# Date 2008-01-16 Time 05:26:14 PST -0800 (1200489974.42 s)
#phil __OFF__

Command line arguments: "../737.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20954
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 737

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 45.9914, 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: 2.78, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95103
Completeness in resolution range: 0.953422
Completeness with d_max=infinity: 0.950553

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95103
Completeness in resolution range: 0.953422
Completeness with d_max=infinity: 0.950553

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1757 [2155/2181]  1943   212   9.8%
  bin  2:  4.1757 -  3.3264 [2081/2100]  1872   209  10.0%
  bin  3:  3.3264 -  2.9094 [2034/2053]  1828   206  10.1%
  bin  4:  2.9094 -  2.6450 [2026/2056]  1828   198   9.8%
  bin  5:  2.6450 -  2.4563 [2037/2056]  1830   207  10.2%
  bin  6:  2.4563 -  2.3121 [1990/2015]  1787   203  10.2%
  bin  7:  2.3121 -  2.1966 [1998/2026]  1801   197   9.9%
  bin  8:  2.1966 -  2.1013 [1984/2020]  1790   194   9.8%
  bin  9:  2.1013 -  2.0206 [1976/2018]  1777   199  10.1%
  bin 10:  2.0206 -  1.9510 [1308/2021]  1174   134  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_737/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: 0.12 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:
        1.51 -     2.19: 27
        2.19 -     2.87: 1261
        2.87 -     3.55: 4570
        3.55 -     4.22: 9399
        4.22 -     4.90: 13625
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.514 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.680 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.702 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.736 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.798 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28877 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_737/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_737/model_refine_001.geo

CPU time processing inputs: 8.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 45.9914 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 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4740   r_free= 0.4792   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.284179                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6578 0.99   1400  158 0.3829 0.3896       6.571      6.6094|
|  2:  4.6578 -  3.7157 0.99   1350  143 0.4163 0.4093      6.8284      6.7621|
|  3:  3.7157 -  3.2515 0.99   1314  147 0.4490 0.4676      6.6886      6.7985|
|  4:  3.2515 -  2.9568 0.99   1329  157 0.4624 0.4423      6.5459      6.5029|
|  5:  2.9568 -  2.7462 0.99   1299  139 0.4985 0.4663      6.3753      6.3511|
|  6:  2.7462 -  2.5852 0.99   1296  148 0.5114 0.5564      6.2866      6.3018|
|  7:  2.5852 -  2.4563 0.99   1313  140 0.4990 0.4999      6.2547      6.1809|
|  8:  2.4563 -  2.3498 0.98   1263  144 0.5134 0.5112      6.1661      6.1831|
|  9:  2.3498 -  2.2597 0.98   1291  149 0.5159 0.5114       6.131      6.1492|
| 10:  2.2597 -  2.1819 0.99   1281  137 0.5043 0.5290      6.0899      6.1033|
| 11:  2.1819 -  2.1139 0.98   1283  138 0.5159 0.5995      6.0442      6.0691|
| 12:  2.1139 -  2.0536 0.97   1255  143 0.5250 0.5630      5.9709      6.0254|
| 13:  2.0536 -  1.9997 0.99   1274  142 0.5185 0.4908      5.8765      5.8172|
| 14:  1.9997 -  1.9510 0.52    682   74 0.5631 0.4616      5.8702      5.7754|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6578  1400   158  0.69  35.50   0.82     0.74      75532.33|
|  2:  4.6578 -  3.7157  1350   143  0.68  36.90   0.90     0.81     117332.63|
|  3:  3.7157 -  3.2515  1314   147  0.57  45.85   0.92     0.78     125185.76|
|  4:  3.2515 -  2.9568  1329   157  0.46  54.72   0.93     0.66     114863.82|
|  5:  2.9568 -  2.7462  1299   139  0.37  62.38   0.88     0.52      89518.50|
|  6:  2.7462 -  2.5852  1296   148  0.30  67.12   0.88     0.44      82133.25|
|  7:  2.5852 -  2.4563  1313   140  0.30  67.18   0.93     0.41      70272.96|
|  8:  2.4563 -  2.3498  1263   144  0.32  65.96   0.90     0.49      62788.15|
|  9:  2.3498 -  2.2597  1291   149  0.35  63.67   0.91     0.51      54299.60|
| 10:  2.2597 -  2.1819  1281   137  0.33  65.52   0.96     0.49      52067.00|
| 11:  2.1819 -  2.1139  1283   138  0.25  71.35   0.96     0.39      52132.70|
| 12:  2.1139 -  2.0536  1255   143  0.25  71.78   0.97     0.40      47285.60|
| 13:  2.0536 -  1.9997  1274   142  0.29  68.46   0.94     0.47      38299.31|
| 14:  1.9997 -  1.9510   682    74  0.41  59.04   0.93     0.62      27147.24|
|alpha:            min =        0.39 max =            0.81 mean =         0.55|
|beta:             min =    27147.24 max =       125185.76 mean =     74074.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.40|
|phase err.(test): min =        0.00 max =           89.94 mean =        59.86|
|-----------------------------------------------------------------------------|

