.180
peak=    3.370 closest distance to " CB  ARG A 190 " =    1.110
peak=    3.370 closest distance to " O   HOH Z  39 " =    1.118
peak=    3.360 closest distance to " O   HOH Z 189 " =    2.841
peak=    3.359 closest distance to " CE1 HIS A 108 " =    1.153
peak=    3.352 closest distance to " CG2 VAL A  78 " =    1.038
peak=    3.352 closest distance to " CB  LEU A   5 " =    1.102
peak=    3.343 closest distance to " CA  ALA A 158 " =    1.206
peak=    3.342 closest distance to " CG  ARG A 219 " =    1.279
peak=    3.340 closest distance to " O   HOH Z 377 " =    1.303
peak=    3.337 closest distance to " O   HOH Z 409 " =    3.196
peak=    3.337 closest distance to " O   HOH Z 438 " =    2.153
peak=    3.332 closest distance to " CB  PRO A  90 " =    1.228
peak=    3.327 closest distance to " O   HOH Z 365 " =    2.851
peak=    3.326 closest distance to " O   HOH Z 250 " =    1.503
peak=    3.325 closest distance to " O   HOH Z 193 " =    1.736
peak=    3.324 closest distance to " CA  ASN A 217 " =    1.372
peak=    3.322 closest distance to " O   HOH Z 427 " =    3.021
peak=    3.313 closest distance to " O   HOH Z 162 " =    2.421
peak=    3.312 closest distance to " O   HOH Z 227 " =    1.783
peak=    3.306 closest distance to " CB  GLU A 277 " =    0.783
peak=    3.305 closest distance to " CA  VAL A 125 " =    1.179
peak=    3.304 closest distance to " CG2 VAL A 126 " =    0.882
peak=    3.304 closest distance to " O   GLY A  91 " =    1.138
peak=    3.301 closest distance to " CA  THR A 221 " =    1.632
peak=    3.298 closest distance to " O   HOH Z 313 " =    1.874
peak=    3.298 closest distance to " O   HOH Z 123 " =    2.091
peak=    3.296 closest distance to " O   HOH Z 255 " =    1.855
peak=    3.289 closest distance to " NH1AARG A 145 " =    1.207
peak=    3.289 closest distance to " O   HOH Z 282 " =    2.112
peak=    3.289 closest distance to " O   HOH Z 387 " =    2.726
peak=    3.289 closest distance to " CB  GLU A  46 " =    0.950
peak=    3.288 closest distance to " OD2 ASP A 298 " =    3.975
peak=    3.278 closest distance to " O   HOH Z 294 " =    1.534
peak=    3.278 closest distance to " N   TYR A 116 " =    1.534
peak=    3.274 closest distance to " O   HOH Z  88 " =    3.617
peak=    3.273 closest distance to " CA  SER A  32 " =    1.651
peak=    3.270 closest distance to " O   HOH Z 423 " =    3.329
peak=    3.270 closest distance to " O   HOH Z 345 " =    2.882
peak=    3.270 closest distance to " O   HOH Z  64 " =    2.074
peak=    3.268 closest distance to " O   HOH Z 130 " =    2.271
peak=    3.268 closest distance to " O   HOH Z 301 " =    1.934
peak=    3.264 closest distance to " CA  ALA A 100 " =    1.215
peak=    3.262 closest distance to " ND2 ASN A 301 " =    1.200
peak=    3.258 closest distance to " CE  LYS A 119 " =    1.026
peak=    3.258 closest distance to " CG  GLN A  77 " =    0.795
peak=    3.256 closest distance to " O   HOH Z 432 " =    1.848
peak=    3.255 closest distance to " O   HOH Z 403 " =    1.539
peak=    3.253 closest distance to " O   HOH Z 325 " =    3.989
peak=    3.250 closest distance to " O   HOH Z 234 " =    1.859
peak=    3.250 closest distance to " CB  ASN A 187 " =    1.173
peak=    3.249 closest distance to " CA  ASN A 215 " =    1.163
peak=    3.249 closest distance to " O   HOH Z 185 " =    1.714
peak=    3.249 closest distance to " O   HOH Z 104 " =    2.695
peak=    3.247 closest distance to " O   HOH Z  88 " =    2.936
peak=    3.246 closest distance to " CB  TYR A 116 " =    1.279
peak=    3.245 closest distance to " CZ3 TRP A 266 " =    1.028
peak=    3.244 closest distance to " CA  GLY A 241 " =    0.837
peak=    3.243 closest distance to " O   HOH Z 435 " =    1.722
peak=    3.239 closest distance to " CD  GLN A 194 " =    1.651
peak=    3.234 closest distance to " CG2 ILE A 120 " =    1.138
peak=    3.234 closest distance to " O   HOH Z 415 " =    1.099
peak=    3.233 closest distance to " O   HOH Z 141 " =    1.642
peak=    3.231 closest distance to " O   HOH Z 139 " =    4.685
peak=    3.224 closest distance to " O   HOH Z 261 " =    1.854
peak=    3.222 closest distance to " CB  GLN A  89 " =    1.229
peak=    3.218 closest distance to " O   HOH Z  46 " =    1.457
