# Date 2008-01-16 Time 04:43:03 PST -0800 (1200487383.43 s)
#phil __OFF__

Command line arguments: "../429.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31196
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 429

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.1647, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95135
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7820
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95135
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7824 -  4.1754 [2183/2211]  1965   218  10.0%
  bin  2:  4.1754 -  3.3266 [2081/2104]  1873   208  10.0%
  bin  3:  3.3266 -  2.9097 [2057/2082]  1847   210  10.2%
  bin  4:  2.9097 -  2.6454 [2051/2067]  1853   198   9.7%
  bin  5:  2.6454 -  2.4567 [2034/2072]  1824   210  10.3%
  bin  6:  2.4567 -  2.3124 [2022/2055]  1829   193   9.5%
  bin  7:  2.3124 -  2.1970 [1997/2034]  1792   205  10.3%
  bin  8:  2.1970 -  2.1016 [1996/2038]  1797   199  10.0%
  bin  9:  2.1016 -  2.0209 [2009/2047]  1808   201  10.0%
  bin 10:  2.0209 -  1.9514 [1159/2024]  1042   117  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_429/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:
        1.41 -     2.10: 23
        2.10 -     2.80: 792
        2.80 -     3.50: 4534
        3.50 -     4.20: 9452
        4.20 -     4.90: 13963
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.406 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.577 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.608 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.684 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.720 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28759 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_429/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_429/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.16465 84.23025 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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3950   r_free= 0.3909   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.189030                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6571 0.99   1412  157 0.3226 0.3323      6.4616      6.4522|
|  2:  4.6571 -  3.7158 0.99   1365  148 0.3249 0.3043      6.6418      6.6065|
|  3:  3.7158 -  3.2518 0.99   1328  154 0.3465 0.3573      6.5192       6.671|
|  4:  3.2518 -  2.9571 0.99   1327  146 0.3705 0.3713      6.3848      6.4009|
|  5:  2.9571 -  2.7466 0.98   1319  147 0.4028 0.3652      6.2614      6.2121|
|  6:  2.7466 -  2.5855 0.99   1301  143 0.4206 0.4233      6.1694      6.1068|
|  7:  2.5855 -  2.4567 0.99   1310  149 0.4239 0.3500       6.163      6.0828|
|  8:  2.4567 -  2.3502 0.99   1289  140 0.4296 0.4497      6.0958       6.139|
|  9:  2.3502 -  2.2600 0.99   1301  146 0.4446 0.4347      6.0615      6.0602|
| 10:  2.2600 -  2.1823 0.98   1292  139 0.4473 0.4802      6.0404      6.0859|
| 11:  2.1823 -  2.1142 0.98   1274  142 0.4705 0.4803      5.9872      6.0459|
| 12:  2.1142 -  2.0540 1.00   1293  144 0.4423 0.4546      5.9142      5.9395|
| 13:  2.0540 -  2.0000 0.96   1265  140 0.4673 0.4850      5.8274        5.84|
| 14:  2.0000 -  1.9514 0.42    554   64 0.5192 0.4696      5.8478      5.6907|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6571  1412   157  0.73  31.14   0.86     0.76      57537.34|
|  2:  4.6571 -  3.7158  1365   148  0.77  28.98   0.95     0.87      74296.44|
|  3:  3.7158 -  3.2518  1328   154  0.71  34.71   0.97     0.90      76865.58|
|  4:  3.2518 -  2.9571  1327   146  0.65  40.06   0.98     0.87      67961.07|
|  5:  2.9571 -  2.7466  1319   147  0.60  43.62   0.94     0.83      54217.32|
|  6:  2.7466 -  2.5855  1301   143  0.60  44.34   0.96     0.81      45385.09|
|  7:  2.5855 -  2.4567  1310   149  0.60  43.65   0.97     0.81      41409.84|
|  8:  2.4567 -  2.3502  1289   140  0.56  47.71   0.97     0.77      40694.11|
|  9:  2.3502 -  2.2600  1301   146  0.51  51.46   0.99     0.71      40379.89|
| 10:  2.2600 -  2.1823  1292   139  0.47  54.34   1.03     0.67      40198.46|
| 11:  2.1823 -  2.1142  1274   142  0.44  56.90   0.99     0.65      38618.52|
| 12:  2.1142 -  2.0540  1293   144  0.44  56.58   1.02     0.68      36395.33|
| 13:  2.0540 -  2.0000  1265   140  0.43  57.48   0.99     0.67      30692.13|
| 14:  2.0000 -  1.9514   554    64  0.47  54.79   0.95     0.67      24170.53|
|alpha:            min =        0.65 max =            0.90 mean =         0.77|
|beta:             min =    24170.53 max =        76865.58 mean =     49071.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.98 mean =        45.52|
|phase err.(test): min =        0.00 max =           89.79 mean =        45.15|
|-----------------------------------------------------------------------------|

============================== 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 = 9.877266              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.994   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.425841              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.945   (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 |  1.406 -  1.755:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.755 -  2.105:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.105 -  2.454:       28 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.454 -  2.803:      764 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.803 -  3.153:     2123 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.153 -  3.502:     2411 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.502 -  3.852:     4606 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.852 -  4.201:     4846 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.201 -  4.551:     6313 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7650 |
|-----------------------------------------------------------------------------|
|-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 |        0.190 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.406 |       0.615 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.532)------------------------------------------|
|    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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3950   r_free= 0.3909   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.189030                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3826   r_free= 0.3763   ksol= 0.30   Bsol= 20.00   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.01,3.36,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.175664                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.200633              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.864   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707027              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.889   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3826      final r-factor (work) = 0.2363          |
| start r-factor (free) = 0.3763      final r-factor (free) = 0.2628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5118 = 8.20 * 0.50 * 6.1756 + 1.00 * 0.1898                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5240 = 8.20 * 0.50 * 5.9546 + 1.00 * 0.1082                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2363      final r-factor (work) = 0.2143          |
| start r-factor (free) = 0.2628      final r-factor (free) = 0.2712          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2162 = 0.71 * 1.00 * 5.9546 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0367 = 0.71 * 1.00 * 5.6923 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.532)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.15   18.09    None  None   None       |
|    all(noH): 2823   0      0.00    91.15   18.09    None  None   None       |
|    Sol.    : 438    0      4.74    80.79   40.92    None  None   None       |
|    Mac.    : 2385   0      0.00    91.15   13.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.115:  810   |   5:    45.574 -  54.689:  114        |
|      1:     9.115 -  18.230: 1131   |   6:    54.689 -  63.803:   57        |
|      2:    18.230 -  27.344:  349   |   7:    63.803 -  72.918:   32        |
|      3:    27.344 -  36.459:  165   |   8:    72.918 -  82.033:   15        |
