# Date 2008-01-16 Time 04:13:12 PST -0800 (1200485592.73 s)
#phil __OFF__

Command line arguments: "../224.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15358
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 224

-------------------------------------------------------------------------------
  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: (68.845, 47.8686, 85.9581, 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: 3.23, per 1000 atoms: 1.14


================================== 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: (68.845, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.96073
Completeness in resolution range: 0.934902
Completeness with d_max=infinity: 0.932099

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9586
                             d_min =   1.9607

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: (68.845, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.96073
Completeness in resolution range: 0.934902
Completeness with d_max=infinity: 0.932099

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9590 -  4.1961 [2207/2236]  1981   226  10.2%
  bin  2:  4.1961 -  3.3428 [2106/2129]  1897   209   9.9%
  bin  3:  3.3428 -  2.9238 [2074/2099]  1868   206   9.9%
  bin  4:  2.9238 -  2.6581 [2055/2072]  1850   205  10.0%
  bin  5:  2.6581 -  2.4685 [2056/2099]  1846   210  10.2%
  bin  6:  2.4685 -  2.3235 [2048/2076]  1853   195   9.5%
  bin  7:  2.3235 -  2.2076 [2023/2059]  1821   202  10.0%
  bin  8:  2.2076 -  2.1117 [2029/2071]  1831   198   9.8%
  bin  9:  2.1117 -  2.0306 [2004/2062]  1797   207  10.3%
  bin 10:  2.0306 -  1.9607 [ 987/2050]   886   101  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_224/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 11
        1.93 -     2.67: 111
        2.67 -     3.42: 4472
        3.42 -     4.16: 9381
        4.16 -     4.90: 14491
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.188 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.430 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.545 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.697 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.712 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28461 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_224/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_224/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 = 68.845 47.8686 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4388   r_free= 0.4280   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.251210                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.6804 0.99   1428  159 0.3538 0.3848      6.5251      6.5852|
|  2:  4.6804 -  3.7340 0.99   1371  153 0.3738 0.3640      6.7571      6.7334|
|  3:  3.7340 -  3.2676 0.99   1362  148 0.4016 0.3754      6.6127      6.6416|
|  4:  3.2676 -  2.9714 0.99   1322  144 0.4202 0.3741      6.4648      6.3717|
|  5:  2.9714 -  2.7599 0.99   1335  152 0.4622 0.4305      6.3269      6.3224|
|  6:  2.7599 -  2.5980 0.99   1330  150 0.4609 0.4560      6.2479      6.1162|
|  7:  2.5980 -  2.4685 0.98   1294  150 0.4796 0.4194      6.2147      6.1253|
|  8:  2.4685 -  2.3615 0.98   1330  135 0.4840 0.5121      6.1571      6.1968|
|  9:  2.3615 -  2.2709 0.99   1313  151 0.5068 0.4911      6.1076      6.1393|
| 10:  2.2709 -  2.1928 0.98   1301  141 0.4819 0.4746       6.085       6.096|
| 11:  2.1928 -  2.1244 0.97   1305  146 0.4994 0.5272      6.0166      6.0222|
| 12:  2.1244 -  2.0639 0.98   1288  147 0.4875 0.4493      5.9261      5.9544|
| 13:  2.0639 -  2.0097 0.91   1188  132 0.4927 0.5044      5.8572      5.8225|
| 14:  2.0097 -  1.9607 0.35    463   51 0.4902 0.5237        5.85      5.7064|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9590 -  4.6804  1428   159  0.68  35.62   0.84     0.71      73736.48|
|  2:  4.6804 -  3.7340  1371   153  0.73  32.50   0.93     0.82      92052.97|
|  3:  3.7340 -  3.2676  1362   148  0.66  38.44   0.93     0.85      90875.10|
|  4:  3.2676 -  2.9714  1322   144  0.62  42.00   0.93     0.82      74179.85|
|  5:  2.9714 -  2.7599  1335   152  0.56  47.17   0.90     0.77      60008.59|
|  6:  2.7599 -  2.5980  1330   150  0.54  48.75   0.92     0.72      52377.33|
|  7:  2.5980 -  2.4685  1294   150  0.51  51.28   0.91     0.69      50483.74|
|  8:  2.4685 -  2.3615  1330   135  0.46  55.55   0.92     0.65      49860.22|
|  9:  2.3615 -  2.2709  1313   151  0.43  57.76   0.92     0.64      48585.00|
| 10:  2.2709 -  2.1928  1301   141  0.42  58.58   0.96     0.60      45163.86|
| 11:  2.1928 -  2.1244  1305   146  0.43  57.99   0.95     0.65      41365.41|
| 12:  2.1244 -  2.0639  1288   147  0.40  59.95   0.95     0.64      38588.89|
| 13:  2.0639 -  2.0097  1188   132  0.37  62.08   0.97     0.59      34101.50|
| 14:  2.0097 -  1.9607   463    51  0.33  65.48   0.95     0.42      29137.03|
|alpha:            min =        0.42 max =            0.85 mean =         0.70|
|beta:             min =    29137.03 max =        92052.97 mean =     57571.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.97 mean =        49.94|
|phase err.(test): min =        0.00 max =           89.84 mean =        49.93|
|-----------------------------------------------------------------------------|