peak=    3.215 closest distance to " O   HOH Z 435 " =    2.947
peak=    3.212 closest distance to " NH1 ARG A  14 " =    1.244
peak=    3.208 closest distance to " CA  LYS A 117 " =    1.329
peak=    3.208 closest distance to " O   HOH Z 343 " =    2.468
peak=    3.207 closest distance to " O   HOH Z 244 " =    1.716
peak=    3.207 closest distance to " CG  PRO A 243 " =    1.174
peak=    3.204 closest distance to " CA  ASP A 132 " =    1.266
peak=    3.204 closest distance to " CB  PRO A 198 " =    0.970
peak=    3.203 closest distance to " CA  PRO A  90 " =    0.979
peak=    3.202 closest distance to " O   HOH Z 156 " =    2.673
peak=    3.201 closest distance to " CA  ALA A  84 " =    1.197
peak=    3.199 closest distance to " N   ARG A 156 " =    1.427
peak=    3.194 closest distance to " CB  PRO A 243 " =    1.213
peak=    3.185 closest distance to " C   SER A  32 " =    1.081
peak=    3.181 closest distance to " CD BLYS A 290 " =    1.089
peak=    3.173 closest distance to " CD1 LEU A 222 " =    0.780
peak=    3.172 closest distance to " N   GLU A  44 " =    2.266
peak=    3.172 closest distance to " OH  TYR A  30 " =    1.412
peak=    3.171 closest distance to " CA  VAL A  41 " =    0.787
peak=    3.171 closest distance to " NH2AARG A 275 " =    3.245
peak=    3.170 closest distance to " N   ASP A 132 " =    1.243
peak=    3.167 closest distance to " CB  SER A  97 " =    1.238
peak=    3.166 closest distance to " CB  ILE A 120 " =    1.330
peak=    3.165 closest distance to " O   HOH Z 240 " =    2.150
peak=    3.164 closest distance to " CG2 THR A  29 " =    1.402
peak=    3.154 closest distance to " O   HOH Z 214 " =    2.192
peak=    3.153 closest distance to " O   HOH Z 145 " =    2.273
peak=    3.152 closest distance to " OE1 GLU A   2 " =    1.659
peak=    3.148 closest distance to " CB  SER A  26 " =    1.789
peak=    3.143 closest distance to " O   HOH Z 126 " =    1.944
peak=    3.137 closest distance to " CG2 THR A  42 " =    0.896
peak=    3.134 closest distance to " CB  ALA A 256 " =    1.397
peak=    3.133 closest distance to " O   HOH Z 173 " =    2.335
peak=    3.122 closest distance to " O   HOH Z 219 " =    5.067
peak=    3.122 closest distance to " CB  ALA A 291 " =    1.213
peak=    3.121 closest distance to " O   HOH Z 402 " =    2.896
peak=    3.118 closest distance to " CB  VAL A 265 " =    1.278
peak=    3.116 closest distance to " O   HOH Z 124 " =    1.207
peak=    3.113 closest distance to " CD  PRO A 213 " =    1.195
peak=    3.113 closest distance to " CA  ARG A  66 " =    1.036
peak=    3.111 closest distance to " O   PHE A  61 " =    1.425
peak=    3.111 closest distance to " O   HOH Z 299 " =    2.267
peak=    3.109 closest distance to " CA  GLN A 223 " =    0.788
peak=    3.106 closest distance to " O   HOH Z  88 " =    3.328
peak=    3.105 closest distance to " CB  ARG A 156 " =    0.993
peak=    3.102 closest distance to " O   HOH Z 146 " =    1.190
peak=    3.100 closest distance to " CG  GLN A  58 " =    2.509
peak=    3.094 closest distance to " CG  GLU A  37 " =    0.994
peak=    3.089 closest distance to " O   TRP A 274 " =    1.798
peak=    3.086 closest distance to " O   HOH Z 413 " =    3.347
peak=    3.080 closest distance to " O   ASP A 200 " =    1.585
peak=    3.077 closest distance to " O   HOH Z 353 " =    2.784
peak=    3.074 closest distance to " C   TYR A 214 " =    1.530
peak=    3.071 closest distance to " O   HOH Z  54 " =    1.550
peak=    3.064 closest distance to " O   HOH Z  99 " =    2.525
peak=    3.061 closest distance to " O   HOH Z  85 " =    2.312
peak=    3.053 closest distance to " O   HOH Z 355 " =    1.707
peak=    3.041 closest distance to " CA  THR A  82 " =    1.530
peak=    3.035 closest distance to " O   HOH Z   7 " =    1.035
peak=    3.029 closest distance to " CB  TRP A 179 " =    1.771
peak=    3.024 closest distance to " O   THR A 251 " =    1.972

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 235         
Filter by distance & map next to the model:
   mapped sites are within: 0.590 - 5.056
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 232 from: 235
   mapped sites are within: 0.792 - 5.056

peak=   -4.626 closest distance to " O   HOH Z 266 " =    5.056