|      4:    36.459 -  45.574:  149   |   9:    82.033 -  91.148:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2143 r_free = 0.2712             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2139 r_free = 0.2713             target_work(ml) = 5.705         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2139   r_free= 0.2713   ksol= 0.30   Bsol= 20.00   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.01,3.36,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.704827                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2092   r_free= 0.2657   ksol= 0.32   Bsol= 35.56   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.22,-0.33,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.690972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.770129              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.101   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.215643              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.504  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2092      final r-factor (work) = 0.1531          |
| start r-factor (free) = 0.2657      final r-factor (free) = 0.2047          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8394 = 3.77 * 0.50 * 5.6929 + 1.00 * 0.1078                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5522 = 3.77 * 0.50 * 5.5662 + 1.00 * 0.0597                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1531      final r-factor (work) = 0.1428          |
| start r-factor (free) = 0.2047      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2123 = 0.22 * 1.00 * 5.5662 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1713 = 0.22 * 1.00 * 5.3855 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.532)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.68   17.46    None  None   None       |
|    all(noH): 2823   0      0.00    90.68   17.46    None  None   None       |
|    Sol.    : 438    0      6.83    80.39   39.85    None  None   None       |
|    Mac.    : 2385   0      0.00    90.68   13.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.068:  743   |   5:    45.340 -  54.408:  116        |
|      1:     9.068 -  18.136: 1315   |   6:    54.408 -  63.476:   44        |
|      2:    18.136 -  27.204:  283   |   7:    63.476 -  72.544:   25        |
|      3:    27.204 -  36.272:  135   |   8:    72.544 -  81.612:   10        |
|      4:    36.272 -  45.340:  151   |   9:    81.612 -  90.680:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1428 r_free = 0.1896             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1896             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1896   ksol= 0.32   Bsol= 35.56   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.22,-0.33,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.344998                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1424   r_free= 0.1883   ksol= 0.32   Bsol= 35.56   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.21,-1.51,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.340458                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.990335              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.279  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.299393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.612   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1424      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1883      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8035 = 3.99 * 0.50 * 5.3849 + 1.00 * 0.0597                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5672 = 3.99 * 0.50 * 5.2614 + 1.00 * 0.0699                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5848 = 0.30 * 1.00 * 5.2614 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5527 = 0.30 * 1.00 * 5.1600 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.532)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    90.45   17.26    None  None   None       |
|    all(noH): 2823   0      1.60    90.45   17.26    None  None   None       |
|    Sol.    : 438    0      6.12    82.92   39.72    None  None   None       |
|    Mac.    : 2385   0      1.60    90.45   13.13    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:     1.598 -  10.484: 1075   |   5:    46.025 -  54.910:  104        |
|      1:    10.484 -  19.369: 1078   |   6:    54.910 -  63.796:   52        |
|      2:    19.369 -  28.254:  225   |   7:    63.796 -  72.681:   19        |
|      3:    28.254 -  37.140:  123   |   8:    72.681 -  81.566:    6        |
|      4:    37.140 -  46.025:  137   |   9:    81.566 -  90.452:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1594             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1593             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1593   ksol= 0.32   Bsol= 35.56   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.21,-1.51,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.147616                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1592   ksol= 0.32   Bsol= 38.55   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.27,-1.93,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149626                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.271566              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.011  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.163083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.216  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3514 = 1.27 * 0.50 * 5.1614 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3275 = 1.27 * 0.50 * 5.1571 + 1.00 * 0.0487                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8489 = 0.16 * 1.00 * 5.1571 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8477 = 0.16 * 1.00 * 5.1550 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.532)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.23    87.34   16.91    None  None   None       |
|    all(noH): 2823   0      2.23    87.34   16.91    None  None   None       |
|    Sol.    : 438    0      5.81    82.25   38.14    None  None   None       |
|    Mac.    : 2385   0      2.23    87.34   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.231 -  10.742: 1133   |   5:    44.784 -  53.295:   99        |
|      1:    10.742 -  19.252: 1033   |   6:    53.295 -  61.805:   46        |
|      2:    19.252 -  27.763:  213   |   7:    61.805 -  70.316:   19        |
|      3:    27.763 -  36.274:  137   |   8:    70.316 -  78.826:    7        |
|      4:    36.274 -  44.784:  131   |   9:    78.826 -  87.337:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1571             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1571             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1571   ksol= 0.32   Bsol= 38.55   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.27,-1.93,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153239                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1570   ksol= 0.32   Bsol= 38.55   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.21,-2.03,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153171                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.173089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.495  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289040              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 164.359  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6496 = 2.17 * 0.50 * 5.1548 + 1.00 * 0.0487                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6343 = 2.17 * 0.50 * 5.1289 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4895 = 0.29 * 1.00 * 5.1289 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4858 = 0.29 * 1.00 * 5.1148 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.532)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.76    86.80   16.84    None  None   None       |
|    all(noH): 2823   0      1.76    86.80   16.84    None  None   None       |
|    Sol.    : 438    0      5.68    82.03   38.27    None  None   None       |
|    Mac.    : 2385   0      1.76    86.80   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.757 -  10.261: 1058   |   5:    44.277 -  52.781:  107        |
|      1:    10.261 -  18.765: 1086   |   6:    52.781 -  61.285:   52        |
|      2:    18.765 -  27.269:  230   |   7:    61.285 -  69.790:   17        |