============================== 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 = 12.250593             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.336   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.587520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.384   (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 |  1.188 -  1.559:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.559 -  1.931:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.931 -  2.302:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.302 -  2.673:       93 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.673 -  3.044:     2150 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.044 -  3.415:     2322 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.415 -  3.786:     4035 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.786 -  4.158:     5346 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.158 -  4.529:     6444 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.529 -  4.900:     8047 |
|-----------------------------------------------------------------------------|
|-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 |        0.193 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.188 |       0.634 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4388   r_free= 0.4280   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.251210                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4298   r_free= 0.4160   ksol= 0.31   Bsol= 26.94   scale= 0.948   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,4.16,-1.62,0.00,-0.00,-0.00); trace/3= 0.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.240401                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.932582             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.040   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.841393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.014   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4298      final r-factor (work) = 0.2884          |
| start r-factor (free) = 0.4160      final r-factor (free) = 0.3143          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.3145 = 10.93 * 0.50 * 6.2422 + 1.00 * 0.1927                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.2389 = 10.93 * 0.50 * 6.0557 + 1.00 * 0.1367                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2884      final r-factor (work) = 0.2608          |
| start r-factor (free) = 0.3143      final r-factor (free) = 0.3231          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1015 = 0.84 * 1.00 * 6.0557 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9554 = 0.84 * 1.00 * 5.8698 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.43   18.07    None  None   None       |
|    all(noH): 2823   0      0.00    87.43   18.07    None  None   None       |
|    Sol.    : 438    0      3.96    87.43   39.19    None  None   None       |
|    Mac.    : 2385   0      0.00    84.00   14.19    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:     0.000 -   8.743:  817   |   5:    43.713 -  52.456:  104        |
|      1:     8.743 -  17.485:  993   |   6:    52.456 -  61.199:   58        |
|      2:    17.485 -  26.228:  417   |   7:    61.199 -  69.941:   42        |
|      3:    26.228 -  34.971:  223   |   8:    69.941 -  78.684:   14        |
|      4:    34.971 -  43.713:  143   |   9:    78.684 -  87.427:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2608 r_free = 0.3231             target_work(ml) = 5.880         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2606 r_free = 0.3234             target_work(ml) = 5.880         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2606   r_free= 0.3234   ksol= 0.31   Bsol= 26.94   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,4.16,-1.62,0.00,-0.00,-0.00); trace/3= 0.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.879713                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2572   r_free= 0.3211   ksol= 0.32   Bsol= 46.22   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,1.24,-1.00,0.00,-0.00,-0.00); trace/3= -0.58                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.872115                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.187267              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.386244              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.923   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2572      final r-factor (work) = 0.1872          |
| start r-factor (free) = 0.3211      final r-factor (free) = 0.2362          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3552 = 5.19 * 0.50 * 5.8675 + 1.00 * 0.1370                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0011 = 5.19 * 0.50 * 5.7559 + 1.00 * 0.0725                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1872      final r-factor (work) = 0.1723          |
| start r-factor (free) = 0.2362      final r-factor (free) = 0.2186          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2398 = 0.39 * 1.00 * 5.7559 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1681 = 0.39 * 1.00 * 5.5453 + 1.00 * 0.0263                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.50  17.79    None  None   None       |
|    all(noH): 2823   0      0.00    119.50  17.79    None  None   None       |
|    Sol.    : 438    0      4.26    85.43   40.04    None  None   None       |
|    Mac.    : 2385   0      0.00    119.50  13.70    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 -  11.950: 1366   |   5:    59.749 -  71.698:   55        |
|      1:    11.950 -  23.899:  836   |   6:    71.698 -  83.648:   20        |
|      2:    23.899 -  35.849:  254   |   7:    83.648 -  95.598:    3        |
|      3:    35.849 -  47.799:  191   |   8:    95.598 - 107.547:    0        |
|      4:    47.799 -  59.749:   97   |   9:   107.547 - 119.497:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1723 r_free = 0.2186             target_work(ml) = 5.512         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1720 r_free = 0.2185             target_work(ml) = 5.511         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1720   r_free= 0.2185   ksol= 0.32   Bsol= 46.22   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,1.24,-1.00,0.00,-0.00,-0.00); trace/3= -0.58                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.510872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1719   r_free= 0.2177   ksol= 0.32   Bsol= 46.22   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-0.17,-0.98,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.510375                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.634574              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.916   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.503776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.811   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1719      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.2177      final r-factor (free) = 0.1870          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1526 = 3.63 * 0.50 * 5.5468 + 1.00 * 0.0725                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9045 = 3.63 * 0.50 * 5.4128 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1281          |
| start r-factor (free) = 0.1870      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7443 = 0.50 * 1.00 * 5.4128 + 1.00 * 0.0174                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6758 = 0.50 * 1.00 * 5.2913 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    86.51   17.42    None  None   None       |
|    all(noH): 2823   0      1.18    86.51   17.42    None  None   None       |
|    Sol.    : 438    0      5.65    86.51   41.47    None  None   None       |
|    Mac.    : 2385   0      1.18    86.42   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.176 -   9.710: 1009   |   5:    43.845 -  52.379:  104        |
|      1:     9.710 -  18.244: 1066   |   6:    52.379 -  60.913:   82        |
|      2:    18.244 -  26.777:  259   |   7:    60.913 -  69.446:   37        |
|      3:    26.777 -  35.311:  123   |   8:    69.446 -  77.980:   25        |
|      4:    35.311 -  43.845:  110   |   9:    77.980 -  86.514:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1281 r_free = 0.1757             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1280 r_free = 0.1757             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1757   ksol= 0.32   Bsol= 46.22   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-0.17,-0.98,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.259754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1755   ksol= 0.32   Bsol= 53.46   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.91,-1.05,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.260421                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.811328              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.826  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.551169              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.916  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1755      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5093 = 2.81 * 0.50 * 5.2939 + 1.00 * 0.0679                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4106 = 2.81 * 0.50 * 5.2252 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8901 = 0.55 * 1.00 * 5.2252 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8660 = 0.55 * 1.00 * 5.1818 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    92.68   17.11    None  None   None       |