peak=   -4.517 closest distance to " CD1 PHE A  59 " =    2.055
peak=   -4.284 closest distance to " CD  GLN A 223 " =    1.511
peak=   -4.274 closest distance to " O   HOH Z 166 " =    1.754
peak=   -4.224 closest distance to " O   VAL A  67 " =    2.809
peak=   -4.221 closest distance to " OXT GLY A 302 " =    3.068
peak=   -4.130 closest distance to " O   HOH Z 155 " =    1.651
peak=   -4.128 closest distance to " CB  PRO A 243 " =    2.752
peak=   -4.097 closest distance to " O   HOH Z 290 " =    0.947
peak=   -4.094 closest distance to " CD  GLN A  58 " =    1.282
peak=   -4.081 closest distance to " O   HOH Z 377 " =    0.954
peak=   -4.074 closest distance to " OG  SER A  97 " =    2.232
peak=   -4.068 closest distance to " CD1 LEU A 167 " =    2.074
peak=   -4.046 closest distance to " O   HOH Z 150 " =    0.949
peak=   -4.040 closest distance to " O   HOH Z  10 " =    1.603
peak=   -4.013 closest distance to " C   HIS A 108 " =    1.128
peak=   -4.002 closest distance to " CG2 ILE A  49 " =    2.717
peak=   -3.981 closest distance to " CE2 TYR A  30 " =    2.588
peak=   -3.971 closest distance to " O   PRO A 163 " =    2.158
peak=   -3.907 closest distance to " NH2 ARG A  66 " =    1.545
peak=   -3.900 closest distance to " CG1 VAL A 112 " =    2.608
peak=   -3.890 closest distance to " ND2 ASN A  45 " =    1.818
peak=   -3.882 closest distance to " O   PRO A 198 " =    1.366
peak=   -3.879 closest distance to " CD  GLN A  88 " =    0.913
peak=   -3.859 closest distance to " CD  ARG A 156 " =    2.140
peak=   -3.852 closest distance to " CD1 LEU A 101 " =    2.526
peak=   -3.841 closest distance to " CD2 LEU A 237 " =    2.728
peak=   -3.825 closest distance to " O   HOH Z  71 " =    1.716
peak=   -3.818 closest distance to " CB  PHE A 208 " =    2.380
peak=   -3.786 closest distance to " CB  SER A 146 " =    2.207
peak=   -3.776 closest distance to " CD  ARG A  14 " =    3.423
peak=   -3.764 closest distance to " OD1 ASP A 191 " =    1.788
peak=   -3.761 closest distance to " CH2 TRP A 179 " =    1.224
peak=   -3.735 closest distance to " O   VAL A  67 " =    2.973
peak=   -3.729 closest distance to " O   HOH Z 252 " =    4.113
peak=   -3.728 closest distance to " O   HOH Z 166 " =    2.510
peak=   -3.723 closest distance to " OG BSER A 210 " =    1.190
peak=   -3.712 closest distance to " ND2 ASN A  45 " =    1.059
peak=   -3.706 closest distance to " C   SER A 206 " =    1.445
peak=   -3.701 closest distance to " O   PHE A 218 " =    1.430
peak=   -3.686 closest distance to " O   HOH Z 234 " =    4.349
peak=   -3.682 closest distance to " OE1 GLN A 223 " =    2.393
peak=   -3.675 closest distance to " O   HOH Z 109 " =    3.495
peak=   -3.665 closest distance to " CD  PRO A 213 " =    2.222
peak=   -3.659 closest distance to " CA  SER A 276 " =    1.510
peak=   -3.656 closest distance to " O   HOH Z 165 " =    1.974
peak=   -3.654 closest distance to " O   HOH Z  15 " =    1.496
peak=   -3.653 closest distance to " NH2BARG A 145 " =    2.383
peak=   -3.646 closest distance to " NE2 GLN A 223 " =    1.087
peak=   -3.634 closest distance to " C   ASN A 285 " =    2.423
peak=   -3.631 closest distance to " O   HOH Z  19 " =    2.252
peak=   -3.625 closest distance to " CA  ASP A 298 " =    1.029
peak=   -3.621 closest distance to " O   HOH Z 351 " =    1.476
peak=   -3.613 closest distance to " CD1 PHE A 130 " =    2.388
peak=   -3.609 closest distance to " CB  ALA A 131 " =    2.372
peak=   -3.602 closest distance to " C   THR A 279 " =    1.059
peak=   -3.597 closest distance to " CD2 PHE A 225 " =    1.308
peak=   -3.580 closest distance to " CB  ALA A  43 " =    2.553
peak=   -3.579 closest distance to " O   HOH Z 171 " =    2.292
peak=   -3.572 closest distance to " OG BSER A 210 " =    2.251
peak=   -3.568 closest distance to " O   TRP A  92 " =    1.943
peak=   -3.558 closest distance to " O   VAL A 189 " =    2.556
peak=   -3.557 closest distance to " CG  ARG A 269 " =    2.331
peak=   -3.553 closest distance to " CA  GLY A 203 " =    2.306
peak=   -3.546 closest distance to " CB  ASP A 162 " =    2.662
peak=   -3.541 closest distance to " CG  PRO A 243 " =    1.711
peak=   -3.540 closest distance to " O   HOH Z 407 " =    0.952
peak=   -3.539 closest distance to " O   HOH Z 283 " =    2.086