|      3:    27.269 -  35.773:  129   |   8:    69.790 -  78.294:    8        |
|      4:    35.773 -  44.277:  131   |   9:    78.294 -  86.798:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1554             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1554             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1554   ksol= 0.32   Bsol= 38.55   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.21,-2.03,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118672                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6571 0.99   1412  157 0.0969 0.1253      5.3521      5.5051|
|  2:  4.6571 -  3.7158 0.99   1365  148 0.0824 0.1080      5.3978       5.618|
|  3:  3.7158 -  3.2518 0.99   1328  154 0.1016 0.1491      5.4334      5.8036|
|  4:  3.2518 -  2.9571 0.99   1327  146 0.1183 0.1500      5.4308      5.5875|
|  5:  2.9571 -  2.7466 0.98   1319  147 0.1217 0.1681      5.2743      5.4599|
|  6:  2.7466 -  2.5855 0.99   1301  143 0.1163 0.1868      5.1676      5.4087|
|  7:  2.5855 -  2.4567 0.99   1310  149 0.1176 0.1636      5.1114      5.3672|
|  8:  2.4567 -  2.3502 0.99   1289  140 0.1118 0.1703      5.0433      5.2591|
|  9:  2.3502 -  2.2600 0.99   1301  146 0.1141 0.1846      5.0092      5.3116|
| 10:  2.2600 -  2.1823 0.98   1292  139 0.1097 0.1777      4.9565      5.2011|
| 11:  2.1823 -  2.1142 0.98   1274  142 0.1077 0.1779      4.9026       5.259|
| 12:  2.1142 -  2.0540 1.00   1293  144 0.1042 0.1588      4.8283      5.0692|
| 13:  2.0540 -  2.0000 0.96   1265  140 0.1097 0.1771      4.7581      5.0466|
| 14:  2.0000 -  1.9514 0.42    554   64 0.1064 0.1639      4.6743      4.8663|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6571  1412   157  0.94   8.40   0.98     0.96       6477.90|
|  2:  4.6571 -  3.7158  1365   148  0.96   7.52   1.02     1.01       8269.76|
|  3:  3.7158 -  3.2518  1328   154  0.94  10.77   1.03     1.03       9703.56|
|  4:  3.2518 -  2.9571  1327   146  0.92  13.68   1.01     0.99      10078.50|
|  5:  2.9571 -  2.7466  1319   147  0.91  15.13   0.99     0.97       7574.68|
|  6:  2.7466 -  2.5855  1301   143  0.91  15.40   0.98     0.96       6519.07|
|  7:  2.5855 -  2.4567  1310   149  0.92  14.39   0.99     0.96       5537.77|
|  8:  2.4567 -  2.3502  1289   140  0.91  15.18   1.00     0.97       5285.69|
|  9:  2.3502 -  2.2600  1301   146  0.91  15.20   1.01     0.98       4842.33|
| 10:  2.2600 -  2.1823  1292   139  0.90  15.56   1.00     0.96       4453.30|
| 11:  2.1823 -  2.1142  1274   142  0.90  16.09   1.00     0.97       4204.50|
| 12:  2.1142 -  2.0540  1293   144  0.92  14.37   1.00     0.99       3623.72|
| 13:  2.0540 -  2.0000  1265   140  0.90  15.90   1.01     1.01       3186.37|
| 14:  2.0000 -  1.9514   554    64  0.91  15.02   0.99     0.95       2582.09|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2582.09 max =        10078.50 mean =      6057.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.64|
|phase err.(test): min =        0.00 max =           89.28 mean =        13.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1554   ksol= 0.32   Bsol= 39.39   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.04,-1.86,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118719                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1554   ksol= 0.32   Bsol= 39.39   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.04,-1.86,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118719                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6571 0.99   1412  157 0.0970 0.1255      5.3541      5.5073|
|  2:  4.6571 -  3.7158 0.99   1365  148 0.0825 0.1080      5.3986      5.6179|
|  3:  3.7158 -  3.2518 0.99   1328  154 0.1016 0.1491      5.4336      5.8039|
|  4:  3.2518 -  2.9571 0.99   1327  146 0.1183 0.1500      5.4308      5.5875|
|  5:  2.9571 -  2.7466 0.98   1319  147 0.1217 0.1681       5.274      5.4596|
|  6:  2.7466 -  2.5855 0.99   1301  143 0.1162 0.1868      5.1673      5.4084|
|  7:  2.5855 -  2.4567 0.99   1310  149 0.1176 0.1636      5.1112      5.3671|
|  8:  2.4567 -  2.3502 0.99   1289  140 0.1118 0.1702       5.043      5.2586|
|  9:  2.3502 -  2.2600 0.99   1301  146 0.1141 0.1846      5.0091      5.3117|
| 10:  2.2600 -  2.1823 0.98   1292  139 0.1097 0.1777      4.9563      5.2007|
| 11:  2.1823 -  2.1142 0.98   1274  142 0.1076 0.1778      4.9024      5.2588|
| 12:  2.1142 -  2.0540 1.00   1293  144 0.1042 0.1587       4.828      5.0689|
| 13:  2.0540 -  2.0000 0.96   1265  140 0.1097 0.1770      4.7577       5.046|
| 14:  2.0000 -  1.9514 0.42    554   64 0.1064 0.1639       4.674      4.8662|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6571  1412   157  0.94   8.42   0.99     0.96       6515.34|
|  2:  4.6571 -  3.7158  1365   148  0.96   7.53   1.03     1.01       8291.34|
|  3:  3.7158 -  3.2518  1328   154  0.94  10.77   1.03     1.03       9707.06|
|  4:  3.2518 -  2.9571  1327   146  0.92  13.69   1.01     0.99      10078.45|
|  5:  2.9571 -  2.7466  1319   147  0.91  15.12   1.00     0.97       7570.72|
|  6:  2.7466 -  2.5855  1301   143  0.91  15.40   0.99     0.96       6514.28|
|  7:  2.5855 -  2.4567  1310   149  0.92  14.39   1.00     0.97       5533.66|
|  8:  2.4567 -  2.3502  1289   140  0.91  15.17   1.00     0.98       5281.58|
|  9:  2.3502 -  2.2600  1301   146  0.91  15.20   1.01     0.98       4840.36|
| 10:  2.2600 -  2.1823  1292   139  0.90  15.56   1.00     0.97       4451.29|
| 11:  2.1823 -  2.1142  1274   142  0.90  16.09   1.01     0.98       4202.32|
| 12:  2.1142 -  2.0540  1293   144  0.92  14.36   1.01     0.99       3620.39|
| 13:  2.0540 -  2.0000  1265   140  0.90  15.90   1.01     1.01       3183.38|
| 14:  2.0000 -  1.9514   554    64  0.91  15.01   1.00     0.96       2579.63|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2579.63 max =        10078.45 mean =      6060.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.64|
|phase err.(test): min =        0.00 max =           89.29 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.532)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    86.73   16.77    None  None   None       |
|    all(noH): 2823   0      1.69    86.73   16.77    None  None   None       |
|    Sol.    : 438    0      5.61    81.97   38.20    None  None   None       |
|    Mac.    : 2385   0      1.69    86.73   12.84    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:     1.694 -  10.198: 1058   |   5:    44.214 -  52.718:  107        |
|      1:    10.198 -  18.702: 1086   |   6:    52.718 -  61.223:   52        |
|      2:    18.702 -  27.206:  230   |   7:    61.223 -  69.727:   17        |
|      3:    27.206 -  35.710:  129   |   8:    69.727 -  78.231:    8        |
|      4:    35.710 -  44.214:  131   |   9:    78.231 -  86.735:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.539 - 5.905
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 300
   mapped sites are within: 0.707 - 5.905

peak=    5.964 closest distance to " O   HOH Z 126 " =    1.909
peak=    5.673 closest distance to " NH2 ARG A  56 " =    2.152
peak=    5.298 closest distance to " CB  SER A  63 " =    1.154
peak=    5.236 closest distance to " CB  GLN A 223 " =    1.404
peak=    5.236 closest distance to " CB  ARG A 275 " =    0.922
peak=    5.213 closest distance to " O   HOH Z 142 " =    1.719
peak=    5.198 closest distance to " CG  PRO A  54 " =    1.176
peak=    4.898 closest distance to " O   HOH Z 124 " =    1.422
peak=    4.871 closest distance to " NE2 GLN A  11 " =    1.065
peak=    4.843 closest distance to " O   HOH Z 232 " =    2.317
peak=    4.761 closest distance to " CG  PRO A 213 " =    1.198
peak=    4.752 closest distance to " O   HOH Z 193 " =    1.760
peak=    4.739 closest distance to " CB  GLN A 183 " =    1.289
peak=    4.730 closest distance to " O   HOH Z  78 " =    1.767
peak=    4.726 closest distance to " O   HOH Z 234 " =    3.666
peak=    4.679 closest distance to " O   HOH Z 236 " =    1.917
peak=    4.631 closest distance to " O   HOH Z 403 " =    1.809
peak=    4.621 closest distance to " O   HOH Z 272 " =    1.843
peak=    4.605 closest distance to " C   PRO A 198 " =    1.514
peak=    4.605 closest distance to " CB  ASN A 148 " =    1.648
peak=    4.582 closest distance to " O   HOH Z 108 " =    1.384
peak=    4.549 closest distance to " CB  GLU A 152 " =    1.187