============================== 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 = 13.843466             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.634   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.269016              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.933   (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 |  1.514 -  1.852:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.852 -  2.191:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.191 -  2.530:       56 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.530 -  2.868:     1205 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.868 -  3.207:     1988 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.207 -  3.545:     2582 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.545 -  3.884:     4726 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.884 -  4.223:     4673 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.223 -  4.561:     6198 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.561 -  4.900:     7427 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.514 |       0.590 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    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 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4740   r_free= 0.4792   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.284179                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4644   r_free= 0.4693   ksol= 0.37   Bsol= 50.00   scale= 0.927   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,1.46,1.78,0.00,0.00,0.00); trace/3= 0.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.280952                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.375103             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.701   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.443756              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.733   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4644      final r-factor (work) = 0.3720          |
| start r-factor (free) = 0.4693      final r-factor (free) = 0.4045          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.7439 = 10.38 * 0.50 * 6.2759 + 1.00 * 0.1875                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.1841 = 10.38 * 0.50 * 6.1781 + 1.00 * 0.1350                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3720      final r-factor (work) = 0.3376          |
| start r-factor (free) = 0.4045      final r-factor (free) = 0.4111          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9256 = 1.44 * 1.00 * 6.1781 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7990 = 1.44 * 1.00 * 6.0798 + 1.00 * 0.0212                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.42   19.29    None  None   None       |
|    all(noH): 2823   0      0.00    95.42   19.29    None  None   None       |
|    Sol.    : 438    0      0.00    95.42   37.14    None  None   None       |
|    Mac.    : 2385   0      0.00    88.75   16.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.542:  815   |   5:    47.712 -  57.254:   78        |
|      1:     9.542 -  19.085:  847   |   6:    57.254 -  66.796:   54        |
|      2:    19.085 -  28.627:  561   |   7:    66.796 -  76.339:   18        |
|      3:    28.627 -  38.169:  282   |   8:    76.339 -  85.881:    7        |
|      4:    38.169 -  47.712:  157   |   9:    85.881 -  95.423:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3376 r_free = 0.4111             target_work(ml) = 6.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3370 r_free = 0.4110             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3370   r_free= 0.4110   ksol= 0.37   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,1.46,1.78,0.00,0.00,0.00); trace/3= 0.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.083400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3362   r_free= 0.4102   ksol= 0.35   Bsol= 53.70   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-0.10,0.38,-0.00,0.00,0.00); trace/3= -0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.083591                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.244663             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.651   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.469007              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.333  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3362      final r-factor (work) = 0.2644          |
| start r-factor (free) = 0.4102      final r-factor (free) = 0.3348          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.2770 = 10.24 * 0.50 * 6.0796 + 1.00 * 0.1350                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.8084 = 10.24 * 0.50 * 5.9962 + 1.00 * 0.0940                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2644      final r-factor (work) = 0.2406          |
| start r-factor (free) = 0.3348      final r-factor (free) = 0.3147          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8333 = 0.47 * 1.00 * 5.9962 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7539 = 0.47 * 1.00 * 5.8496 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.85   17.91    None  None   None       |