peak=   -3.525 closest distance to " NH2 ARG A 159 " =    2.411
peak=   -3.524 closest distance to " C   ALA A 158 " =    1.360
peak=   -3.523 closest distance to " O   SER A 276 " =    1.730
peak=   -3.521 closest distance to " O   ALA A   1 " =    1.929
peak=   -3.517 closest distance to " O   HOH Z   7 " =    1.263
peak=   -3.517 closest distance to " O   HOH Z 185 " =    2.461
peak=   -3.511 closest distance to " ND2 ASN A 187 " =    1.748
peak=   -3.510 closest distance to " ND2 ASN A  60 " =    1.612
peak=   -3.507 closest distance to " O   HOH Z 422 " =    1.665
peak=   -3.505 closest distance to " CB  ALA A 161 " =    2.634
peak=   -3.502 closest distance to " O   HOH Z 136 " =    2.098
peak=   -3.498 closest distance to " O   ALA A  34 " =    2.499
peak=   -3.494 closest distance to " O   HOH Z 422 " =    1.228
peak=   -3.487 closest distance to " OE1 GLN A  88 " =    0.959
peak=   -3.487 closest distance to " NH2 ARG A  79 " =    2.020
peak=   -3.487 closest distance to " CB  ALA A  10 " =    2.055
peak=   -3.484 closest distance to " CG  ASP A 231 " =    0.809
peak=   -3.481 closest distance to " CB  SER A 210 " =    1.173
peak=   -3.477 closest distance to " CD  GLN A  58 " =    0.792
peak=   -3.471 closest distance to " OD1 ASN A 148 " =    1.557
peak=   -3.467 closest distance to " O   HOH Z  90 " =    1.973
peak=   -3.466 closest distance to " O   HOH Z 137 " =    1.314
peak=   -3.463 closest distance to " OD2 ASP A 171 " =    1.912
peak=   -3.446 closest distance to " O   HOH Z 128 " =    4.390
peak=   -3.440 closest distance to " CD2 LEU A 300 " =    2.847
peak=   -3.440 closest distance to " CA  GLY A 241 " =    2.386
peak=   -3.439 closest distance to " CA  VAL A 197 " =    0.957
peak=   -3.438 closest distance to " O  BHOH Z 338 " =    1.161
peak=   -3.437 closest distance to " O   HOH Z 106 " =    2.299
peak=   -3.432 closest distance to " CD1 LEU A  25 " =    2.501
peak=   -3.432 closest distance to " O   HOH Z   6 " =    1.521
peak=   -3.429 closest distance to " OD1 ASP A 298 " =    1.988
peak=   -3.429 closest distance to " O   HOH Z 426 " =    1.686
peak=   -3.427 closest distance to " O   HOH Z 109 " =    3.324
peak=   -3.423 closest distance to " O   HOH Z  52 " =    1.848
peak=   -3.421 closest distance to " CG  GLU A  53 " =    1.420
peak=   -3.415 closest distance to " CD  ARG A 195 " =    5.020
peak=   -3.414 closest distance to " N   ALA A  43 " =    2.830
peak=   -3.413 closest distance to " NE2 GLN A 194 " =    1.913
peak=   -3.406 closest distance to " O   ALA A  10 " =    1.780
peak=   -3.405 closest distance to " O   HOH Z 292 " =    4.700
peak=   -3.399 closest distance to " CG2 VAL A 189 " =    2.173
peak=   -3.386 closest distance to " O   HOH Z 200 " =    1.262
peak=   -3.372 closest distance to " O   HOH Z 418 " =    1.307
peak=   -3.369 closest distance to " O   HOH Z 117 " =    4.551
peak=   -3.367 closest distance to " O   VAL A 174 " =    2.132
peak=   -3.367 closest distance to " O   HOH Z 377 " =    2.266
peak=   -3.358 closest distance to " O   HOH Z 275 " =    1.509
peak=   -3.356 closest distance to " OG1 THR A  82 " =    1.529
peak=   -3.356 closest distance to " OE1 GLN A  88 " =    0.896
peak=   -3.343 closest distance to " O   SER A 210 " =    1.913
peak=   -3.340 closest distance to " O   HOH Z 197 " =    1.958
peak=   -3.339 closest distance to " O   HOH Z 111 " =    1.466
peak=   -3.338 closest distance to " CE2 PHE A  61 " =    2.613
peak=   -3.329 closest distance to " O   GLY A  75 " =    2.059
peak=   -3.327 closest distance to " CG2 THR A 221 " =    2.388
peak=   -3.326 closest distance to " OG  SER A  26 " =    1.442
peak=   -3.321 closest distance to " O   ALA A  34 " =    2.045
peak=   -3.319 closest distance to " CG  MET A 105 " =    0.918
peak=   -3.315 closest distance to " CG1 VAL A  78 " =    2.788
peak=   -3.314 closest distance to " N   THR A 157 " =    1.768
peak=   -3.312 closest distance to " O   ASN A 187 " =    1.644
peak=   -3.311 closest distance to " CD2 HIS A 115 " =    1.027
peak=   -3.308 closest distance to " ND2 ASN A 249 " =    2.271
peak=   -3.308 closest distance to " CB  ASP A 132 " =    2.440
peak=   -3.307 closest distance to " NE2 GLN A 103 " =    1.739