peak=    4.531 closest distance to " O   HOH Z  93 " =    2.472
peak=    4.493 closest distance to " CB  SER A   3 " =    1.297
peak=    4.451 closest distance to " O   HOH Z 427 " =    2.740
peak=    4.407 closest distance to " O   HOH Z 368 " =    1.937
peak=    4.402 closest distance to " O   HOH Z 203 " =    1.740
peak=    4.378 closest distance to " O   HOH Z 278 " =    1.048
peak=    4.377 closest distance to " O   HOH Z  54 " =    1.718
peak=    4.369 closest distance to " O   HOH Z 298 " =    1.846
peak=    4.346 closest distance to " NZ  LYS A 119 " =    1.855
peak=    4.329 closest distance to " OD2 ASP A 286 " =    2.713
peak=    4.324 closest distance to " CB  TYR A 169 " =    0.793
peak=    4.311 closest distance to " O   HOH Z 389 " =    1.818
peak=    4.286 closest distance to " CB  ARG A  79 " =    1.430
peak=    4.260 closest distance to " O   HOH Z  97 " =    1.901
peak=    4.228 closest distance to " OD1 ASN A  69 " =    2.637
peak=    4.227 closest distance to " CA  TYR A  30 " =    0.965
peak=    4.222 closest distance to " CA  ALA A  21 " =    1.107
peak=    4.218 closest distance to " O   HOH Z 344 " =    2.935
peak=    4.215 closest distance to " O   HOH Z 128 " =    1.937
peak=    4.206 closest distance to " O   HOH Z   6 " =    2.172
peak=    4.205 closest distance to " CG  PRO A  90 " =    1.120
peak=    4.201 closest distance to " O   SER A  87 " =    2.213
peak=    4.168 closest distance to " O   HOH Z 326 " =    1.546
peak=    4.162 closest distance to " NH2BARG A 145 " =    1.989
peak=    4.158 closest distance to " O   HOH Z  15 " =    2.067
peak=    4.154 closest distance to " O   HOH Z 132 " =    1.024
peak=    4.111 closest distance to " CB  GLU A 128 " =    1.102
peak=    4.106 closest distance to " CB  TRP A 179 " =    1.289
peak=    4.101 closest distance to " O   HOH Z 207 " =    1.866
peak=    4.061 closest distance to " ND2 ASN A 187 " =    1.554
peak=    3.998 closest distance to " O   HOH Z 197 " =    2.751
peak=    3.986 closest distance to " O   HOH Z 134 " =    1.442
peak=    3.973 closest distance to " O   HOH Z 371 " =    3.337
peak=    3.968 closest distance to " O   HOH Z 144 " =    2.100
peak=    3.965 closest distance to " CB  GLU A 277 " =    3.455
peak=    3.962 closest distance to " CB  PRO A  54 " =    0.910
peak=    3.958 closest distance to " CG1 ILE A  33 " =    1.252
peak=    3.943 closest distance to " O   HOH Z 173 " =    1.988
peak=    3.930 closest distance to " O   HOH Z 303 " =    1.882
peak=    3.930 closest distance to " CB  LEU A 228 " =    1.090
peak=    3.930 closest distance to " O   HOH Z 316 " =    2.930
peak=    3.918 closest distance to " NZ  LYS A 117 " =    3.162
peak=    3.915 closest distance to " CA  THR A 221 " =    0.957
peak=    3.913 closest distance to " O   HOH Z 209 " =    2.255
peak=    3.905 closest distance to " O   HOH Z 426 " =    1.467
peak=    3.887 closest distance to " O   HOH Z 346 " =    1.662
peak=    3.875 closest distance to " O   HOH Z 193 " =    2.119
peak=    3.867 closest distance to " O   HOH Z  10 " =    1.840
peak=    3.861 closest distance to " CB  ARG A 139 " =    1.020
peak=    3.852 closest distance to " O   HOH Z  40 " =    1.517
peak=    3.834 closest distance to " CA  ASN A 215 " =    1.203
peak=    3.832 closest distance to " O   HOH Z 227 " =    1.592
peak=    3.814 closest distance to " O   MET A 105 " =    1.860
peak=    3.811 closest distance to " O   HOH Z 279 " =    2.058
peak=    3.804 closest distance to " O   HOH Z 407 " =    2.626
peak=    3.803 closest distance to " O   HOH Z 402 " =    1.392
peak=    3.784 closest distance to " O   HOH Z 172 " =    3.845
peak=    3.776 closest distance to " CB  SER A 141 " =    1.068
peak=    3.776 closest distance to " O   HOH Z  88 " =    3.143
peak=    3.763 closest distance to " CB  VAL A 202 " =    1.611
peak=    3.750 closest distance to " O   HOH Z 411 " =    3.732
peak=    3.744 closest distance to " O   HOH Z 261 " =    1.646
peak=    3.744 closest distance to " OG BSER A 164 " =    2.467
peak=    3.742 closest distance to " CG2 ILE A  20 " =    1.450
peak=    3.738 closest distance to " O   HOH Z 250 " =    1.369
peak=    3.735 closest distance to " O   HOH Z 180 " =    2.232
peak=    3.734 closest distance to " O   HOH Z  49 " =    2.045
peak=    3.731 closest distance to " O   HOH Z 125 " =    2.287
peak=    3.731 closest distance to " O   HOH Z 284 " =    2.827
peak=    3.716 closest distance to " O   HOH Z  71 " =    1.333
peak=    3.714 closest distance to " CD2 LEU A 297 " =    0.924
peak=    3.711 closest distance to " O   HOH Z  21 " =    1.718
peak=    3.700 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.692 closest distance to " NH2AARG A 190 " =    1.241
peak=    3.691 closest distance to " O   HOH Z  44 " =    2.025
peak=    3.689 closest distance to " O   HOH Z 334 " =    1.390
peak=    3.685 closest distance to " N   ASN A  39 " =    1.213
peak=    3.684 closest distance to " CB  SER A  26 " =    1.587
peak=    3.675 closest distance to " O   HOH Z 313 " =    1.673
peak=    3.674 closest distance to " O   HOH Z 132 " =    2.395
peak=    3.668 closest distance to " CG  GLN A  77 " =    1.895
peak=    3.666 closest distance to " CB  TYR A 169 " =    0.838
peak=    3.665 closest distance to " O   HOH Z 423 " =    2.026
peak=    3.659 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.657 closest distance to " O   HOH Z 214 " =    2.024
peak=    3.657 closest distance to " CB  VAL A 265 " =    1.299
peak=    3.653 closest distance to " O   HOH Z 327 " =    1.716
peak=    3.652 closest distance to " O   HOH Z  61 " =    1.583
peak=    3.647 closest distance to " O   HOH Z 369 " =    1.968
peak=    3.645 closest distance to " O   HOH Z  19 " =    2.090
peak=    3.643 closest distance to " CZ2 TRP A 179 " =    1.684
peak=    3.643 closest distance to " O   HOH Z 183 " =    1.541
peak=    3.639 closest distance to " O   HOH Z  43 " =    2.041
peak=    3.638 closest distance to " CG  ARG A  66 " =    2.631
peak=    3.635 closest distance to " CB  ARG A 190 " =    1.705
peak=    3.634 closest distance to " O   HOH Z  59 " =    2.137
peak=    3.630 closest distance to " CB  ASN A  39 " =    0.859
peak=    3.623 closest distance to " CG1BVAL A  72 " =    1.570
peak=    3.618 closest distance to " O   HOH Z 365 " =    2.918
peak=    3.616 closest distance to " NH1BARG A 145 " =    1.378
peak=    3.609 closest distance to " O   HOH Z  66 " =    2.156
peak=    3.601 closest distance to " O   HOH Z 108 " =    1.976
peak=    3.593 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.588 closest distance to " CG  PRO A 243 " =    1.216
peak=    3.570 closest distance to " O   HOH Z 427 " =    3.101
peak=    3.570 closest distance to " CG  PRO A 198 " =    1.299
peak=    3.570 closest distance to " O   HOH Z  85 " =    1.694
peak=    3.568 closest distance to " O   HOH Z 273 " =    2.725
peak=    3.567 closest distance to " O   HOH Z 163 " =    1.967
peak=    3.566 closest distance to " CA  ASN A 176 " =    1.097
peak=    3.555 closest distance to " O   HOH Z 374 " =    2.466
peak=    3.555 closest distance to " O   HOH Z 281 " =    4.348
peak=    3.555 closest distance to " CA  MET A  40 " =    1.016
peak=    3.543 closest distance to " O   HOH Z 263 " =    2.289
peak=    3.542 closest distance to " CG2 THR A 221 " =    1.097
peak=    3.539 closest distance to " O   HOH Z  68 " =    1.650
peak=    3.532 closest distance to " O   HOH Z 260 " =    1.174
peak=    3.522 closest distance to " CG2 ILE A 120 " =    1.132
peak=    3.519 closest distance to " O   HOH Z 299 " =    4.328
peak=    3.516 closest distance to " O   HOH Z 286 " =    2.198
peak=    3.514 closest distance to " O   HOH Z 345 " =    3.047
peak=    3.509 closest distance to " O   HOH Z 185 " =    1.622
peak=    3.506 closest distance to " CG  GLN A  11 " =    1.548
peak=    3.496 closest distance to " O   HOH Z 133 " =    2.270
peak=    3.479 closest distance to " CG  GLN A  58 " =    2.532
peak=    3.477 closest distance to " CG  GLU A 277 " =    2.213
peak=    3.473 closest distance to " NH1AARG A 145 " =    1.076
peak=    3.472 closest distance to " O   HOH Z 189 " =    1.476
peak=    3.471 closest distance to " O   HOH Z 291 " =    1.563
peak=    3.468 closest distance to " O   HOH Z  48 " =    1.510
peak=    3.463 closest distance to " OG  SER A  22 " =    2.630
peak=    3.460 closest distance to " O   HOH Z  30 " =    2.119