|    all(noH): 2823   0      0.85    92.68   17.11    None  None   None       |
|    Sol.    : 438    0      1.43    87.00   41.06    None  None   None       |
|    Mac.    : 2385   0      0.85    92.68   12.71    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:     0.851 -  10.034: 1112   |   5:    46.766 -  55.949:  101        |
|      1:    10.034 -  19.217: 1059   |   6:    55.949 -  65.132:   68        |
|      2:    19.217 -  28.400:  202   |   7:    65.132 -  74.315:   27        |
|      3:    28.400 -  37.583:  120   |   8:    74.315 -  83.498:   11        |
|      4:    37.583 -  46.766:  118   |   9:    83.498 -  92.681:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1630             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1631             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1631   ksol= 0.32   Bsol= 53.46   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.91,-1.05,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1631   ksol= 0.32   Bsol= 53.46   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-0.96,-0.90,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.512963              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.856  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.483262              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.103  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9856 = 1.51 * 0.50 * 5.1818 + 1.00 * 0.0657                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9718 = 1.51 * 0.50 * 5.1824 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6968 = 1.48 * 1.00 * 5.1824 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6945 = 1.48 * 1.00 * 5.1803 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.03  17.07    None  None   None       |
|    all(noH): 2823   0      0.00    104.03  17.07    None  None   None       |
|    Sol.    : 438    0      1.78    90.43   41.42    None  None   None       |
|    Mac.    : 2385   0      0.00    104.03  12.60    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 -  10.403: 1239   |   5:    52.017 -  62.420:   90        |
|      1:    10.403 -  20.807:  994   |   6:    62.420 -  72.823:   49        |
|      2:    20.807 -  31.210:  186   |   7:    72.823 -  83.226:   13        |
|      3:    31.210 -  41.613:  124   |   8:    83.226 -  93.630:    6        |
|      4:    41.613 -  52.017:  119   |   9:    93.630 - 104.033:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1641             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1641             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1641   ksol= 0.32   Bsol= 53.46   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-0.96,-0.90,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183224                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.6804 0.99   1428  159 0.0986 0.1302      5.3809      5.5596|
|  2:  4.6804 -  3.7340 0.99   1371  153 0.0842 0.1060      5.4273      5.6248|
|  3:  3.7340 -  3.2676 0.99   1362  148 0.1086 0.1543      5.4792       5.839|
|  4:  3.2676 -  2.9714 0.99   1322  144 0.1293 0.1689      5.4905       5.659|
|  5:  2.9714 -  2.7599 0.99   1335  152 0.1379 0.1804       5.359      5.5492|
|  6:  2.7599 -  2.5980 0.99   1330  150 0.1331 0.2175      5.2702      5.5352|
|  7:  2.5980 -  2.4685 0.98   1294  150 0.1274 0.1610      5.1925       5.364|
|  8:  2.4685 -  2.3615 0.98   1330  135 0.1239 0.1732      5.1247      5.3372|
|  9:  2.3615 -  2.2709 0.99   1313  151 0.1199 0.1998      5.0553      5.3779|
| 10:  2.2709 -  2.1928 0.98   1301  141 0.1161 0.1690      4.9971      5.2043|
| 11:  2.1928 -  2.1244 0.97   1305  146 0.1166 0.1977      4.9536      5.2748|
| 12:  2.1244 -  2.0639 0.98   1288  147 0.1197 0.1587      4.8901      5.1169|
| 13:  2.0639 -  2.0097 0.91   1188  132 0.1151 0.1955      4.8245       5.158|
| 14:  2.0097 -  1.9607 0.35    463   51 0.1091 0.1881      4.7567      4.9525|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9590 -  4.6804  1428   159  0.94   9.16   0.97     0.95       7079.00|
|  2:  4.6804 -  3.7340  1371   153  0.95   7.90   1.02     1.01       8952.03|
|  3:  3.7340 -  3.2676  1362   148  0.93  11.69   1.03     1.02      10533.02|
|  4:  3.2676 -  2.9714  1322   144  0.91  14.60   1.01     1.00      11120.78|
|  5:  2.9714 -  2.7599  1335   152  0.89  16.93   1.00     0.98       9105.62|
|  6:  2.7599 -  2.5980  1330   150  0.89  17.23   0.98     0.94       7762.58|
|  7:  2.5980 -  2.4685  1294   150  0.90  16.40   0.99     0.95       6696.20|
|  8:  2.4685 -  2.3615  1330   135  0.90  16.38   1.00     0.96       6048.69|
|  9:  2.3615 -  2.2709  1313   151  0.90  16.59   1.00     0.95       5368.68|
| 10:  2.2709 -  2.1928  1301   141  0.90  16.53   0.99     0.95       4873.36|
| 11:  2.1928 -  2.1244  1305   146  0.90  16.74   0.99     0.95       4598.80|
| 12:  2.1244 -  2.0639  1288   147  0.90  16.38   0.99     0.97       4071.74|
| 13:  2.0639 -  2.0097  1188   132  0.89  17.29   0.99     0.98       3735.98|
| 14:  2.0097 -  1.9607   463    51  0.89  16.78   0.97     0.91       3134.11|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3134.11 max =        11120.78 mean =      6871.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.87|
|phase err.(test): min =        0.00 max =           89.63 mean =        14.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1641   ksol= 0.32   Bsol= 53.97   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-0.87,-0.72,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.183281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1641   ksol= 0.32   Bsol= 53.97   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-0.87,-0.72,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.183281                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.6804 0.99   1428  159 0.0985 0.1300      5.3809      5.5608|
|  2:  4.6804 -  3.7340 0.99   1371  153 0.0844 0.1061      5.4283      5.6256|
|  3:  3.7340 -  3.2676 0.99   1362  148 0.1086 0.1543      5.4798      5.8393|
|  4:  3.2676 -  2.9714 0.99   1322  144 0.1293 0.1690      5.4903       5.659|
|  5:  2.9714 -  2.7599 0.99   1335  152 0.1379 0.1803      5.3586      5.5486|
|  6:  2.7599 -  2.5980 0.99   1330  150 0.1331 0.2173      5.2699      5.5344|
|  7:  2.5980 -  2.4685 0.98   1294  150 0.1274 0.1611      5.1923       5.364|
|  8:  2.4685 -  2.3615 0.98   1330  135 0.1238 0.1731      5.1246      5.3371|
|  9:  2.3615 -  2.2709 0.99   1313  151 0.1199 0.1998      5.0554      5.3779|
| 10:  2.2709 -  2.1928 0.98   1301  141 0.1161 0.1691      4.9973      5.2051|
| 11:  2.1928 -  2.1244 0.97   1305  146 0.1166 0.1976      4.9538      5.2745|
| 12:  2.1244 -  2.0639 0.98   1288  147 0.1197 0.1589      4.8902      5.1175|
| 13:  2.0639 -  2.0097 0.91   1188  132 0.1152 0.1954      4.8244      5.1569|
| 14:  2.0097 -  1.9607 0.35    463   51 0.1091 0.1883      4.7566      4.9525|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9590 -  4.6804  1428   159  0.94   9.16   0.97     0.95       7077.08|
|  2:  4.6804 -  3.7340  1371   153  0.95   7.90   1.02     1.01       8964.79|
|  3:  3.7340 -  3.2676  1362   148  0.93  11.70   1.03     1.02      10551.92|
|  4:  3.2676 -  2.9714  1322   144  0.91  14.60   1.02     1.01      11120.26|
|  5:  2.9714 -  2.7599  1335   152  0.89  16.92   1.01     0.98       9094.05|
|  6:  2.7599 -  2.5980  1330   150  0.89  17.22   0.98     0.95       7753.88|
|  7:  2.5980 -  2.4685  1294   150  0.90  16.39   0.99     0.96       6690.07|
|  8:  2.4685 -  2.3615  1330   135  0.90  16.38   1.00     0.97       6047.58|
|  9:  2.3615 -  2.2709  1313   151  0.90  16.60   1.00     0.96       5370.23|
| 10:  2.2709 -  2.1928  1301   141  0.90  16.54   1.00     0.96       4874.63|
| 11:  2.1928 -  2.1244  1305   146  0.90  16.75   1.00     0.96       4600.44|
| 12:  2.1244 -  2.0639  1288   147  0.90  16.39   1.00     0.98       4072.56|
| 13:  2.0639 -  2.0097  1188   132  0.89  17.29   1.00     0.99       3733.93|
| 14:  2.0097 -  1.9607   463    51  0.89  16.77   0.98     0.92       3129.20|
|alpha:            min =        0.92 max =            1.02 mean =         0.98|
|beta:             min =     3129.20 max =        11120.26 mean =      6871.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.87|
|phase err.(test): min =        0.00 max =           89.60 mean =        14.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.04  17.08    None  None   None       |
|    all(noH): 2823   0      0.00    104.04  17.08    None  None   None       |
|    Sol.    : 438    0      1.78    90.44   41.42    None  None   None       |
|    Mac.    : 2385   0      0.00    104.04  12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.406: 1239   |   5:    52.020 -  62.423:   90        |
|      1:    10.406 -  20.810:  994   |   6:    62.423 -  72.826:   49        |
|      2:    20.810 -  31.213:  186   |   7:    72.826 -  83.229:   13        |
|      3:    31.213 -  41.616:  124   |   8:    83.229 -  93.633:    6        |
|      4:    41.616 -  52.020:  119   |   9:    93.633 - 104.036:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.523 - 3.910
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 317
   mapped sites are within: 0.750 - 3.910