peak=   -3.305 closest distance to " OG  SER A   3 " =    1.793
peak=   -3.304 closest distance to " N   GLN A  58 " =    1.414
peak=   -3.301 closest distance to " O   HOH Z 353 " =    2.330
peak=   -3.296 closest distance to " O   HOH Z 151 " =    1.542
peak=   -3.293 closest distance to " CE2 PHE A  38 " =    1.941
peak=   -3.293 closest distance to " NH2 ARG A  66 " =    4.071
peak=   -3.283 closest distance to " O   HOH Z  58 " =    1.245
peak=   -3.276 closest distance to " O   HOH Z 264 " =    1.776
peak=   -3.276 closest distance to " O   HOH Z 396 " =    1.753
peak=   -3.270 closest distance to " CG2AVAL A  41 " =    2.921
peak=   -3.269 closest distance to " CG1 VAL A 197 " =    2.213
peak=   -3.268 closest distance to " O   HOH Z 388 " =    1.886
peak=   -3.268 closest distance to " CD2 TYR A 293 " =    1.799
peak=   -3.263 closest distance to " O   HOH Z 313 " =    1.484
peak=   -3.261 closest distance to " O   HOH Z 118 " =    1.522
peak=   -3.258 closest distance to " O   HOH Z 423 " =    2.363
peak=   -3.257 closest distance to " CG2 ILE A 263 " =    2.204
peak=   -3.255 closest distance to " NH2 ARG A  66 " =    1.319
peak=   -3.252 closest distance to " CD2 PHE A  61 " =    2.038
peak=   -3.251 closest distance to " CZ  TYR A 169 " =    1.805
peak=   -3.250 closest distance to " NE2 GLN A  94 " =    1.793
peak=   -3.247 closest distance to " CE3 TRP A 274 " =    2.472
peak=   -3.245 closest distance to " O   HOH Z 150 " =    1.898
peak=   -3.238 closest distance to " SG  CYS A 168 " =    0.868
peak=   -3.234 closest distance to " NH1 ARG A 195 " =    2.334
peak=   -3.234 closest distance to " CG2BVAL A  41 " =    1.453
peak=   -3.232 closest distance to " N   ASP A 272 " =    1.206
peak=   -3.226 closest distance to " O   HOH Z 384 " =    1.659
peak=   -3.225 closest distance to " O   HOH Z 133 " =    1.732
peak=   -3.222 closest distance to " CG  GLN A  11 " =    1.458
peak=   -3.222 closest distance to " O   HOH Z  78 " =    1.700
peak=   -3.222 closest distance to " O   HOH Z 397 " =    1.151
peak=   -3.221 closest distance to " CB  ALA A 291 " =    2.483
peak=   -3.218 closest distance to " CD2 PHE A  59 " =    2.385
peak=   -3.215 closest distance to " OE1 GLN A  77 " =    2.103
peak=   -3.207 closest distance to " N   ALA A 226 " =    2.015
peak=   -3.204 closest distance to " O   HOH Z 372 " =    2.584
peak=   -3.203 closest distance to " O   HOH Z  49 " =    1.108
peak=   -3.203 closest distance to " O   HOH Z 392 " =    1.222
peak=   -3.200 closest distance to " CD2 LEU A 237 " =    2.656
peak=   -3.199 closest distance to " O   HOH Z 331 " =    1.189
peak=   -3.196 closest distance to " CD  ARG A 139 " =    1.577
peak=   -3.195 closest distance to " CB  ALA A 291 " =    2.293
peak=   -3.193 closest distance to " CB  PHE A 192 " =    2.014
peak=   -3.191 closest distance to " O   HOH Z 298 " =    2.864
peak=   -3.190 closest distance to " O   HOH Z  11 " =    1.724
peak=   -3.188 closest distance to " OG  SER A  87 " =    1.703
peak=   -3.187 closest distance to " O   HOH Z 166 " =    2.252
peak=   -3.186 closest distance to " NH2 ARG A  79 " =    1.780
peak=   -3.183 closest distance to " ND2 ASN A  60 " =    1.780
peak=   -3.182 closest distance to " O   HOH Z 128 " =    2.552
peak=   -3.181 closest distance to " O   HOH Z 236 " =    1.857
peak=   -3.180 closest distance to " CZ  PHE A  38 " =    2.406
peak=   -3.178 closest distance to " O   HOH Z 409 " =    5.036
peak=   -3.177 closest distance to " CE BMET A  47 " =    1.924
peak=   -3.176 closest distance to " O   HOH Z 210 " =    1.236
peak=   -3.176 closest distance to " CB  ALA A 248 " =    2.238
peak=   -3.176 closest distance to " C   ARG A  79 " =    2.703
peak=   -3.175 closest distance to " CE  LYS A 119 " =    2.056
peak=   -3.173 closest distance to " O   HOH Z 246 " =    1.159
peak=   -3.159 closest distance to " O   HOH Z 424 " =    3.100
peak=   -3.158 closest distance to " CB  ASP A 286 " =    2.021
peak=   -3.154 closest distance to " OD1 ASN A 249 " =    1.781
peak=   -3.153 closest distance to " CH2 TRP A 177 " =    1.975
peak=   -3.147 closest distance to " O   HOH Z  37 " =    1.745
peak=   -3.145 closest distance to " CD2 LEU A 167 " =    1.776