peak=    3.458 closest distance to " O   HOH Z 147 " =    1.680
peak=    3.457 closest distance to " C   ALA A   1 " =    1.650
peak=    3.450 closest distance to " O   SER A  26 " =    1.680
peak=    3.448 closest distance to " CE1 TYR A 186 " =    1.227
peak=    3.439 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.430 closest distance to " O   HOH Z 380 " =    2.080
peak=    3.428 closest distance to " NH2 ARG A 156 " =    1.154
peak=    3.428 closest distance to " O   HOH Z  85 " =    2.106
peak=    3.427 closest distance to " O   HOH Z 425 " =    1.924
peak=    3.426 closest distance to " CD  ARG A 269 " =    0.989
peak=    3.424 closest distance to " N   ARG A 156 " =    1.320
peak=    3.422 closest distance to " NH2 ARG A 219 " =    1.906
peak=    3.419 closest distance to " CG AARG A 275 " =    1.023
peak=    3.418 closest distance to " O   ALA A   1 " =    1.443
peak=    3.407 closest distance to " O   HOH Z 368 " =    3.643
peak=    3.393 closest distance to " O   HOH Z 251 " =    1.571
peak=    3.390 closest distance to " CG2BVAL A  41 " =    0.871
peak=    3.389 closest distance to " CG  MET A 185 " =    1.156
peak=    3.389 closest distance to " O   HOH Z 214 " =    2.352
peak=    3.386 closest distance to " O   HOH Z   1 " =    1.984
peak=    3.385 closest distance to " OE1 GLU A 277 " =    1.967
peak=    3.378 closest distance to " O   HOH Z 158 " =    3.029
peak=    3.367 closest distance to " CA  GLY A  80 " =    0.833
peak=    3.367 closest distance to " CB  TRP A 266 " =    1.001
peak=    3.367 closest distance to " O   HOH Z 189 " =    1.568
peak=    3.366 closest distance to " O   ALA A 165 " =    1.406
peak=    3.365 closest distance to " CA  ARG A  36 " =    1.065
peak=    3.358 closest distance to " OD1 ASP A 286 " =    1.540
peak=    3.357 closest distance to " O   HOH Z 145 " =    2.401
peak=    3.355 closest distance to " CA  ASP A 140 " =    1.088
peak=    3.352 closest distance to " CD BLYS A 290 " =    1.221
peak=    3.350 closest distance to " O   HOH Z 337 " =    3.588
peak=    3.334 closest distance to " O   HOH Z 357 " =    1.851
peak=    3.332 closest distance to " O   HOH Z 267 " =    2.090
peak=    3.326 closest distance to " CD2 LEU A 255 " =    1.158
peak=    3.325 closest distance to " CD1 ILE A 106 " =    0.974
peak=    3.317 closest distance to " O   HOH Z 106 " =    2.328
peak=    3.316 closest distance to " CB  ALA A 291 " =    1.307
peak=    3.315 closest distance to " O   HOH Z 266 " =    1.574
peak=    3.315 closest distance to " CB  SER A  62 " =    1.263
peak=    3.315 closest distance to " O   TRP A 274 " =    1.889
peak=    3.307 closest distance to " CA  ALA A  84 " =    1.327
peak=    3.307 closest distance to " CE  LYS A 119 " =    1.164
peak=    3.305 closest distance to " OE1 GLN A  11 " =    1.924
peak=    3.303 closest distance to " CB  GLN A  89 " =    1.175
peak=    3.301 closest distance to " O   HOH Z  63 " =    1.864
peak=    3.298 closest distance to " O   HOH Z 353 " =    2.535
peak=    3.297 closest distance to " CB  ALA A   1 " =    1.165
peak=    3.296 closest distance to " O   HOH Z 430 " =    5.561
peak=    3.295 closest distance to " O   HOH Z 194 " =    1.915
peak=    3.287 closest distance to " O   HOH Z 102 " =    1.222
peak=    3.282 closest distance to " CB  PRO A 198 " =    1.033
peak=    3.281 closest distance to " O   HOH Z  50 " =    1.420
peak=    3.276 closest distance to " CB  ALA A   9 " =    1.537
peak=    3.274 closest distance to " CA  ASN A  74 " =    1.138
peak=    3.274 closest distance to " O   HOH Z 148 " =    3.046
peak=    3.273 closest distance to " CD  LYS A 166 " =    1.313
peak=    3.264 closest distance to " CA  ASP A 162 " =    1.128
peak=    3.263 closest distance to " CA  ALA A 248 " =    1.189
peak=    3.263 closest distance to " CA  ALA A 291 " =    0.887
peak=    3.259 closest distance to " O   HOH Z 292 " =    1.588
peak=    3.257 closest distance to " OG  SER A  62 " =    2.945
peak=    3.252 closest distance to " CA  ILE A  33 " =    1.452
peak=    3.252 closest distance to " O   HOH Z 435 " =    1.877
peak=    3.252 closest distance to " CB  GLU A  46 " =    1.050
peak=    3.252 closest distance to " CG  MET A 185 " =    1.019
peak=    3.249 closest distance to " O   HOH Z 409 " =    3.263
peak=    3.246 closest distance to " O   HOH Z 133 " =    1.334
peak=    3.246 closest distance to " O   HOH Z 368 " =    2.476
peak=    3.245 closest distance to " N   PHE A 130 " =    1.381
peak=    3.242 closest distance to " O   HOH Z 291 " =    1.811
peak=    3.241 closest distance to " CA  THR A 264 " =    0.826
peak=    3.240 closest distance to " CB  ASP A 140 " =    0.787
peak=    3.237 closest distance to " O   HOH Z 403 " =    1.363
peak=    3.236 closest distance to " N   SER A 135 " =    1.294
peak=    3.235 closest distance to " CD  LYS A 119 " =    1.375
peak=    3.234 closest distance to " CA  ALA A 233 " =    1.205
peak=    3.233 closest distance to " CD  ARG A 159 " =    0.707
peak=    3.230 closest distance to " CB  ALA A 100 " =    1.128
peak=    3.228 closest distance to " C   ALA A 299 " =    0.947
peak=    3.228 closest distance to " O   HOH Z 417 " =    3.123
peak=    3.222 closest distance to " O   HOH Z 118 " =    1.123
peak=    3.217 closest distance to " O   HOH Z 255 " =    1.596
peak=    3.210 closest distance to " OH  TYR A  30 " =    1.059
peak=    3.210 closest distance to " CB  ILE A 120 " =    1.344
peak=    3.209 closest distance to " CG  ARG A  66 " =    0.937
peak=    3.207 closest distance to " O   HOH Z 329 " =    3.302
peak=    3.205 closest distance to " O   HOH Z 411 " =    1.692
peak=    3.205 closest distance to " CA  ALA A  51 " =    0.835
peak=    3.197 closest distance to " CE BLYS A 290 " =    1.090
peak=    3.191 closest distance to " CB  ALA A  71 " =    1.215
peak=    3.188 closest distance to " CA  ASN A 217 " =    1.247
peak=    3.182 closest distance to " CB  THR A  31 " =    1.770
peak=    3.181 closest distance to " ND2 ASN A 301 " =    1.444
peak=    3.177 closest distance to " OD1 ASP A 231 " =    1.894
peak=    3.175 closest distance to " O   HOH Z 336 " =    1.789
peak=    3.171 closest distance to " CB  GLN A 278 " =    0.850
peak=    3.171 closest distance to " O   HOH Z 189 " =    1.775
peak=    3.168 closest distance to " O   HOH Z 163 " =    1.721
peak=    3.165 closest distance to " OD1 ASP A 238 " =    0.976
peak=    3.159 closest distance to " CA  LEU A 282 " =    1.198
peak=    3.157 closest distance to " CA  ALA A  43 " =    1.212
peak=    3.156 closest distance to " SD AMET A  47 " =    1.223
peak=    3.156 closest distance to " O   HOH Z 245 " =    1.321
peak=    3.153 closest distance to " NZ  LYS A  76 " =    1.221
peak=    3.149 closest distance to " O   HOH Z 421 " =    1.476
peak=    3.148 closest distance to " OE1 GLN A  58 " =    5.905
peak=    3.147 closest distance to " CG  LYS A  76 " =    1.139
peak=    3.146 closest distance to " CZ2 TRP A 274 " =    1.590
peak=    3.146 closest distance to " CB  GLN A 205 " =    1.341
peak=    3.143 closest distance to " O   HOH Z 175 " =    2.181
peak=    3.141 closest distance to " CG  GLN A  89 " =    1.508
peak=    3.141 closest distance to " O   HOH Z 192 " =    1.815
peak=    3.138 closest distance to " O   HOH Z 258 " =    1.639
peak=    3.133 closest distance to " CA  VAL A 126 " =    1.060
peak=    3.132 closest distance to " CD2 HIS A  81 " =    1.220
peak=    3.130 closest distance to " CG2 VAL A 257 " =    0.854
peak=    3.127 closest distance to " O   HOH Z 266 " =    2.919
peak=    3.127 closest distance to " O   HOH Z 247 " =    1.291
peak=    3.126 closest distance to " O   HOH Z  66 " =    1.981
peak=    3.126 closest distance to " O   HOH Z 211 " =    2.460
peak=    3.125 closest distance to " CG  MET A  93 " =    0.952
peak=    3.123 closest distance to " CB  SER A 216 " =    0.719
peak=    3.119 closest distance to " O   HOH Z 227 " =    2.203
peak=    3.110 closest distance to " CB  ASN A 215 " =    1.106
peak=    3.109 closest distance to " N   ASP A 162 " =    1.269
peak=    3.108 closest distance to " CG2 VAL A 126 " =    1.934
peak=    3.104 closest distance to " O   HOH Z 327 " =    2.525
peak=    3.096 closest distance to " CA  VAL A  41 " =    0.897
peak=    3.094 closest distance to " CA  ARG A  56 " =    1.654
peak=    3.091 closest distance to " O   HOH Z  11 " =    1.264
peak=    3.083 closest distance to " CA  GLU A  46 " =    0.710