peak=    5.344 closest distance to " NH2 ARG A  56 " =    2.298
peak=    5.311 closest distance to " CB  ARG A 275 " =    0.916
peak=    5.239 closest distance to " CA  TYR A  30 " =    0.934
peak=    5.209 closest distance to " CG  PRO A  54 " =    1.317
peak=    5.198 closest distance to " CB  GLN A 223 " =    1.406
peak=    5.028 closest distance to " CG  PRO A  90 " =    1.196
peak=    4.962 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.730 closest distance to " CB  SER A  63 " =    1.141
peak=    4.721 closest distance to " CG  PRO A 213 " =    1.325
peak=    4.714 closest distance to " O   HOH Z 102 " =    1.368
peak=    4.701 closest distance to " O   HOH Z 403 " =    1.902
peak=    4.534 closest distance to " O   HOH Z 232 " =    2.321
peak=    4.510 closest distance to " O   HOH Z  97 " =    1.926
peak=    4.501 closest distance to " O   HOH Z  80 " =    1.809
peak=    4.474 closest distance to " CB  GLN A 183 " =    1.289
peak=    4.467 closest distance to " CB  PRO A  54 " =    0.987
peak=    4.458 closest distance to " O   HOH Z 234 " =    3.728
peak=    4.454 closest distance to " C   PRO A 198 " =    1.511
peak=    4.430 closest distance to " NH2BARG A 145 " =    2.114
peak=    4.423 closest distance to " O   HOH Z 124 " =    1.401
peak=    4.408 closest distance to " O   HOH Z 389 " =    1.940
peak=    4.406 closest distance to " CB  ARG A 190 " =    1.770
peak=    4.380 closest distance to " NZ  LYS A 117 " =    3.062
peak=    4.369 closest distance to " O   HOH Z 193 " =    1.694
peak=    4.364 closest distance to " O  BHOH Z  74 " =    1.282
peak=    4.342 closest distance to " O   HOH Z 154 " =    1.629
peak=    4.335 closest distance to " O   HOH Z 298 " =    1.822
peak=    4.327 closest distance to " O   HOH Z 402 " =    1.497
peak=    4.315 closest distance to " CG  ARG A  66 " =    1.019
peak=    4.300 closest distance to " O   SER A  87 " =    2.158
peak=    4.286 closest distance to " O   HOH Z 209 " =    2.294
peak=    4.222 closest distance to " CB  GLU A 128 " =    1.160
peak=    4.216 closest distance to " O   HOH Z  59 " =    2.167
peak=    4.190 closest distance to " O   GLY A  23 " =    2.378
peak=    4.187 closest distance to " O   HOH Z 134 " =    1.597
peak=    4.186 closest distance to " O   HOH Z  15 " =    2.145
peak=    4.184 closest distance to " O   HOH Z  39 " =    1.432
peak=    4.176 closest distance to " O   HOH Z 189 " =    2.100
peak=    4.162 closest distance to " O   HOH Z  63 " =    1.970
peak=    4.161 closest distance to " O   HOH Z 130 " =    2.634
peak=    4.144 closest distance to " O   HOH Z 357 " =    1.989
peak=    4.138 closest distance to " O   HOH Z 423 " =    1.878
peak=    4.137 closest distance to " O   HOH Z  44 " =    2.120
peak=    4.119 closest distance to " CG  PRO A 243 " =    1.191
peak=    4.118 closest distance to " O   HOH Z 247 " =    1.429
peak=    4.109 closest distance to " CG1 ILE A  33 " =    1.222
peak=    4.098 closest distance to " CG2BVAL A  41 " =    0.772
peak=    4.086 closest distance to " O   HOH Z 406 " =    1.571
peak=    4.053 closest distance to " CD  ARG A 269 " =    1.020
peak=    4.041 closest distance to " CB  TRP A 179 " =    1.181
peak=    4.029 closest distance to " O   HOH Z 368 " =    2.078
peak=    4.026 closest distance to " CD2 TRP A 179 " =    1.399
peak=    4.015 closest distance to " O   HOH Z 272 " =    1.876
peak=    4.007 closest distance to " O   HOH Z 227 " =    1.857
peak=    4.005 closest distance to " N   ASN A  39 " =    1.200
peak=    3.996 closest distance to " O   HOH Z  43 " =    1.585
peak=    3.996 closest distance to " O   HOH Z 142 " =    1.519
peak=    3.987 closest distance to " CB  SER A   3 " =    1.236
peak=    3.980 closest distance to " CA  ALA A  51 " =    0.989
peak=    3.976 closest distance to " O   HOH Z 245 " =    1.371
peak=    3.961 closest distance to " O   HOH Z 369 " =    2.505
peak=    3.955 closest distance to " CG2 ILE A 120 " =    1.172
peak=    3.954 closest distance to " CA  ARG A  36 " =    1.031
peak=    3.949 closest distance to " CB  ARG A  79 " =    1.373
peak=    3.927 closest distance to " CB  GLU A 277 " =    3.613
peak=    3.922 closest distance to " O   HOH Z 203 " =    1.857
peak=    3.915 closest distance to " O   HOH Z 345 " =    1.808
peak=    3.909 closest distance to " O   HOH Z 132 " =    2.175
peak=    3.890 closest distance to " CA  ASN A 176 " =    1.228
peak=    3.877 closest distance to " CB  GLU A 152 " =    1.125
peak=    3.871 closest distance to " CB  SER A 141 " =    1.021
peak=    3.869 closest distance to " CA  ARG A 195 " =    1.292
peak=    3.857 closest distance to " O   HOH Z 279 " =    2.089
peak=    3.836 closest distance to " NE2 GLN A  11 " =    0.952
peak=    3.835 closest distance to " CB  ASN A 148 " =    1.371
peak=    3.825 closest distance to " O   HOH Z 361 " =    3.087
peak=    3.811 closest distance to " CD  LYS A 166 " =    1.408
peak=    3.810 closest distance to " O   HOH Z 346 " =    1.642
peak=    3.810 closest distance to " O   HOH Z 265 " =    2.127
peak=    3.807 closest distance to " CB  SER A  62 " =    0.871
peak=    3.806 closest distance to " O   HOH Z 345 " =    2.575
peak=    3.803 closest distance to " CG AARG A 275 " =    1.182
peak=    3.776 closest distance to " C   ILE A 106 " =    1.819
peak=    3.776 closest distance to " O   HOH Z 128 " =    2.307
peak=    3.776 closest distance to " CE  LYS A 119 " =    1.158
peak=    3.774 closest distance to " O   HOH Z  20 " =    1.368
peak=    3.771 closest distance to " O   HOH Z 250 " =    1.429
peak=    3.763 closest distance to " O   HOH Z 316 " =    2.901
peak=    3.761 closest distance to " O   HOH Z 421 " =    2.009
peak=    3.755 closest distance to " O   HOH Z 334 " =    1.461
peak=    3.754 closest distance to " O   HOH Z 433 " =    1.442
peak=    3.748 closest distance to " O   HOH Z 126 " =    1.550
peak=    3.731 closest distance to " CB  ARG A 269 " =    0.838
peak=    3.728 closest distance to " O   HOH Z 414 " =    1.699
peak=    3.722 closest distance to " O   HOH Z 261 " =    1.952
peak=    3.719 closest distance to " CZ  PHE A  38 " =    1.309
peak=    3.708 closest distance to " O   HOH Z 298 " =    2.207
peak=    3.707 closest distance to " ND2 ASN A 187 " =    1.627
peak=    3.697 closest distance to " CZ  PHE A 218 " =    1.088
peak=    3.694 closest distance to " CB  ALA A 248 " =    1.358
peak=    3.691 closest distance to " OE1 GLU A   2 " =    2.192
peak=    3.688 closest distance to " NH2AARG A 145 " =    2.200
peak=    3.686 closest distance to " O   HOH Z 426 " =    1.429
peak=    3.685 closest distance to " CD2 LEU A 297 " =    0.956
peak=    3.681 closest distance to " CB  TYR A 169 " =    0.777
peak=    3.677 closest distance to " O   HOH Z 128 " =    1.970
peak=    3.676 closest distance to " O   HOH Z 365 " =    2.545
peak=    3.675 closest distance to " CB  VAL A 202 " =    1.471
peak=    3.672 closest distance to " O   HOH Z  21 " =    1.824
peak=    3.663 closest distance to " O   HOH Z  40 " =    1.860
peak=    3.663 closest distance to " O   HOH Z 126 " =    1.906
peak=    3.662 closest distance to " O   HOH Z 132 " =    1.101
peak=    3.661 closest distance to " O   ASN A  74 " =    1.830
peak=    3.659 closest distance to " O   HOH Z 173 " =    2.222
peak=    3.656 closest distance to " CA  ALA A  21 " =    1.294
peak=    3.652 closest distance to " O   HOH Z  61 " =    1.529
peak=    3.645 closest distance to " O   HOH Z 303 " =    2.121
peak=    3.644 closest distance to " O   HOH Z 109 " =    1.609
peak=    3.638 closest distance to " O   HOH Z 411 " =    3.624
peak=    3.635 closest distance to " C   GLY A  80 " =    1.149
peak=    3.634 closest distance to " O   HOH Z 380 " =    1.809
peak=    3.633 closest distance to " CD  ARG A 159 " =    0.827
peak=    3.632 closest distance to " CB  ASN A 285 " =    0.996
peak=    3.630 closest distance to " CG2 ILE A  20 " =    1.379
peak=    3.620 closest distance to " O   HOH Z 185 " =    1.745
peak=    3.612 closest distance to " CA  ASP A 162 " =    1.186
peak=    3.612 closest distance to " CB  LEU A 228 " =    1.128
peak=    3.611 closest distance to " OG BSER A 212 " =    2.598
peak=    3.606 closest distance to " O   HOH Z  78 " =    1.707
peak=    3.606 closest distance to " CB  SER A  26 " =    1.756
peak=    3.602 closest distance to " O   HOH Z 336 " =    1.704
peak=    3.601 closest distance to " O   HOH Z 371 " =    3.067
peak=    3.599 closest distance to " O   HOH Z  97 " =    2.303
peak=    3.591 closest distance to " O   HOH Z 408 " =    1.817
peak=    3.584 closest distance to " O   HOH Z 141 " =    1.730
peak=    3.582 closest distance to " CA  ALA A 160 " =    0.869
peak=    3.575 closest distance to " CD1 LEU A  96 " =    0.814
peak=    3.562 closest distance to " O   HOH Z 284 " =    2.879
peak=    3.543 closest distance to " O   HOH Z 427 " =    2.811
peak=    3.538 closest distance to " CG  GLN A  11 " =    1.344
peak=    3.538 closest distance to " CA  ALA A 248 " =    1.269
peak=    3.536 closest distance to " O   HOH Z 327 " =    1.652
peak=    3.529 closest distance to " CA  GLU A 152 " =    0.867
peak=    3.523 closest distance to " NH1AARG A 145 " =    1.285
peak=    3.523 closest distance to " CG1BVAL A  72 " =    1.747
peak=    3.523 closest distance to " O   HOH Z 158 " =    2.946
peak=    3.520 closest distance to " CB  THR A  52 " =    0.828
peak=    3.519 closest distance to " O   HOH Z  35 " =    2.148
peak=    3.516 closest distance to " CG2 VAL A 197 " =    1.171
peak=    3.509 closest distance to " O   HOH Z 287 " =    1.790
peak=    3.497 closest distance to " O   HOH Z 417 " =    3.072
peak=    3.495 closest distance to " CD  GLN A 194 " =    1.639
peak=    3.488 closest distance to " O   HOH Z 427 " =    3.017
peak=    3.487 closest distance to " NZ  LYS A  48 " =    1.190
peak=    3.483 closest distance to " CA  ALA A  84 " =    1.109
peak=    3.482 closest distance to " O   HOH Z 214 " =    1.347