peak=   -3.143 closest distance to " O   HOH Z 414 " =    1.497
peak=   -3.137 closest distance to " CG2 THR A   4 " =    1.816
peak=   -3.135 closest distance to " CD1 ILE A 263 " =    2.019
peak=   -3.132 closest distance to " O   HOH Z 423 " =    1.367
peak=   -3.129 closest distance to " O   HOH Z 252 " =    3.838
peak=   -3.127 closest distance to " CG1 VAL A 112 " =    2.405
peak=   -3.127 closest distance to " O   HOH Z 126 " =    1.919
peak=   -3.123 closest distance to " ND2 ASN A 301 " =    1.977
peak=   -3.122 closest distance to " O   HOH Z 222 " =    1.249
peak=   -3.112 closest distance to " CA  GLY A 241 " =    3.240
peak=   -3.107 closest distance to " O   HOH Z  56 " =    1.279
peak=   -3.106 closest distance to " CE  MET A  93 " =    1.956
peak=   -3.094 closest distance to " O   HOH Z 385 " =    3.797
peak=   -3.091 closest distance to " O   HOH Z 246 " =    1.650
peak=   -3.088 closest distance to " CG  TRP A 266 " =    1.895
peak=   -3.086 closest distance to " OE2 GLU A   2 " =    1.483
peak=   -3.086 closest distance to " CE  MET A 105 " =    2.316
peak=   -3.085 closest distance to " O   THR A  18 " =    1.466
peak=   -3.085 closest distance to " OE1 GLN A  88 " =    1.166
peak=   -3.080 closest distance to " C   GLN A  11 " =    1.215
peak=   -3.074 closest distance to " O   HOH Z 134 " =    2.143
peak=   -3.070 closest distance to " O   HOH Z  40 " =    3.019
peak=   -3.065 closest distance to " O   HOH Z 280 " =    2.269
peak=   -3.064 closest distance to " O   GLY A 118 " =    2.342
peak=   -3.053 closest distance to " O   HOH Z 198 " =    1.182
peak=   -3.047 closest distance to " CD1 ILE A 151 " =    2.345
peak=   -3.047 closest distance to " O   HOH Z  91 " =    2.179
peak=   -3.045 closest distance to " CA  TRP A 274 " =    1.368
peak=   -3.040 closest distance to " NE1 TRP A 177 " =    2.108
peak=   -3.039 closest distance to " CB  PHE A  16 " =    2.488
peak=   -3.038 closest distance to " OD2 ASP A 171 " =    2.249
peak=   -3.015 closest distance to " O   HOH Z 150 " =    1.354

================= 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    :  0.4077 0.3889   6.229720e+00   6.185076e+00
   1_bss:  0.3924 0.3726   6.213915e+00   6.167002e+00
   1_xyz:  0.3362 0.3611   6.084721e+00   6.127989e+00
   1_adp:  0.3120 0.3684   6.039550e+00   6.137581e+00
   1_occ:  0.3118 0.3679   6.038592e+00   6.137017e+00
   2_bss:  0.3105 0.3665   6.040283e+00   6.138499e+00
   2_xyz:  0.2553 0.3057   5.862081e+00   5.998991e+00
   2_adp:  0.2406 0.3021   5.830701e+00   5.988282e+00
   2_occ:  0.2404 0.3020   5.830317e+00   5.988365e+00
   3_bss:  0.2401 0.3004   5.830567e+00   5.988430e+00
   3_xyz:  0.1982 0.2516   5.645642e+00   5.828509e+00
   3_adp:  0.1853 0.2358   5.588234e+00   5.773877e+00
   3_occ:  0.1851 0.2357   5.587663e+00   5.773457e+00
   4_bss:  0.1853 0.2355   5.588365e+00   5.772843e+00
   4_xyz:  0.1469 0.1910   5.370017e+00   5.576202e+00
   4_adp:  0.1356 0.1832   5.307092e+00   5.528024e+00
   4_occ:  0.1356 0.1833   5.306772e+00   5.527865e+00
   5_bss:  0.1358 0.1833   5.308157e+00   5.528491e+00
   5_xyz:  0.1207 0.1715   5.223735e+00   5.467837e+00
   5_adp:  0.1191 0.1667   5.202495e+00   5.438405e+00
   5_occ:  0.1189 0.1666   5.201524e+00   5.437816e+00
   5_bss:  0.1189 0.1666   5.201340e+00   5.437718e+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:  0.292  34.583  -3.320   6.177  -2.015   0.000  -0.000  -0.000
   1_xyz:  0.292  34.583  -3.320   6.177  -2.015   0.000  -0.000  -0.000
   1_adp:  0.292  34.583  -3.320   6.177  -2.015   0.000  -0.000  -0.000
   1_occ:  0.292  34.583  -3.320   6.177  -2.015   0.000  -0.000  -0.000
   2_bss:  0.286  49.935  -1.884   3.438  -0.703   0.000  -0.000  -0.000
   2_xyz:  0.286  49.935  -1.884   3.438  -0.703   0.000  -0.000  -0.000
   2_adp:  0.286  49.935  -1.884   3.438  -0.703   0.000  -0.000  -0.000
   2_occ:  0.286  49.935  -1.884   3.438  -0.703   0.000  -0.000  -0.000
   3_bss:  0.314  63.755  -1.025   2.227   0.059   0.000   0.000   0.000
   3_xyz:  0.314  63.755  -1.025   2.227   0.059   0.000   0.000   0.000
   3_adp:  0.314  63.755  -1.025   2.227   0.059   0.000   0.000   0.000
   3_occ:  0.314  63.755  -1.025   2.227   0.059   0.000   0.000   0.000