peak=    3.080 closest distance to " OE2 GLU A  53 " =    2.127
peak=    3.075 closest distance to " O   HOH Z 438 " =    1.775
peak=    3.075 closest distance to " CB  GLN A 103 " =    0.798
peak=    3.070 closest distance to " O   HOH Z 425 " =    1.284
peak=    3.067 closest distance to " O   HOH Z 368 " =    2.518
peak=    3.057 closest distance to " O   HOH Z 195 " =    1.814
peak=    3.047 closest distance to " O   HOH Z 299 " =    2.235
peak=    3.041 closest distance to " O   HOH Z  71 " =    1.715
peak=    3.041 closest distance to " N   ASN A 127 " =    1.252
peak=    3.030 closest distance to " NE2 GLN A  58 " =    2.480
peak=    2.981 closest distance to " O   HOH Z 286 " =    2.214

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.652 - 5.971
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 217
   mapped sites are within: 0.838 - 5.971

peak=   -4.699 closest distance to " O   HOH Z 266 " =    4.206
peak=   -4.595 closest distance to " O   HOH Z 372 " =    2.298
peak=   -4.320 closest distance to " SG  CYS A 254 " =    3.307
peak=   -4.282 closest distance to " O   HOH Z 290 " =    0.941
peak=   -4.275 closest distance to " OXT GLY A 302 " =    2.663
peak=   -4.265 closest distance to " N   GLN A  58 " =    1.616
peak=   -4.206 closest distance to " C   HIS A 108 " =    1.114
peak=   -4.198 closest distance to " CB  PRO A 243 " =    2.523
peak=   -4.196 closest distance to " O   HOH Z  13 " =    1.523
peak=   -4.130 closest distance to " N   ALA A 248 " =    1.674
peak=   -4.052 closest distance to " O   PRO A 163 " =    2.037
peak=   -4.033 closest distance to " CD  ARG A 156 " =    1.957
peak=   -4.032 closest distance to " CH2 TRP A 179 " =    1.371
peak=   -4.025 closest distance to " CB  ALA A 161 " =    2.523
peak=   -4.003 closest distance to " O   VAL A  67 " =    2.691
peak=   -3.970 closest distance to " O   HOH Z 198 " =    2.117
peak=   -3.970 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.964 closest distance to " CD1 LEU A 101 " =    2.455
peak=   -3.957 closest distance to " CZ  TYR A 169 " =    1.793
peak=   -3.945 closest distance to " O   VAL A 153 " =    2.316
peak=   -3.914 closest distance to " O   VAL A  67 " =    2.723
peak=   -3.909 closest distance to " CG  ASP A 231 " =    0.838
peak=   -3.906 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.901 closest distance to " CB  ALA A 291 " =    2.385
peak=   -3.897 closest distance to " O   HOH Z  11 " =    1.816
peak=   -3.884 closest distance to " O   HOH Z 407 " =    2.966
peak=   -3.882 closest distance to " O   HOH Z 231 " =    2.207
peak=   -3.882 closest distance to " O   HOH Z  92 " =    1.788
peak=   -3.881 closest distance to " CD2 LEU A 300 " =    2.847
peak=   -3.868 closest distance to " O   HOH Z  10 " =    1.478
peak=   -3.860 closest distance to " OG  SER A  97 " =    2.130
peak=   -3.859 closest distance to " O   HOH Z 388 " =    2.058
peak=   -3.852 closest distance to " NE2 GLN A  58 " =    1.097
peak=   -3.832 closest distance to " O   HOH Z 377 " =    2.070
peak=   -3.824 closest distance to " C   ALA A 158 " =    1.166
peak=   -3.797 closest distance to " CB  TYR A  15 " =    2.199
peak=   -3.766 closest distance to " OG BSER A 134 " =    1.267
peak=   -3.755 closest distance to " NH2 ARG A  79 " =    1.860
peak=   -3.753 closest distance to " O   HOH Z  43 " =    1.611
peak=   -3.742 closest distance to " O   HOH Z 126 " =    1.813
peak=   -3.742 closest distance to " O   HOH Z 353 " =    2.228
peak=   -3.721 closest distance to " CB  ASN A  39 " =    2.231
peak=   -3.715 closest distance to " O   HOH Z 166 " =    1.430
peak=   -3.715 closest distance to " O   HOH Z 118 " =    2.874
peak=   -3.698 closest distance to " N   HIS A 115 " =    1.878
peak=   -3.686 closest distance to " CG  GLN A 223 " =    2.146
peak=   -3.686 closest distance to " ND2 ASN A  45 " =    0.992
peak=   -3.676 closest distance to " CG  ASP A  50 " =    2.372
peak=   -3.657 closest distance to " O   HOH Z 362 " =    5.971
peak=   -3.656 closest distance to " O   HOH Z 234 " =    4.086
peak=   -3.651 closest distance to " CD1 PHE A  59 " =    1.871
peak=   -3.649 closest distance to " N   ALA A 248 " =    2.202
peak=   -3.631 closest distance to " O   HOH Z 311 " =    3.411
peak=   -3.624 closest distance to " O   SER A 210 " =    1.898
peak=   -3.624 closest distance to " O   VAL A 174 " =    1.983
peak=   -3.617 closest distance to " O   SER A 146 " =    0.937
peak=   -3.617 closest distance to " O   HOH Z 185 " =    2.194
peak=   -3.615 closest distance to " O   SER A 135 " =    1.581
peak=   -3.607 closest distance to " CD1 LEU A 228 " =    2.131
peak=   -3.598 closest distance to " N   SER A 276 " =    1.252
peak=   -3.592 closest distance to " OG BSER A 134 " =    1.678
peak=   -3.588 closest distance to " O   HOH Z 395 " =    5.103
peak=   -3.584 closest distance to " OXT GLY A 302 " =    3.175
peak=   -3.579 closest distance to " O   HOH Z 435 " =    2.665
peak=   -3.574 closest distance to " N   GLN A 122 " =    1.471
peak=   -3.572 closest distance to " O   TRP A  92 " =    1.812
peak=   -3.566 closest distance to " N   ASP A 286 " =    2.342
peak=   -3.561 closest distance to " O   ALA A 161 " =    1.591
peak=   -3.559 closest distance to " CB  CYS A 201 " =    2.581
peak=   -3.552 closest distance to " OE2 GLU A   2 " =    1.984
peak=   -3.551 closest distance to " ND2 ASN A 187 " =    1.470
peak=   -3.537 closest distance to " O   HOH Z 165 " =    2.062
peak=   -3.525 closest distance to " C   LEU A 143 " =    1.100
peak=   -3.522 closest distance to " CG  PHE A 283 " =    2.607
peak=   -3.515 closest distance to " O   HOH Z  15 " =    1.572
peak=   -3.515 closest distance to " OG  SER A  62 " =    1.430
peak=   -3.512 closest distance to " O   HOH Z  52 " =    1.432
peak=   -3.512 closest distance to " N   ALA A  43 " =    2.450
peak=   -3.510 closest distance to " O   HOH Z 385 " =    1.995
peak=   -3.497 closest distance to " CD2 LEU A 237 " =    2.590
peak=   -3.494 closest distance to " CA  GLY A 133 " =    1.834
peak=   -3.492 closest distance to " O   HOH Z  11 " =    1.844
peak=   -3.482 closest distance to " O   HOH Z 292 " =    4.423
peak=   -3.477 closest distance to " ND2 ASN A 209 " =    1.688
peak=   -3.474 closest distance to " OG  SER A   3 " =    1.545
peak=   -3.469 closest distance to " OG ASER A 134 " =    1.214
peak=   -3.467 closest distance to " CE  MET A 105 " =    1.995
peak=   -3.461 closest distance to " CG  GLU A  53 " =    1.430
peak=   -3.460 closest distance to " CE2 TYR A  30 " =    2.871
peak=   -3.447 closest distance to " O   HOH Z  93 " =    1.556
peak=   -3.438 closest distance to " O   HOH Z  76 " =    1.890
peak=   -3.437 closest distance to " OD2 ASP A 171 " =    2.281
peak=   -3.423 closest distance to " O   ASN A  45 " =    1.832
peak=   -3.411 closest distance to " O   HOH Z 309 " =    2.450
peak=   -3.401 closest distance to " O   GLY A 196 " =    0.981
peak=   -3.396 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.391 closest distance to " ND2 ASN A  39 " =    1.286
peak=   -3.388 closest distance to " O   HOH Z 281 " =    2.801
peak=   -3.385 closest distance to " CZ  PHE A  59 " =    1.596
peak=   -3.381 closest distance to " CB  ASP A 132 " =    2.289
peak=   -3.380 closest distance to " O   HOH Z  47 " =    1.532
peak=   -3.379 closest distance to " SG ACYS A 201 " =    2.073
peak=   -3.377 closest distance to " O   HOH Z 250 " =    1.427
peak=   -3.376 closest distance to " N   SER A 206 " =    1.867
peak=   -3.372 closest distance to " O   HOH Z 417 " =    2.472
peak=   -3.358 closest distance to " CB  CYS A 254 " =    2.535
peak=   -3.357 closest distance to " CB  PHE A 192 " =    1.859
peak=   -3.356 closest distance to " CD1 LEU A  25 " =    2.452
peak=   -3.351 closest distance to " O   MET A  40 " =    2.754
peak=   -3.348 closest distance to " CE  LYS A  76 " =    2.897
peak=   -3.344 closest distance to " O   HOH Z 283 " =    1.707
peak=   -3.342 closest distance to " O   HOH Z  19 " =    2.173
peak=   -3.342 closest distance to " NH2 ARG A  66 " =    4.605
peak=   -3.341 closest distance to " O   PRO A 198 " =    1.246
peak=   -3.334 closest distance to " NH1 ARG A 195 " =    2.525
peak=   -3.334 closest distance to " CE2 TYR A 186 " =    2.130
peak=   -3.332 closest distance to " CA  TYR A  68 " =    2.948
peak=   -3.322 closest distance to " OG1 THR A 178 " =    1.206