peak=    3.477 closest distance to " OH  TYR A 116 " =    1.127
peak=    3.475 closest distance to " N   CYS A 260 " =    0.807
peak=    3.465 closest distance to " CB  TRP A 266 " =    1.092
peak=    3.464 closest distance to " O   HOH Z 291 " =    1.451
peak=    3.461 closest distance to " O   HOH Z 258 " =    2.225
peak=    3.458 closest distance to " CB  MET A  47 " =    0.946
peak=    3.455 closest distance to " O   HOH Z 163 " =    1.445
peak=    3.452 closest distance to " O   HOH Z 403 " =    1.434
peak=    3.449 closest distance to " OG  SER A  62 " =    2.824
peak=    3.444 closest distance to " CG2 THR A 221 " =    1.127
peak=    3.441 closest distance to " O   HOH Z  68 " =    1.913
peak=    3.438 closest distance to " CB  PRO A 198 " =    1.076
peak=    3.438 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.437 closest distance to " O   HOH Z 108 " =    2.705
peak=    3.436 closest distance to " O   HOH Z 132 " =    2.539
peak=    3.435 closest distance to " O   HOH Z 150 " =    1.467
peak=    3.422 closest distance to " O   HOH Z  66 " =    2.142
peak=    3.421 closest distance to " O   HOH Z 183 " =    1.550
peak=    3.420 closest distance to " NE2 GLN A  77 " =    3.230
peak=    3.419 closest distance to " O   HOH Z 374 " =    2.607
peak=    3.418 closest distance to " O   HOH Z 214 " =    2.403
peak=    3.415 closest distance to " CA  ASP A 191 " =    1.262
peak=    3.402 closest distance to " CB  TYR A 247 " =    0.968
peak=    3.400 closest distance to " CG2 VAL A 257 " =    0.801
peak=    3.397 closest distance to " CB  PHE A  16 " =    1.025
peak=    3.395 closest distance to " CA  LYS A 117 " =    1.295
peak=    3.389 closest distance to " O   HOH Z 193 " =    2.204
peak=    3.385 closest distance to " O   ALA A 165 " =    1.372
peak=    3.385 closest distance to " O   HOH Z 422 " =    2.613
peak=    3.384 closest distance to " OD2 ASP A 286 " =    2.803
peak=    3.383 closest distance to " CA  SER A  87 " =    1.044
peak=    3.383 closest distance to " CD  PRO A  54 " =    1.184
peak=    3.382 closest distance to " CD  ARG A 195 " =    0.931
peak=    3.380 closest distance to " CB  ASN A  39 " =    0.809
peak=    3.380 closest distance to " NH2 ARG A 156 " =    1.129
peak=    3.377 closest distance to " O   HOH Z 250 " =    1.844
peak=    3.376 closest distance to " O   HOH Z 313 " =    1.894
peak=    3.374 closest distance to " OG BSER A 164 " =    2.353
peak=    3.366 closest distance to " O   HOH Z 402 " =    2.907
peak=    3.364 closest distance to " CG  MET A 185 " =    1.147
peak=    3.364 closest distance to " CB  ARG A  79 " =    0.799
peak=    3.361 closest distance to " CA  ASN A 215 " =    1.083
peak=    3.358 closest distance to " O   THR A 220 " =    1.143
peak=    3.358 closest distance to " CB  ASP A 140 " =    1.001
peak=    3.356 closest distance to " O   HOH Z 147 " =    1.815
peak=    3.355 closest distance to " O   HOH Z 359 " =    1.514
peak=    3.351 closest distance to " OG  SER A 276 " =    1.431
peak=    3.350 closest distance to " O   HOH Z 344 " =    2.989
peak=    3.350 closest distance to " CB  VAL A 265 " =    1.208
peak=    3.347 closest distance to " CB  GLN A 278 " =    0.893
peak=    3.344 closest distance to " OG BSER A 258 " =    3.078
peak=    3.343 closest distance to " O   HOH Z 145 " =    2.447
peak=    3.335 closest distance to " O   HOH Z 419 " =    1.596
peak=    3.333 closest distance to " O   HOH Z 393 " =    3.368
peak=    3.333 closest distance to " NZ  LYS A 119 " =    1.608
peak=    3.332 closest distance to " OE1 GLN A  11 " =    1.880
peak=    3.330 closest distance to " CG2 THR A 220 " =    0.800
peak=    3.329 closest distance to " N   TRP A 150 " =    1.179
peak=    3.328 closest distance to " O   HOH Z  88 " =    3.296
peak=    3.328 closest distance to " CD  LYS A 119 " =    1.744
peak=    3.326 closest distance to " O   HOH Z 409 " =    3.429
peak=    3.324 closest distance to " O   SER A  26 " =    1.636
peak=    3.323 closest distance to " O   HOH Z 130 " =    2.563
peak=    3.319 closest distance to " CG  LEU A 167 " =    1.117
peak=    3.318 closest distance to " CA  LEU A  83 " =    1.249
peak=    3.317 closest distance to " O   HOH Z 358 " =    2.095
peak=    3.315 closest distance to " O   HOH Z 438 " =    2.111
peak=    3.307 closest distance to " CA  ARG A  66 " =    1.050
peak=    3.306 closest distance to " O   HOH Z 280 " =    2.554
peak=    3.301 closest distance to " CB  ALA A 291 " =    1.194
peak=    3.299 closest distance to " CA  THR A 221 " =    0.973
peak=    3.296 closest distance to " CB  MET A  40 " =    0.923
peak=    3.294 closest distance to " O   HOH Z 339 " =    1.238
peak=    3.290 closest distance to " CE1 TYR A 186 " =    1.328
peak=    3.282 closest distance to " O   HOH Z 437 " =    1.376
peak=    3.281 closest distance to " CG  GLN A  58 " =    2.455
peak=    3.280 closest distance to " C   PHE A  59 " =    0.785
peak=    3.278 closest distance to " CB  ASN A 215 " =    1.172
peak=    3.273 closest distance to " CA  ALA A 100 " =    1.200
peak=    3.271 closest distance to " CG2 VAL A  78 " =    0.806
peak=    3.266 closest distance to " O   HOH Z 282 " =    2.085
peak=    3.260 closest distance to " OD2 ASP A 298 " =    3.910
peak=    3.256 closest distance to " CA  PRO A  90 " =    0.931
peak=    3.256 closest distance to " CA  TRP A  85 " =    1.099
peak=    3.254 closest distance to " ND2 ASN A 209 " =    3.660
peak=    3.251 closest distance to " OD1 ASN A 148 " =    2.059
peak=    3.248 closest distance to " NH1AARG A 275 " =    0.976
peak=    3.248 closest distance to " O   HOH Z 130 " =    1.077
peak=    3.247 closest distance to " O   HOH Z  46 " =    1.357
peak=    3.247 closest distance to " CA  ASP A 191 " =    0.917
peak=    3.245 closest distance to " O   HOH Z 130 " =    2.443
peak=    3.233 closest distance to " O   HOH Z 171 " =    1.920
peak=    3.230 closest distance to " CA  THR A  82 " =    1.815
peak=    3.228 closest distance to " CB  SER A 273 " =    0.848
peak=    3.227 closest distance to " O   HOH Z 392 " =    2.380
peak=    3.222 closest distance to " OH  TYR A  30 " =    1.223
peak=    3.222 closest distance to " ND2 ASN A 249 " =    0.887
peak=    3.222 closest distance to " O   TRP A 274 " =    1.917
peak=    3.218 closest distance to " CA  VAL A  41 " =    0.929
peak=    3.207 closest distance to " O   HOH Z 353 " =    2.726
peak=    3.203 closest distance to " CG  ARG A 219 " =    1.268
peak=    3.193 closest distance to " O   ALA A 242 " =    1.037
peak=    3.192 closest distance to " OD1 ASP A 171 " =    1.313
peak=    3.191 closest distance to " O   HOH Z 425 " =    1.404
peak=    3.189 closest distance to " CD  ARG A 139 " =    1.219
peak=    3.184 closest distance to " O   CYS A 168 " =    1.451
peak=    3.183 closest distance to " NE1 TRP A 274 " =    0.860
peak=    3.182 closest distance to " CD1 LEU A 300 " =    1.241
peak=    3.178 closest distance to " OG1 THR A 221 " =    1.295
peak=    3.177 closest distance to " O   ALA A 158 " =    1.125
peak=    3.176 closest distance to " O   THR A 251 " =    1.207
peak=    3.174 closest distance to " O   HOH Z 383 " =    2.183
peak=    3.174 closest distance to " CG2 ILE A 106 " =    0.946
peak=    3.173 closest distance to " O   HOH Z  48 " =    1.619
peak=    3.169 closest distance to " CD2 HIS A  81 " =    1.098
peak=    3.166 closest distance to " CA  THR A  42 " =    0.944
peak=    3.166 closest distance to " O   HOH Z 156 " =    2.631
peak=    3.162 closest distance to " CD  GLN A 240 " =    1.425
peak=    3.158 closest distance to " N   TYR A 116 " =    1.603
peak=    3.158 closest distance to " CA  ASP A 140 " =    1.107
peak=    3.156 closest distance to " O   HOH Z 423 " =    3.448
peak=    3.155 closest distance to " CZ3 TRP A 266 " =    1.061
peak=    3.148 closest distance to " CD1 LEU A 222 " =    0.770
peak=    3.144 closest distance to " NH1 ARG A  14 " =    1.230
peak=    3.144 closest distance to " O   HOH Z  47 " =    1.436
peak=    3.143 closest distance to " OG BSER A 134 " =    2.877
peak=    3.140 closest distance to " CB  THR A  31 " =    1.685
peak=    3.139 closest distance to " CB  HIS A 108 " =    0.836
peak=    3.138 closest distance to " CG AARG A 190 " =    1.324
peak=    3.137 closest distance to " O   HOH Z 375 " =    2.145
peak=    3.137 closest distance to " O   HOH Z 305 " =    3.601
peak=    3.131 closest distance to " O   HOH Z   9 " =    2.422
peak=    3.129 closest distance to " O   HOH Z 250 " =    1.879
peak=    3.126 closest distance to " CA  ALA A 291 " =    0.818
peak=    3.125 closest distance to " CA  GLY A 196 " =    1.060
peak=    3.121 closest distance to " O   HOH Z 394 " =    1.616
peak=    3.119 closest distance to " OG  SER A 245 " =    1.489
peak=    3.113 closest distance to " NH1 ARG A 269 " =    0.752
peak=    3.108 closest distance to " O   ILE A  33 " =    1.329
peak=    3.101 closest distance to " CA  THR A 221 " =    1.313
peak=    3.099 closest distance to " O   GLY A  91 " =    1.294
peak=    3.093 closest distance to " CB  LYS A 289 " =    0.999
peak=    3.092 closest distance to " NZ  LYS A 117 " =    2.021
peak=    3.092 closest distance to " O   HOH Z 112 " =    2.977
peak=    3.087 closest distance to " CB  ALA A  71 " =    1.287
peak=    3.087 closest distance to " O   HOH Z 236 " =    1.433
peak=    3.086 closest distance to " O   TYR A 116 " =    1.536
peak=    3.077 closest distance to " ND1 HIS A  81 " =    1.487
peak=    3.073 closest distance to " O   HOH Z 298 " =    1.932
peak=    3.072 closest distance to " CB  ALA A 114 " =    0.750
peak=    3.061 closest distance to " O   HOH Z 152 " =    1.699
peak=    3.060 closest distance to " CA  VAL A 126 " =    1.166
peak=    3.050 closest distance to " OD1 ASN A  69 " =    2.451
peak=    3.041 closest distance to " OE1 GLN A  58 " =    3.269
peak=    3.040 closest distance to " O   HOH Z 129 " =    3.498
peak=    3.034 closest distance to " O   HOH Z 111 " =    1.731