   4_bss:  0.322  70.125  -1.098   1.040  -0.002   0.000  -0.000  -0.000
   4_xyz:  0.322  70.125  -1.098   1.040  -0.002   0.000  -0.000  -0.000
   4_adp:  0.322  70.125  -1.098   1.040  -0.002   0.000  -0.000  -0.000
   4_occ:  0.322  70.125  -1.098   1.040  -0.002   0.000  -0.000  -0.000
   5_bss:  0.329  73.323  -1.098   0.359   0.105   0.000   0.000   0.000
   5_xyz:  0.329  73.323  -1.098   0.359   0.105   0.000   0.000   0.000
   5_adp:  0.329  73.323  -1.098   0.359   0.105   0.000   0.000   0.000
   5_occ:  0.329  73.323  -1.098   0.359   0.105   0.000   0.000   0.000
   5_bss:  0.324  66.885  -1.067   0.050   0.190   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.248 0.6070  0.7718    48132.676
   1_bss:  42.417 0.6156  0.7836    44553.249
   1_xyz:  41.225 0.6281  0.7949    39723.997
   1_adp:  41.598 0.6234  0.7785    40390.646
   1_occ:  41.573 0.6236  0.7777    40309.505
   2_bss:  41.236 0.6280  0.7886    40228.000
   2_xyz:  33.014 0.7233  0.8910    26093.946
   2_adp:  32.405 0.7303  0.8790    25357.359
   2_occ:  32.402 0.7303  0.8786    25349.291
   3_bss:  32.251 0.7322  0.8873    25232.838
   3_xyz:  25.731 0.8034  0.9505    16696.923
   3_adp:  23.611 0.8261  0.9521    14760.746
   3_occ:  23.588 0.8263  0.9523    14741.462
   4_bss:  23.511 0.8271  0.9396    14685.407
   4_xyz:  18.397 0.8762  0.9712     9275.182
   4_adp:  17.122 0.8882  0.9680     8430.479
   4_occ:  17.117 0.8883  0.9679     8430.243
   5_bss:  17.116 0.8883  0.9619     8441.437
   5_xyz:  15.751 0.9004  0.9691     7461.389
   5_adp:  15.099 0.9062  0.9658     7135.897
   5_occ:  15.082 0.9063  0.9659     7126.547
   5_bss:  15.079 0.9063  0.9632     7122.176
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6697e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6697e-01
   1_xyz:   1.410  0.010  0.087 15.826  0.005  4.113   1.0220e-01
   1_adp:   1.410  0.010  0.087 15.826  0.005  4.113   1.0220e-01
   1_occ:   1.410  0.010  0.087 15.826  0.005  4.113   1.0220e-01
   2_bss:   1.410  0.010  0.087 15.826  0.005  4.113   1.0220e-01
   2_xyz:   1.293  0.010  0.082 14.785  0.006  4.114   9.3788e-02
   2_adp:   1.293  0.010  0.082 14.785  0.006  4.114   9.3788e-02
   2_occ:   1.293  0.010  0.082 14.785  0.006  4.114   9.3788e-02
   3_bss:   1.293  0.010  0.082 14.785  0.006  4.114   9.3788e-02
   3_xyz:   0.961  0.007  0.066 14.408  0.004  4.125   5.9231e-02
   3_adp:   0.961  0.007  0.066 14.408  0.004  4.125   5.9231e-02
   3_occ:   0.961  0.007  0.066 14.408  0.004  4.125   5.9231e-02
   4_bss:   0.961  0.007  0.066 14.408  0.004  4.125   5.9231e-02
   4_xyz:   1.120  0.009  0.080 14.579  0.004  4.114   7.2347e-02
   4_adp:   1.120  0.009  0.080 14.579  0.004  4.114   7.2347e-02
   4_occ:   1.120  0.009  0.080 14.579  0.004  4.114   7.2347e-02
   5_bss:   1.120  0.009  0.080 14.579  0.004  4.114   7.2347e-02
   5_xyz:   1.153  0.011  0.083 14.744  0.004  4.123   8.0475e-02
   5_adp:   1.153  0.011  0.083 14.744  0.004  4.123   8.0475e-02
   5_occ:   1.153  0.011  0.083 14.744  0.004  4.123   8.0475e-02
   5_bss:   1.153  0.011  0.083 14.744  0.004  4.123   8.0475e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.710   2.4373e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.710   2.4373e-01
   1_xyz:   9.718  0.081  0.455 89.485  0.038  2.147   7.3520e-02
   1_adp:   9.718  0.081  0.455 89.485  0.038  2.147   7.3520e-02
   1_occ:   9.718  0.081  0.455 89.485  0.038  2.147   7.3520e-02
   2_bss:   9.718  0.081  0.455 89.485  0.038  2.147   7.3520e-02
   2_xyz:   8.237  0.054  0.323 84.854  0.064  2.295   1.8385e-01
   2_adp:   8.237  0.054  0.323 84.854  0.064  2.295   1.8385e-01
   2_occ:   8.237  0.054  0.323 84.854  0.064  2.295   1.8385e-01
   3_bss:   8.237  0.054  0.323 84.854  0.064  2.295   1.8385e-01
   3_xyz:   7.247  0.046  0.211 84.241  0.047  2.271   8.5142e-02
   3_adp:   7.247  0.046  0.211 84.241  0.047  2.271   8.5142e-02
   3_occ:   7.247  0.046  0.211 84.241  0.047  2.271   8.5142e-02
   4_bss:   7.247  0.046  0.211 84.241  0.047  2.271   8.5142e-02
   4_xyz:   8.028  0.066  0.245 86.281  0.030  2.205   5.7209e-02
   4_adp:   8.028  0.066  0.245 86.281  0.030  2.205   5.7209e-02
   4_occ:   8.028  0.066  0.245 86.281  0.030  2.205   5.7209e-02