peak=   -3.322 closest distance to " CD  GLN A  58 " =    1.411
peak=   -3.313 closest distance to " O   HOH Z  97 " =    1.650
peak=   -3.303 closest distance to " O   HOH Z 427 " =    1.413
peak=   -3.302 closest distance to " CG1 VAL A 112 " =    2.619
peak=   -3.298 closest distance to " OD1 ASP A 191 " =    1.752
peak=   -3.297 closest distance to " O   ASP A 231 " =    2.518
peak=   -3.287 closest distance to " O   HOH Z 265 " =    1.921
peak=   -3.284 closest distance to " OD1 ASN A 176 " =    1.132
peak=   -3.279 closest distance to " O   HOH Z  24 " =    1.578
peak=   -3.279 closest distance to " O   HOH Z  71 " =    1.472
peak=   -3.278 closest distance to " CA  GLY A  98 " =    2.020
peak=   -3.274 closest distance to " C   GLY A  80 " =    2.368
peak=   -3.261 closest distance to " CD1 ILE A 239 " =    2.481
peak=   -3.260 closest distance to " CZ3 TRP A 274 " =    1.059
peak=   -3.259 closest distance to " OD1 ASP A 200 " =    1.199
peak=   -3.258 closest distance to " O   HOH Z 166 " =    1.881
peak=   -3.258 closest distance to " O   HOH Z 378 " =    1.647
peak=   -3.257 closest distance to " O   HOH Z 263 " =    2.892
peak=   -3.253 closest distance to " O   HOH Z 360 " =    2.499
peak=   -3.252 closest distance to " O   HOH Z  41 " =    2.284
peak=   -3.249 closest distance to " CD2 TYR A 293 " =    2.073
peak=   -3.246 closest distance to " O   HOH Z  90 " =    2.883
peak=   -3.245 closest distance to " O   HOH Z  63 " =    1.421
peak=   -3.244 closest distance to " NH2AARG A 275 " =    5.106
peak=   -3.243 closest distance to " O   ALA A 292 " =    1.990
peak=   -3.241 closest distance to " CE  MET A  93 " =    1.157
peak=   -3.241 closest distance to " O   PHE A 218 " =    1.599
peak=   -3.239 closest distance to " NH1 ARG A  56 " =    2.584
peak=   -3.236 closest distance to " OD2 ASP A 191 " =    1.449
peak=   -3.235 closest distance to " O   HOH Z  88 " =    1.765
peak=   -3.234 closest distance to " O   SER A 273 " =    1.368
peak=   -3.234 closest distance to " O   ALA A 160 " =    1.431
peak=   -3.232 closest distance to " OG BSER A 210 " =    1.909
peak=   -3.231 closest distance to " C   PRO A  90 " =    1.446
peak=   -3.230 closest distance to " O   HOH Z  38 " =    1.658
peak=   -3.222 closest distance to " O   LEU A 167 " =    1.571
peak=   -3.222 closest distance to " O   HOH Z 313 " =    0.978
peak=   -3.217 closest distance to " CG  GLU A 152 " =    0.849
peak=   -3.215 closest distance to " O   HOH Z 148 " =    3.432
peak=   -3.211 closest distance to " O   HOH Z 385 " =    2.109
peak=   -3.210 closest distance to " OG  SER A  26 " =    1.190
peak=   -3.206 closest distance to " CG  GLU A 152 " =    2.197
peak=   -3.204 closest distance to " O   HOH Z 351 " =    1.576
peak=   -3.204 closest distance to " CG2 THR A 178 " =    2.245
peak=   -3.203 closest distance to " O   HOH Z 297 " =    2.770
peak=   -3.203 closest distance to " CG  GLU A 277 " =    1.184
peak=   -3.199 closest distance to " OH  TYR A 214 " =    1.306
peak=   -3.195 closest distance to " CG  PRO A 163 " =    2.566
peak=   -3.194 closest distance to " O   ALA A  51 " =    1.347
peak=   -3.192 closest distance to " O   HOH Z 198 " =    1.452
peak=   -3.190 closest distance to " OG  SER A 206 " =    1.682
peak=   -3.190 closest distance to " CE3 TRP A 274 " =    2.467
peak=   -3.189 closest distance to " O   ALA A   1 " =    1.829
peak=   -3.186 closest distance to " CD2 LEU A 237 " =    2.702
peak=   -3.180 closest distance to " CB  SER A 258 " =    2.076
peak=   -3.179 closest distance to " O   HOH Z 407 " =    3.399
peak=   -3.178 closest distance to " O   HOH Z 137 " =    1.533
peak=   -3.172 closest distance to " N   GLN A  58 " =    1.266
peak=   -3.167 closest distance to " OD1 ASP A 171 " =    1.627
peak=   -3.161 closest distance to " OD1 ASP A 191 " =    1.490
peak=   -3.161 closest distance to " CG  ASN A 110 " =    1.187
peak=   -3.159 closest distance to " OD1 ASN A 148 " =    1.637
peak=   -3.158 closest distance to " N   ALA A 226 " =    1.938
peak=   -3.157 closest distance to " CG2 VAL A 189 " =    2.117
peak=   -3.152 closest distance to " CB  ASP A 132 " =    2.315
peak=   -3.145 closest distance to " O   HOH Z 191 " =    5.447
peak=   -3.129 closest distance to " CB  ALA A 248 " =    1.959
peak=   -3.124 closest distance to " O   HOH Z 145 " =    3.028
peak=   -3.123 closest distance to " O   HOH Z 423 " =    2.276
peak=   -3.123 closest distance to " NE2 GLN A 103 " =    1.605
peak=   -3.121 closest distance to " O   HOH Z 317 " =    2.625
peak=   -3.120 closest distance to " ND2 ASN A 249 " =    2.259
peak=   -3.112 closest distance to " O   ARG A  56 " =    1.568
peak=   -3.108 closest distance to " CE3 TRP A 123 " =    1.243
peak=   -3.107 closest distance to " CZ  PHE A 130 " =    0.853
peak=   -3.103 closest distance to " CG2 ILE A  20 " =    2.859
peak=   -3.102 closest distance to " OG1 THR A 279 " =    1.304
peak=   -3.101 closest distance to " O   HOH Z 396 " =    1.585
peak=   -3.101 closest distance to " OG  SER A  87 " =    1.283
peak=   -3.099 closest distance to " O   ALA A 256 " =    1.497
peak=   -3.095 closest distance to " CE1 HIS A  81 " =    1.392
peak=   -3.094 closest distance to " CA  GLY A 241 " =    3.206
peak=   -3.093 closest distance to " OE1 GLN A  77 " =    1.677
peak=   -3.093 closest distance to " CB  PHE A 208 " =    2.206
peak=   -3.093 closest distance to " NZ  LYS A 119 " =    3.469
peak=   -3.092 closest distance to " O   LYS A 117 " =    1.540
peak=   -3.086 closest distance to " CG2 ILE A 263 " =    2.182
peak=   -3.085 closest distance to " OD1 ASN A 249 " =    1.327
peak=   -3.084 closest distance to " N   VAL A 296 " =    2.492
peak=   -3.082 closest distance to " CD1 TYR A 247 " =    2.366
peak=   -3.081 closest distance to " CA  SER A 245 " =    2.435
peak=   -3.074 closest distance to " O   HOH Z 412 " =    4.397
peak=   -3.074 closest distance to " O   HOH Z 210 " =    1.006
peak=   -3.068 closest distance to " O   GLY A 111 " =    1.102
peak=   -3.059 closest distance to " N   VAL A 189 " =    1.643
peak=   -3.041 closest distance to " O   HOH Z 310 " =    3.496
peak=   -3.035 closest distance to " CG  ARG A 269 " =    2.161
peak=   -3.008 closest distance to " OE1 GLN A  88 " =    1.273

================= 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    :  0.3950 0.3909   6.189030e+00   6.192544e+00
   1_bss:  0.3826 0.3763   6.175664e+00   6.164910e+00
   1_xyz:  0.2363 0.2628   5.758456e+00   5.849694e+00
   1_adp:  0.2143 0.2712   5.705528e+00   5.876606e+00
   1_occ:  0.2139 0.2713   5.704827e+00   5.875813e+00
   2_bss:  0.2092 0.2657   5.690972e+00   5.862527e+00
   2_xyz:  0.1531 0.2047   5.414703e+00   5.628409e+00
   2_adp:  0.1428 0.1896   5.346080e+00   5.553050e+00
   2_occ:  0.1425 0.1896   5.344998e+00   5.552345e+00
   3_bss:  0.1424 0.1883   5.340458e+00   5.546591e+00
   3_xyz:  0.1178 0.1621   5.179808e+00   5.406687e+00
   3_adp:  0.1127 0.1594   5.148388e+00   5.384262e+00
   3_occ:  0.1126 0.1593   5.147616e+00   5.383708e+00
   4_bss:  0.1130 0.1592   5.149626e+00   5.384070e+00
   4_xyz:  0.1138 0.1576   5.153958e+00   5.378571e+00
   4_adp:  0.1140 0.1571   5.153584e+00   5.377164e+00
   4_occ:  0.1139 0.1571   5.153239e+00   5.377080e+00
   5_bss:  0.1139 0.1570   5.153171e+00   5.376997e+00
   5_xyz:  0.1080 0.1546   5.118598e+00   5.359824e+00
   5_adp:  0.1073 0.1554   5.118635e+00   5.364962e+00
   5_occ:  0.1072 0.1554   5.118672e+00   5.365237e+00
   5_bss:  0.1072 0.1554   5.118719e+00   5.365232e+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:  0.300  20.000  -2.447  -2.009   3.359  -0.000   0.000   0.000
   1_xyz:  0.300  20.000  -2.447  -2.009   3.359  -0.000   0.000   0.000
   1_adp:  0.300  20.000  -2.447  -2.009   3.359  -0.000   0.000   0.000
   1_occ:  0.300  20.000  -2.447  -2.009   3.359  -0.000   0.000   0.000
   2_bss:  0.316  35.560  -2.878  -2.221  -0.329  -0.000  -0.000  -0.000
   2_xyz:  0.316  35.560  -2.878  -2.221  -0.329  -0.000  -0.000  -0.000
   2_adp:  0.316  35.560  -2.878  -2.221  -0.329  -0.000  -0.000  -0.000
   2_occ:  0.316  35.560  -2.878  -2.221  -0.329  -0.000  -0.000  -0.000
   3_bss:  0.316  35.558  -2.886  -2.206  -1.508  -0.000  -0.000  -0.000
   3_xyz:  0.316  35.558  -2.886  -2.206  -1.508  -0.000  -0.000  -0.000
   3_adp:  0.316  35.558  -2.886  -2.206  -1.508  -0.000  -0.000  -0.000