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.823 - 5.710
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.823 - 5.710

peak=   -4.908 closest distance to " O   HOH Z 266 " =    4.675
peak=   -4.720 closest distance to " C   HIS A 108 " =    1.021
peak=   -4.423 closest distance to " O   HOH Z 210 " =    0.823
peak=   -4.345 closest distance to " CD  ARG A 156 " =    2.066
peak=   -4.260 closest distance to " OXT GLY A 302 " =    2.892
peak=   -4.202 closest distance to " SG  CYS A 254 " =    3.328
peak=   -4.178 closest distance to " O   HOH Z  13 " =    1.730
peak=   -4.175 closest distance to " CA  VAL A  67 " =    2.896
peak=   -4.090 closest distance to " CG  MET A  93 " =    2.465
peak=   -4.037 closest distance to " C   THR A 279 " =    1.181
peak=   -4.027 closest distance to " O   PRO A 163 " =    2.064
peak=   -4.026 closest distance to " CG  GLN A  58 " =    1.046
peak=   -4.015 closest distance to " O   HOH Z 165 " =    1.926
peak=   -3.955 closest distance to " CG2 ILE A  49 " =    2.658
peak=   -3.938 closest distance to " O   PRO A 198 " =    1.330
peak=   -3.936 closest distance to " ND2 ASN A  45 " =    1.062
peak=   -3.908 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.907 closest distance to " OG BSER A 134 " =    1.453
peak=   -3.904 closest distance to " O   HOH Z 422 " =    1.276
peak=   -3.902 closest distance to " O   HOH Z 377 " =    2.022
peak=   -3.899 closest distance to " CG  GLN A  58 " =    1.190
peak=   -3.880 closest distance to " O   PHE A 218 " =    1.456
peak=   -3.870 closest distance to " OG  SER A  97 " =    2.144
peak=   -3.868 closest distance to " O   HOH Z 166 " =    1.840
peak=   -3.846 closest distance to " O   HOH Z 372 " =    2.294
peak=   -3.823 closest distance to " O   ALA A  34 " =    2.309
peak=   -3.806 closest distance to " O   VAL A  67 " =    2.708
peak=   -3.778 closest distance to " ND2 ASN A  69 " =    1.561
peak=   -3.778 closest distance to " CZ  TYR A 169 " =    1.854
peak=   -3.770 closest distance to " OD2 ASP A 171 " =    2.361
peak=   -3.765 closest distance to " CB  ALA A 161 " =    2.577
peak=   -3.765 closest distance to " CB  PHE A 192 " =    1.965
peak=   -3.756 closest distance to " CG  GLU A  53 " =    1.277
peak=   -3.744 closest distance to " CG  ARG A 219 " =    2.417
peak=   -3.738 closest distance to " CB  PHE A 208 " =    2.325
peak=   -3.712 closest distance to " CD2 LEU A 237 " =    2.239
peak=   -3.675 closest distance to " O   SER A 210 " =    1.866
peak=   -3.668 closest distance to " CD2 LEU A 237 " =    2.449
peak=   -3.667 closest distance to " CE2 TYR A  30 " =    2.735
peak=   -3.649 closest distance to " O   TRP A  92 " =    1.886
peak=   -3.642 closest distance to " O   HOH Z 351 " =    1.444
peak=   -3.636 closest distance to " O   HOH Z 353 " =    2.176
peak=   -3.636 closest distance to " ND2 ASN A 187 " =    1.513
peak=   -3.616 closest distance to " O   HOH Z  71 " =    1.805
peak=   -3.615 closest distance to " O   VAL A 174 " =    2.039
peak=   -3.611 closest distance to " CB  ALA A  10 " =    2.251
peak=   -3.606 closest distance to " O   HOH Z 196 " =    1.764
peak=   -3.602 closest distance to " CD  ARG A 139 " =    1.613
peak=   -3.593 closest distance to " CA  TYR A  68 " =    2.859
peak=   -3.591 closest distance to " O   HOH Z 198 " =    1.854
peak=   -3.573 closest distance to " CG1 VAL A 112 " =    2.687
peak=   -3.568 closest distance to " CH2 TRP A 179 " =    1.307
peak=   -3.565 closest distance to " O   ALA A 256 " =    1.521
peak=   -3.562 closest distance to " CA  GLY A 133 " =    1.917
peak=   -3.556 closest distance to " O   HOH Z  15 " =    1.530
peak=   -3.553 closest distance to " O   GLN A  11 " =    1.238
peak=   -3.539 closest distance to " N   ALA A  43 " =    2.690
peak=   -3.538 closest distance to " O   HOH Z 234 " =    4.048
peak=   -3.536 closest distance to " O   ALA A   1 " =    2.010
peak=   -3.533 closest distance to " CD1 LEU A  25 " =    2.487
peak=   -3.519 closest distance to " N   ALA A 248 " =    1.754
peak=   -3.513 closest distance to " CD  LYS A 289 " =    2.458
peak=   -3.510 closest distance to " O   HOH Z  88 " =    4.470
peak=   -3.504 closest distance to " CD  GLN A 223 " =    1.533
peak=   -3.502 closest distance to " CD  ARG A 195 " =    5.084
peak=   -3.500 closest distance to " ND2 ASN A  45 " =    1.124
peak=   -3.497 closest distance to " CD1 PHE A  59 " =    1.969
peak=   -3.494 closest distance to " O   GLY A  80 " =    2.412
peak=   -3.491 closest distance to " CG1 VAL A  78 " =    2.814
peak=   -3.490 closest distance to " OE2 GLU A   2 " =    1.617
peak=   -3.488 closest distance to " N   SER A 276 " =    1.410
peak=   -3.487 closest distance to " O   HOH Z 407 " =    2.951
peak=   -3.472 closest distance to " CE1 TYR A 247 " =    2.542
peak=   -3.472 closest distance to " CG1AVAL A  41 " =    2.553
peak=   -3.470 closest distance to " CB  ALA A 184 " =    2.321
peak=   -3.467 closest distance to " NE2 GLN A  88 " =    1.716
peak=   -3.465 closest distance to " CE  LYS A 166 " =    2.899
peak=   -3.465 closest distance to " CH2 TRP A 150 " =    1.072
peak=   -3.464 closest distance to " NE2 GLN A 223 " =    1.304
peak=   -3.459 closest distance to " O   HOH Z 197 " =    1.913
peak=   -3.457 closest distance to " CG  PRO A 243 " =    1.613
peak=   -3.456 closest distance to " O   HOH Z  56 " =    1.077
peak=   -3.455 closest distance to " CB  LEU A 167 " =    2.194
peak=   -3.443 closest distance to " CA  GLY A 203 " =    2.344
peak=   -3.441 closest distance to " O   HOH Z  11 " =    1.742
peak=   -3.434 closest distance to " ND2 ASN A  39 " =    1.155
peak=   -3.433 closest distance to " O  BHOH Z 338 " =    1.264
peak=   -3.430 closest distance to " CD  PRO A 198 " =    1.215
peak=   -3.422 closest distance to " O   HOH Z   5 " =    1.568
peak=   -3.420 closest distance to " O   HOH Z 392 " =    1.418
peak=   -3.417 closest distance to " N   THR A  52 " =    1.706
peak=   -3.417 closest distance to " CG  ASP A 132 " =    2.327
peak=   -3.414 closest distance to " O   HOH Z 126 " =    1.990
peak=   -3.413 closest distance to " O   HOH Z 418 " =    1.429
peak=   -3.411 closest distance to " CB  ALA A 248 " =    2.168
peak=   -3.408 closest distance to " O   HOH Z 290 " =    1.056
peak=   -3.406 closest distance to " N   THR A 235 " =    1.341
peak=   -3.405 closest distance to " CZ  ARG A  66 " =    1.058
peak=   -3.402 closest distance to " O   HOH Z 102 " =    1.749
peak=   -3.397 closest distance to " CB  PRO A 213 " =    1.548