   5_bss:   8.028  0.066  0.245 86.281  0.030  2.205   5.7209e-02
   5_xyz:   8.276  0.055  0.296 81.539  0.035  2.309   6.4691e-02
   5_adp:   8.276  0.055  0.296 81.539  0.035  2.309   6.4691e-02
   5_occ:   8.276  0.055  0.296 81.539  0.035  2.309   6.4691e-02
   5_bss:   8.276  0.055  0.296 81.539  0.035  2.309   6.4691e-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:  86.71   0.00  17.30  79.72   0.00  14.20  86.71   2.75  34.14
   1_occ:  86.71   0.00  17.30  79.72   0.00  14.20  86.71   2.75  34.14
   2_bss:  86.71   0.00  17.30  79.72   0.00  14.20  86.71   2.75  34.14
   2_xyz:  86.71   0.00  17.30  79.72   0.00  14.20  86.71   2.75  34.14
   2_adp:  94.24   0.00  17.73  94.24   0.00  14.05  92.65   0.95  37.76
   2_occ:  94.24   0.00  17.73  94.24   0.00  14.05  92.65   0.95  37.76
   3_bss:  94.24   0.00  17.73  94.24   0.00  14.05  92.65   0.95  37.76
   3_xyz:  94.24   0.00  17.73  94.24   0.00  14.05  92.65   0.95  37.76
   3_adp:  98.52   0.00  17.18  98.52   0.00  12.88  92.58   3.51  40.60
   3_occ:  98.52   0.00  17.18  98.52   0.00  12.88  92.58   3.51  40.60
   4_bss:  98.52   0.00  17.18  98.52   0.00  12.88  92.58   3.51  40.60
   4_xyz:  98.52   0.00  17.18  98.52   0.00  12.88  92.58   3.51  40.60
   4_adp: 110.94   0.00  17.07 110.94   0.00  12.20 103.55   1.48  43.56
   4_occ: 110.94   0.00  17.07 110.94   0.00  12.20 103.55   1.48  43.56
   5_bss: 110.94   0.00  17.07 110.94   0.00  12.20 103.55   1.48  43.56
   5_xyz: 110.94   0.00  17.07 110.94   0.00  12.20 103.55   1.48  43.56
   5_adp: 105.94   0.83  16.31 105.94   0.83  11.72 103.17   4.12  41.32
   5_occ: 105.94   0.83  16.31 105.94   0.83  11.72 103.17   4.12  41.32
   5_bss: 105.91   0.80  16.28 105.91   0.80  11.69 103.14   4.09  41.29
------------------------------------------------------------------------
 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:    1.637    0.012    0.279
   1_adp:    1.637    0.012    0.279
   1_occ:    1.637    0.012    0.279
   2_bss:    1.637    0.012    0.279
   2_xyz:    1.351    0.019    0.450
   2_adp:    1.351    0.019    0.450
   2_occ:    1.351    0.019    0.450
   3_bss:    1.351    0.019    0.450
   3_xyz:    1.394    0.044    0.596
   3_adp:    1.394    0.044    0.596
   3_occ:    1.394    0.044    0.596
   4_bss:    1.394    0.044    0.596
   4_xyz:    1.619    0.082    0.700
   4_adp:    1.619    0.082    0.700
   4_occ:    1.619    0.082    0.700
   5_bss:    1.619    0.082    0.700
   5_xyz:    1.561    0.096    0.742
   5_adp:    1.561    0.096    0.742
   5_occ:    1.561    0.096    0.742
   5_bss:    1.561    0.096    0.742
------------------------------------------------------------------------

CPU time actual refinement: 330.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_841/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_841/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_841/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_841/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_841/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.11 
  Macro-tasks:
    bulk solvent and scale       = 41.50  
    individual site refinement   = 132.82 
    weights calculation          = 29.42  
    collect and process          = 6.56   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 210.39 
  Micro-tasks:
    mask                            = 2.25   
    f_calc                          = 106.55 
    alpha_beta                      = 8.33   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 108.96 
    fmodel                         = 6.65   
    r_factors                      = 0.20   
    phase_errors                   = 11.68  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 246.00 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.768 micro seconds
Total CPU time: 5.72 minutes
from_scatterers_fft:    618 calls, 106.13 s
gradients_fft:          563 calls,  98.25 s

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

# Date 2008-01-16 Time 05:47:35 PST -0800 (1200491255.80 s)
Start R-work = 0.4077, R-free = 0.3889 (no bulk solvent and anisotropic scale)
Final R-work = 0.1352, R-free = 0.1810 (no bulk solvent and anisotropic scale)

Start R-work = 0.3924, R-free = 0.3726
Final R-work = 0.1189, R-free = 0.1666