   3_occ:  0.316  35.558  -2.886  -2.206  -1.508  -0.000  -0.000  -0.000
   4_bss:  0.316  38.546  -2.947  -2.275  -1.932  -0.000  -0.000  -0.000
   4_xyz:  0.316  38.546  -2.947  -2.275  -1.932  -0.000  -0.000  -0.000
   4_adp:  0.316  38.546  -2.947  -2.275  -1.932  -0.000  -0.000  -0.000
   4_occ:  0.316  38.546  -2.947  -2.275  -1.932  -0.000  -0.000  -0.000
   5_bss:  0.318  38.546  -2.938  -2.215  -2.027  -0.000  -0.000  -0.000
   5_xyz:  0.318  38.546  -2.938  -2.215  -2.027  -0.000  -0.000  -0.000
   5_adp:  0.318  38.546  -2.938  -2.215  -2.027  -0.000  -0.000  -0.000
   5_occ:  0.318  38.546  -2.938  -2.215  -2.027  -0.000  -0.000  -0.000
   5_bss:  0.321  39.386  -2.752  -2.040  -1.861  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.485 0.5778  0.7682    49073.101
   1_bss:  43.759 0.5970  0.7840    44399.133
   1_xyz:  26.011 0.8016  0.9904    17759.845
   1_adp:  27.268 0.7873  0.9816    18977.929
   1_occ:  27.257 0.7874  0.9816    18950.653
   2_bss:  26.637 0.7939  0.9397    18223.268
   2_xyz:  19.747 0.8632  0.9873    10503.716
   2_adp:  17.760 0.8826  0.9953     9070.140
   2_occ:  17.741 0.8827  0.9951     9050.882
   3_bss:  17.556 0.8843  0.9819     8913.665
   3_xyz:  14.671 0.9089  0.9942     6617.485
   3_adp:  14.147 0.9135  0.9937     6360.654
   3_occ:  14.129 0.9137  0.9937     6348.563
   4_bss:  14.144 0.9136  0.9867     6378.909
   4_xyz:  13.931 0.9155  0.9868     6244.629
   4_adp:  13.832 0.9165  0.9854     6222.708
   4_occ:  13.824 0.9166  0.9854     6220.102
   5_bss:  13.823 0.9166  0.9850     6221.373
   5_xyz:  13.521 0.9188  0.9851     6007.392
   5_adp:  13.605 0.9182  0.9808     6055.368
   5_occ:  13.606 0.9182  0.9807     6057.793
   5_bss:  13.606 0.9182  0.9848     6060.479
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8980e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8980e-01
   1_xyz:   1.371  0.012  0.084 15.777  0.006  4.108   1.0815e-01
   1_adp:   1.371  0.012  0.084 15.777  0.006  4.108   1.0815e-01
   1_occ:   1.371  0.012  0.084 15.777  0.006  4.108   1.0815e-01
   2_bss:   1.371  0.012  0.084 15.777  0.006  4.108   1.0815e-01
   2_xyz:   1.048  0.006  0.068 14.381  0.004  4.112   5.9660e-02
   2_adp:   1.048  0.006  0.068 14.381  0.004  4.112   5.9660e-02
   2_occ:   1.048  0.006  0.068 14.381  0.004  4.112   5.9660e-02
   3_bss:   1.048  0.006  0.068 14.381  0.004  4.112   5.9660e-02
   3_xyz:   1.121  0.008  0.077 14.879  0.005  4.115   6.9892e-02
   3_adp:   1.121  0.008  0.077 14.879  0.005  4.115   6.9892e-02
   3_occ:   1.121  0.008  0.077 14.879  0.005  4.115   6.9892e-02
   4_bss:   1.121  0.008  0.077 14.879  0.005  4.115   6.9892e-02
   4_xyz:   0.895  0.005  0.065 14.318  0.004  4.114   4.8710e-02
   4_adp:   0.895  0.005  0.065 14.318  0.004  4.114   4.8710e-02
   4_occ:   0.895  0.005  0.065 14.318  0.004  4.114   4.8710e-02
   5_bss:   0.895  0.005  0.065 14.318  0.004  4.114   4.8710e-02
   5_xyz:   1.042  0.007  0.074 14.705  0.004  4.107   6.1461e-02
   5_adp:   1.042  0.007  0.074 14.705  0.004  4.107   6.1461e-02
   5_occ:   1.042  0.007  0.074 14.705  0.004  4.107   6.1461e-02
   5_bss:   1.042  0.007  0.074 14.705  0.004  4.107   6.1461e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.406   2.3938e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.406   2.3938e-01
   1_xyz:   8.856  0.097  0.275 89.497  0.037  2.164   1.0990e-01
   1_adp:   8.856  0.097  0.275 89.497  0.037  2.164   1.0990e-01
   1_occ:   8.856  0.097  0.275 89.497  0.037  2.164   1.0990e-01
   2_bss:   8.856  0.097  0.275 89.497  0.037  2.164   1.0990e-01
   2_xyz:   6.808  0.037  0.263 85.169  0.041  2.377   4.2310e-02
   2_adp:   6.808  0.037  0.263 85.169  0.041  2.377   4.2310e-02
   2_occ:   6.808  0.037  0.263 85.169  0.041  2.377   4.2310e-02
   3_bss:   6.808  0.037  0.263 85.169  0.041  2.377   4.2310e-02
   3_xyz:   6.944  0.045  0.264 82.865  0.039  2.278   6.8913e-02
   3_adp:   6.944  0.045  0.264 82.865  0.039  2.278   6.8913e-02
   3_occ:   6.944  0.045  0.264 82.865  0.039  2.278   6.8913e-02
   4_bss:   6.944  0.045  0.264 82.865  0.039  2.278   6.8913e-02
   4_xyz:   6.128  0.037  0.202 82.285  0.038  2.386   3.1156e-02
   4_adp:   6.128  0.037  0.202 82.285  0.038  2.386   3.1156e-02
   4_occ:   6.128  0.037  0.202 82.285  0.038  2.386   3.1156e-02
   5_bss:   6.128  0.037  0.202 82.285  0.038  2.386   3.1156e-02
   5_xyz:   7.074  0.036  0.239 82.946  0.035  2.280   4.3075e-02
   5_adp:   7.074  0.036  0.239 82.946  0.035  2.280   4.3075e-02
   5_occ:   7.074  0.036  0.239 82.946  0.035  2.280   4.3075e-02
   5_bss:   7.074  0.036  0.239 82.946  0.035  2.280   4.3075e-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:  91.15   0.00  18.09  91.15   0.00  13.90  80.79   4.74  40.92
   1_occ:  91.15   0.00  18.09  91.15   0.00  13.90  80.79   4.74  40.92
   2_bss:  91.15   0.00  18.09  91.15   0.00  13.90  80.79   4.74  40.92
   2_xyz:  91.15   0.00  18.09  91.15   0.00  13.90  80.79   4.74  40.92
   2_adp:  90.68   0.00  17.46  90.68   0.00  13.35  80.39   6.83  39.85
   2_occ:  90.68   0.00  17.46  90.68   0.00  13.35  80.39   6.83  39.85
   3_bss:  90.68   0.00  17.46  90.68   0.00  13.35  80.39   6.83  39.85
   3_xyz:  90.68   0.00  17.46  90.68   0.00  13.35  80.39   6.83  39.85
   3_adp:  90.45   1.60  17.26  90.45   1.60  13.13  82.92   6.12  39.72
   3_occ:  90.45   1.60  17.26  90.45   1.60  13.13  82.92   6.12  39.72
   4_bss:  90.45   1.60  17.26  90.45   1.60  13.13  82.92   6.12  39.72
   4_xyz:  90.45   1.60  17.26  90.45   1.60  13.13  82.92   6.12  39.72
   4_adp:  87.34   2.23  16.91  87.34   2.23  13.01  82.25   5.81  38.14
   4_occ:  87.34   2.23  16.91  87.34   2.23  13.01  82.25   5.81  38.14
   5_bss:  87.34   2.23  16.91  87.34   2.23  13.01  82.25   5.81  38.14
   5_xyz:  87.34   2.23  16.91  87.34   2.23  13.01  82.25   5.81  38.14
   5_adp:  86.80   1.76  16.84  86.80   1.76  12.90  82.03   5.68  38.27
   5_occ:  86.80   1.76  16.84  86.80   1.76  12.90  82.03   5.68  38.27
   5_bss:  86.73   1.69  16.77  86.73   1.69  12.84  81.97   5.61  38.20
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.757    0.005    0.413
   1_adp:    1.757    0.005    0.413
   1_occ:    1.757    0.005    0.413
   2_bss:    1.757    0.005    0.413
   2_xyz:    1.304    0.052    0.477
   2_adp:    1.304    0.052    0.477
   2_occ:    1.304    0.052    0.477
   3_bss:    1.304    0.052    0.477
   3_xyz:    1.367    0.028    0.538
   3_adp:    1.367    0.028    0.538
   3_occ:    1.367    0.028    0.538
   4_bss:    1.367    0.028    0.538
   4_xyz:    1.500    0.029    0.543
   4_adp:    1.500    0.029    0.543
   4_occ:    1.500    0.029    0.543
   5_bss:    1.500    0.029    0.543
   5_xyz:    1.500    0.059    0.558
   5_adp:    1.500    0.059    0.558
   5_occ:    1.500    0.059    0.558
   5_bss:    1.500    0.059    0.558
------------------------------------------------------------------------

CPU time actual refinement: 347.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_429/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_429/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_429/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_429/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_429/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.19 
  Macro-tasks:
    bulk solvent and scale       = 43.07  
    individual site refinement   = 148.65 
    weights calculation          = 28.97  
    collect and process          = 6.13   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 226.94 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 110.57 
    alpha_beta                      = 8.53   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 121.47 
    fmodel                         = 7.41   
    r_factors                      = 0.24   
    phase_errors                   = 10.95  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 262.44 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.793 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    665 calls, 110.28 s
gradients_fft:          610 calls, 107.04 s

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

# Date 2008-01-16 Time 04:49:02 PST -0800 (1200487742.90 s)
Start R-work = 0.3950, R-free = 0.3909 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1775 (no bulk solvent and anisotropic scale)

Start R-work = 0.3826, R-free = 0.3763
Final R-work = 0.1072, R-free = 0.1554