peak=   -3.389 closest distance to " C   SER A 206 " =    1.623
peak=   -3.380 closest distance to " OD1 ASN A 148 " =    1.528
peak=   -3.379 closest distance to " CD2 PHE A  61 " =    2.129
peak=   -3.371 closest distance to " OG BSER A 210 " =    2.319
peak=   -3.361 closest distance to " O   ALA A 160 " =    1.516
peak=   -3.359 closest distance to " OD1 ASN A  39 " =    2.219
peak=   -3.357 closest distance to " NH2 ARG A  66 " =    5.545
peak=   -3.356 closest distance to " CB  ALA A 291 " =    2.348
peak=   -3.353 closest distance to " OD2 ASP A 191 " =    1.497
peak=   -3.352 closest distance to " O   SER A  95 " =    1.661
peak=   -3.351 closest distance to " NE2 GLN A 194 " =    1.868
peak=   -3.351 closest distance to " OG  SER A   3 " =    1.599
peak=   -3.336 closest distance to " O   HOH Z 145 " =    2.264
peak=   -3.335 closest distance to " O   GLU A 152 " =    1.436
peak=   -3.332 closest distance to " O   HOH Z 377 " =    1.901
peak=   -3.327 closest distance to " O   HOH Z 171 " =    2.216
peak=   -3.320 closest distance to " O   HOH Z 301 " =    2.263
peak=   -3.319 closest distance to " O   HOH Z 114 " =    3.498
peak=   -3.316 closest distance to " O   ASN A  45 " =    1.788
peak=   -3.303 closest distance to " O   SER A 135 " =    1.565
peak=   -3.300 closest distance to " CD1 ILE A 106 " =    2.175
peak=   -3.299 closest distance to " O   HOH Z 265 " =    2.329
peak=   -3.294 closest distance to " O   HOH Z 401 " =    0.918
peak=   -3.291 closest distance to " O   HOH Z 427 " =    1.410
peak=   -3.290 closest distance to " CD2 TYR A 293 " =    1.816
peak=   -3.281 closest distance to " O   LEU A 300 " =    2.470
peak=   -3.280 closest distance to " O   ALA A 161 " =    1.450
peak=   -3.278 closest distance to " N   GLN A  58 " =    1.601
peak=   -3.278 closest distance to " O   SER A   3 " =    1.046
peak=   -3.277 closest distance to " CD2 TYR A 247 " =    2.329
peak=   -3.277 closest distance to " CD1 TRP A 179 " =    1.158
peak=   -3.277 closest distance to " O   HOH Z 174 " =    3.661
peak=   -3.268 closest distance to " O   HOH Z 150 " =    2.173
peak=   -3.267 closest distance to " NE2 GLN A  88 " =    1.108
peak=   -3.266 closest distance to " OG1 THR A   4 " =    1.818
peak=   -3.266 closest distance to " O   ASN A 187 " =    1.465
peak=   -3.263 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.263 closest distance to " OD1 ASP A 191 " =    1.456
peak=   -3.262 closest distance to " CE3 TRP A 150 " =    2.246
peak=   -3.260 closest distance to " O   HOH Z 135 " =    1.584
peak=   -3.259 closest distance to " CA  VAL A 197 " =    0.990
peak=   -3.257 closest distance to " N   GLY A  17 " =    1.660
peak=   -3.248 closest distance to " CG  PHE A 225 " =    1.364
peak=   -3.244 closest distance to " O   GLY A  75 " =    1.806
peak=   -3.239 closest distance to " O   GLY A 196 " =    0.965
peak=   -3.238 closest distance to " NE2 GLN A 103 " =    1.678
peak=   -3.237 closest distance to " CD1 LEU A 228 " =    2.179
peak=   -3.233 closest distance to " O   LEU A 282 " =    2.176
peak=   -3.232 closest distance to " CG2 VAL A 189 " =    2.219
peak=   -3.230 closest distance to " O   HOH Z 396 " =    1.666
peak=   -3.227 closest distance to " O   HOH Z 423 " =    2.362
peak=   -3.224 closest distance to " O   HOH Z 361 " =    3.403
peak=   -3.222 closest distance to " NH1 ARG A 195 " =    2.331
peak=   -3.220 closest distance to " CG  LYS A 119 " =    2.897
peak=   -3.215 closest distance to " N   SER A 134 " =    1.224
peak=   -3.211 closest distance to " O   HOH Z 414 " =    1.971
peak=   -3.206 closest distance to " CZ  PHE A  38 " =    2.003
peak=   -3.200 closest distance to " O   SER A 146 " =    1.061
peak=   -3.196 closest distance to " CD2 LEU A 300 " =    2.757
peak=   -3.192 closest distance to " O   HOH Z 185 " =    2.387
peak=   -3.182 closest distance to " O   HOH Z 366 " =    1.723
peak=   -3.180 closest distance to " O   HOH Z 283 " =    1.992
peak=   -3.179 closest distance to " O   HOH Z 281 " =    2.376
peak=   -3.178 closest distance to " C   ASN A 285 " =    2.209
peak=   -3.178 closest distance to " O   VAL A 189 " =    2.598
peak=   -3.174 closest distance to " O   HOH Z  19 " =    2.307
peak=   -3.173 closest distance to " OE1 GLN A 183 " =    1.468
peak=   -3.169 closest distance to " CG  ASP A 231 " =    0.867
peak=   -3.167 closest distance to " O   HOH Z 252 " =    3.181
peak=   -3.164 closest distance to " NH2 ARG A  66 " =    1.769
peak=   -3.161 closest distance to " CB  GLU A 277 " =    1.388
peak=   -3.160 closest distance to " CB  ASP A 286 " =    1.982
peak=   -3.157 closest distance to " C   GLY A  91 " =    1.281
peak=   -3.152 closest distance to " OG1 THR A  82 " =    1.308
peak=   -3.150 closest distance to " O   HOH Z 389 " =    1.692
peak=   -3.150 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.147 closest distance to " O   HOH Z 109 " =    5.710
peak=   -3.143 closest distance to " NH1 ARG A 195 " =    2.620
peak=   -3.142 closest distance to " N   VAL A 189 " =    1.658
peak=   -3.141 closest distance to " O   HOH Z 252 " =    4.150
peak=   -3.140 closest distance to " N   ALA A 226 " =    1.892
peak=   -3.136 closest distance to " O   HOH Z   6 " =    1.804
peak=   -3.131 closest distance to " O   HOH Z  78 " =    1.713
peak=   -3.126 closest distance to " O   HOH Z 111 " =    3.656
peak=   -3.125 closest distance to " O   HOH Z 166 " =    1.626
peak=   -3.121 closest distance to " CB  SER A 210 " =    1.189
peak=   -3.116 closest distance to " O   HOH Z 280 " =    2.287
peak=   -3.110 closest distance to " O   HOH Z 120 " =    1.341
peak=   -3.110 closest distance to " OG  SER A 273 " =    2.160
peak=   -3.107 closest distance to " O   VAL A 189 " =    1.893
peak=   -3.103 closest distance to " O   HOH Z  41 " =    2.208
peak=   -3.102 closest distance to " C   ALA A 158 " =    1.354
peak=   -3.101 closest distance to " OG  SER A  26 " =    1.297
peak=   -3.081 closest distance to " O   HOH Z 222 " =    1.345
peak=   -3.072 closest distance to " CA  GLU A   2 " =    2.470
peak=   -3.067 closest distance to " CD1 ILE A 239 " =    2.282
peak=   -3.066 closest distance to " CB  GLN A  11 " =    1.594
peak=   -3.066 closest distance to " O   HOH Z 139 " =    3.291
peak=   -3.063 closest distance to " OD2 ASP A 171 " =    1.754
peak=   -3.054 closest distance to " CB  TRP A  85 " =    2.452
peak=   -3.046 closest distance to " CB  ALA A  43 " =    2.403
peak=   -3.026 closest distance to " O   HOH Z 422 " =    1.467
peak=   -3.026 closest distance to " C   ALA A 242 " =    1.893

================= 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    :  0.4388 0.4280   6.251210e+00   6.233908e+00
   1_bss:  0.4298 0.4160   6.240401e+00   6.219156e+00
   1_xyz:  0.2884 0.3143   5.933325e+00   6.003073e+00
   1_adp:  0.2608 0.3231   5.880079e+00   6.024418e+00
   1_occ:  0.2606 0.3234   5.879713e+00   6.024471e+00
   2_bss:  0.2572 0.3211   5.872115e+00   6.018779e+00
   2_xyz:  0.1872 0.2362   5.582442e+00   5.762773e+00
   2_adp:  0.1723 0.2186   5.511746e+00   5.697611e+00
   2_occ:  0.1720 0.2185   5.510872e+00   5.697391e+00
   3_bss:  0.1719 0.2177   5.510375e+00   5.694778e+00
   3_xyz:  0.1383 0.1870   5.325182e+00   5.544210e+00
   3_adp:  0.1281 0.1757   5.260145e+00   5.486214e+00
   3_occ:  0.1280 0.1757   5.259754e+00   5.485796e+00
   4_bss:  0.1283 0.1755   5.260421e+00   5.484607e+00
   4_xyz:  0.1176 0.1648   5.190763e+00   5.425978e+00
   4_adp:  0.1151 0.1630   5.175366e+00   5.414486e+00
   4_occ:  0.1151 0.1631   5.175328e+00   5.414636e+00
   5_bss:  0.1150 0.1631   5.175362e+00   5.414707e+00
   5_xyz:  0.1162 0.1633   5.183964e+00   5.418576e+00
   5_adp:  0.1156 0.1641   5.183439e+00   5.423361e+00
   5_occ:  0.1156 0.1641   5.183224e+00   5.423237e+00
   5_bss:  0.1155 0.1641   5.183281e+00   5.423323e+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:  0.308  26.941  -0.736   4.160  -1.622   0.000  -0.000  -0.000
   1_xyz:  0.308  26.941  -0.736   4.160  -1.622   0.000  -0.000  -0.000
   1_adp:  0.308  26.941  -0.736   4.160  -1.622   0.000  -0.000  -0.000
   1_occ:  0.308  26.941  -0.736   4.160  -1.622   0.000  -0.000  -0.000
   2_bss:  0.317  46.225  -1.984   1.235  -1.004   0.000  -0.000  -0.000
   2_xyz:  0.317  46.225  -1.984   1.235  -1.004   0.000  -0.000  -0.000
   2_adp:  0.317  46.225  -1.984   1.235  -1.004   0.000  -0.000  -0.000
   2_occ:  0.317  46.225  -1.984   1.235  -1.004   0.000  -0.000  -0.000
   3_bss:  0.320  46.225  -2.488  -0.168  -0.975  -0.000  -0.000  -0.000
   3_xyz:  0.320  46.225  -2.488  -0.168  -0.975  -0.000  -0.000  -0.000
   3_adp:  0.320  46.225  -2.488  -0.168  -0.975  -0.000  -0.000  -0.000
   3_occ:  0.320  46.225  -2.488  -0.168  -0.975  -0.000  -0.000  -0.000
   4_bss:  0.324  53.462  -2.724  -0.910  -1.053  -0.000  -0.000  -0.000
   4_xyz:  0.324  53.462  -2.724  -0.910  -1.053  -0.000  -0.000  -0.000
   4_adp:  0.324  53.462  -2.724  -0.910  -1.053  -0.000  -0.000  -0.000
   4_occ:  0.324  53.462  -2.724  -0.910  -1.053  -0.000  -0.000  -0.000
   5_bss:  0.324  53.462  -2.614  -0.962  -0.904  -0.000  -0.000  -0.000
   5_xyz:  0.324  53.462  -2.614  -0.962  -0.904  -0.000  -0.000  -0.000
   5_adp:  0.324  53.462  -2.614  -0.962  -0.904  -0.000  -0.000  -0.000
   5_occ:  0.324  53.462  -2.614  -0.962  -0.904  -0.000  -0.000  -0.000
   5_bss:  0.322  53.969  -2.448  -0.865  -0.720  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.935 0.5228  0.6972    57563.628
   1_bss:  48.682 0.5371  0.7330    53924.795
   1_xyz:  33.634 0.7170  0.9281    27192.727
   1_adp:  34.842 0.7023  0.9071    28815.335
   1_occ:  34.863 0.7020  0.9060    28827.875
   2_bss:  34.372 0.7075  0.8790    28087.315
   2_xyz:  23.854 0.8221  0.9784    14404.419
   2_adp:  21.444 0.8476  0.9901    12388.227
   2_occ:  21.435 0.8476  0.9901    12370.067
   3_bss:  21.336 0.8485  0.9694    12253.695
   3_xyz:  17.710 0.8826  0.9892     8843.144
   3_adp:  16.380 0.8947  0.9872     7903.951
   3_occ:  16.369 0.8948  0.9872     7894.693
   4_bss:  16.326 0.8952  0.9760     7858.196
   4_xyz:  15.071 0.9060  0.9801     6959.488
   4_adp:  14.778 0.9086  0.9746     6839.744
   4_occ:  14.779 0.9086  0.9745     6839.729
   5_bss:  14.778 0.9086  0.9771     6839.985
   5_xyz:  14.755 0.9090  0.9772     6825.792
   5_adp:  14.828 0.9084  0.9698     6873.635
   5_occ:  14.822 0.9085  0.9697     6870.686
   5_bss:  14.824 0.9085  0.9750     6870.996
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9267e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9267e-01
   1_xyz:   1.597  0.014  0.095 15.986  0.007  4.105   1.3675e-01
   1_adp:   1.597  0.014  0.095 15.986  0.007  4.105   1.3675e-01
   1_occ:   1.597  0.014  0.095 15.986  0.007  4.105   1.3675e-01
   2_bss:   1.597  0.014  0.095 15.986  0.007  4.105   1.3675e-01
   2_xyz:   1.143  0.008  0.076 14.650  0.005  4.121   7.2488e-02
   2_adp:   1.143  0.008  0.076 14.650  0.005  4.121   7.2488e-02
   2_occ:   1.143  0.008  0.076 14.650  0.005  4.121   7.2488e-02
   3_bss:   1.143  0.008  0.076 14.650  0.005  4.121   7.2488e-02
   3_xyz:   1.088  0.008  0.073 14.794  0.004  4.108   6.7850e-02
   3_adp:   1.088  0.008  0.073 14.794  0.004  4.108   6.7850e-02
   3_occ:   1.088  0.008  0.073 14.794  0.004  4.108   6.7850e-02
   4_bss:   1.088  0.008  0.073 14.794  0.004  4.108   6.7850e-02
   4_xyz:   1.070  0.008  0.076 14.770  0.004  4.113   6.5724e-02
   4_adp:   1.070  0.008  0.076 14.770  0.004  4.113   6.5724e-02
   4_occ:   1.070  0.008  0.076 14.770  0.004  4.113   6.5724e-02
   5_bss:   1.070  0.008  0.076 14.770  0.004  4.113   6.5724e-02
   5_xyz:   0.925  0.006  0.068 14.431  0.004  4.113   5.1355e-02
   5_adp:   0.925  0.006  0.068 14.431  0.004  4.113   5.1355e-02
   5_occ:   0.925  0.006  0.068 14.431  0.004  4.113   5.1355e-02
   5_bss:   0.925  0.006  0.068 14.431  0.004  4.113   5.1355e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.188   2.4177e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.188   2.4177e-01
   1_xyz:   9.593  0.131  0.368 84.631  0.051  1.995   1.2652e-01
   1_adp:   9.593  0.131  0.368 84.631  0.051  1.995   1.2652e-01
   1_occ:   9.593  0.131  0.368 84.631  0.051  1.995   1.2652e-01
   2_bss:   9.593  0.131  0.368 84.631  0.051  1.995   1.2652e-01
   2_xyz:   8.669  0.045  0.260 83.252  0.054  2.271   1.0613e-01
   2_adp:   8.669  0.045  0.260 83.252  0.054  2.271   1.0613e-01
   2_occ:   8.669  0.045  0.260 83.252  0.054  2.271   1.0613e-01
   3_bss:   8.669  0.045  0.260 83.252  0.054  2.271   1.0613e-01
   3_xyz:   8.354  0.052  0.243 81.914  0.045  2.299   6.2285e-02
   3_adp:   8.354  0.052  0.243 81.914  0.045  2.299   6.2285e-02
   3_occ:   8.354  0.052  0.243 81.914  0.045  2.299   6.2285e-02
   4_bss:   8.354  0.052  0.243 81.914  0.045  2.299   6.2285e-02
   4_xyz:   7.434  0.050  0.236 82.214  0.038  2.270   4.7575e-02
   4_adp:   7.434  0.050  0.236 82.214  0.038  2.270   4.7575e-02
   4_occ:   7.434  0.050  0.236 82.214  0.038  2.270   4.7575e-02
   5_bss:   7.434  0.050  0.236 82.214  0.038  2.270   4.7575e-02
   5_xyz:   6.758  0.045  0.216 81.039  0.033  2.410   2.9719e-02
   5_adp:   6.758  0.045  0.216 81.039  0.033  2.410   2.9719e-02
   5_occ:   6.758  0.045  0.216 81.039  0.033  2.410   2.9719e-02
   5_bss:   6.758  0.045  0.216 81.039  0.033  2.410   2.9719e-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:  87.43   0.00  18.07  84.00   0.00  14.19  87.43   3.96  39.19
   1_occ:  87.43   0.00  18.07  84.00   0.00  14.19  87.43   3.96  39.19
   2_bss:  87.43   0.00  18.07  84.00   0.00  14.19  87.43   3.96  39.19
   2_xyz:  87.43   0.00  18.07  84.00   0.00  14.19  87.43   3.96  39.19
   2_adp: 119.50   0.00  17.79 119.50   0.00  13.70  85.43   4.26  40.04
   2_occ: 119.50   0.00  17.79 119.50   0.00  13.70  85.43   4.26  40.04
   3_bss: 119.50   0.00  17.79 119.50   0.00  13.70  85.43   4.26  40.04
   3_xyz: 119.50   0.00  17.79 119.50   0.00  13.70  85.43   4.26  40.04
   3_adp:  86.51   1.18  17.42  86.42   1.18  13.00  86.51   5.65  41.47
   3_occ:  86.51   1.18  17.42  86.42   1.18  13.00  86.51   5.65  41.47
   4_bss:  86.51   1.18  17.42  86.42   1.18  13.00  86.51   5.65  41.47
   4_xyz:  86.51   1.18  17.42  86.42   1.18  13.00  86.51   5.65  41.47
   4_adp:  92.68   0.85  17.11  92.68   0.85  12.71  87.00   1.43  41.06
   4_occ:  92.68   0.85  17.11  92.68   0.85  12.71  87.00   1.43  41.06
   5_bss:  92.68   0.85  17.11  92.68   0.85  12.71  87.00   1.43  41.06
   5_xyz:  92.68   0.85  17.11  92.68   0.85  12.71  87.00   1.43  41.06
   5_adp: 104.03   0.00  17.07 104.03   0.00  12.60  90.43   1.78  41.42
   5_occ: 104.03   0.00  17.07 104.03   0.00  12.60  90.43   1.78  41.42
   5_bss: 104.04   0.00  17.08 104.04   0.00  12.61  90.44   1.78  41.42
------------------------------------------------------------------------
 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:    2.178    0.032    0.469
   1_adp:    2.178    0.032    0.469
   1_occ:    2.178    0.032    0.469
   2_bss:    2.178    0.032    0.469
   2_xyz:    1.973    0.035    0.584
   2_adp:    1.973    0.035    0.584
   2_occ:    1.973    0.035    0.584
   3_bss:    1.973    0.035    0.584
   3_xyz:    1.799    0.052    0.681
   3_adp:    1.799    0.052    0.681
   3_occ:    1.799    0.052    0.681
   4_bss:    1.799    0.052    0.681
   4_xyz:    1.589    0.041    0.709
   4_adp:    1.589    0.041    0.709
   4_occ:    1.589    0.041    0.709
   5_bss:    1.589    0.041    0.709
   5_xyz:    1.547    0.060    0.718
   5_adp:    1.547    0.060    0.718
   5_occ:    1.547    0.060    0.718
   5_bss:    1.547    0.060    0.718
------------------------------------------------------------------------

CPU time actual refinement: 350.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_224/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_224/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_224/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_224/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_224/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.67 
  Macro-tasks:
    bulk solvent and scale       = 39.68  
    individual site refinement   = 151.61 
    weights calculation          = 30.44  
    collect and process          = 6.66   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 228.49 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 112.92 
    alpha_beta                      = 8.40   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 123.14 
    fmodel                         = 6.63   
    r_factors                      = 0.23   
    phase_errors                   = 10.85  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 265.40 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.862 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    665 calls, 112.46 s
gradients_fft:          610 calls, 108.84 s

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

# Date 2008-01-16 Time 04:19:15 PST -0800 (1200485955.87 s)
Start R-work = 0.4388, R-free = 0.4280 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1811 (no bulk solvent and anisotropic scale)

Start R-work = 0.4298, R-free = 0.4160
Final R-work = 0.1155, R-free = 0.1641