|    all(noH): 2823   0      0.00    92.85   17.91    None  None   None       |
|    Sol.    : 438    0      2.21    92.85   38.43    None  None   None       |
|    Mac.    : 2385   0      0.00    91.72   14.14    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 -   9.285:  823   |   5:    46.425 -  55.709:   82        |
|      1:     9.285 -  18.570: 1076   |   6:    55.709 -  64.994:   46        |
|      2:    18.570 -  27.855:  397   |   7:    64.994 -  74.279:   19        |
|      3:    27.855 -  37.140:  228   |   8:    74.279 -  83.564:    0        |
|      4:    37.140 -  46.425:  145   |   9:    83.564 -  92.849:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2406 r_free = 0.3147             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2402 r_free = 0.3146             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2402   r_free= 0.3146   ksol= 0.35   Bsol= 53.70   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-0.10,0.38,-0.00,0.00,0.00); trace/3= -0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.817501                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2399   r_free= 0.3132   ksol= 0.35   Bsol= 53.70   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,-1.37,-0.53,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.814389                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.244992              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.523  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.319519              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.087  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2399      final r-factor (work) = 0.1912          |
| start r-factor (free) = 0.3132      final r-factor (free) = 0.2492          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5839 = 3.24 * 0.50 * 5.8490 + 1.00 * 0.0940                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3434 = 3.24 * 0.50 * 5.7256 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1773          |
| start r-factor (free) = 0.2492      final r-factor (free) = 0.2349          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8397 = 0.32 * 1.00 * 5.7256 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7909 = 0.32 * 1.00 * 5.5765 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.11    89.67   17.55    None  None   None       |
|    all(noH): 2823   0      1.11    89.67   17.55    None  None   None       |
|    Sol.    : 438    0      4.79    87.39   40.89    None  None   None       |
|    Mac.    : 2385   0      1.11    89.67   13.26    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:     1.108 -   9.964: 1021   |   5:    45.388 -  54.244:  103        |
|      1:     9.964 -  18.820: 1025   |   6:    54.244 -  63.100:   70        |
|      2:    18.820 -  27.676:  274   |   7:    63.100 -  71.956:   21        |
|      3:    27.676 -  36.532:  156   |   8:    71.956 -  80.812:    5        |
|      4:    36.532 -  45.388:  142   |   9:    80.812 -  89.669:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1773 r_free = 0.2349             target_work(ml) = 5.550         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1771 r_free = 0.2345             target_work(ml) = 5.549         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1771   r_free= 0.2345   ksol= 0.35   Bsol= 53.70   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,-1.37,-0.53,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.548900                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1772   r_free= 0.2339   ksol= 0.32   Bsol= 44.14   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.19,-1.32,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.548521                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.010329              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.640  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.531112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.729  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1772      final r-factor (work) = 0.1413          |
| start r-factor (free) = 0.2339      final r-factor (free) = 0.1897          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4506 = 3.01 * 0.50 * 5.5787 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2683 = 3.01 * 0.50 * 5.4545 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1413      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.1897      final r-factor (free) = 0.1799          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9060 = 0.53 * 1.00 * 5.4545 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8264 = 0.53 * 1.00 * 5.3036 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.35    93.67   17.61    None  None   None       |
|    all(noH): 2823   0      0.35    93.67   17.61    None  None   None       |
|    Sol.    : 438    0      6.09    86.00   43.38    None  None   None       |
|    Mac.    : 2385   0      0.35    93.67   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.349 -   9.682: 1010   |   5:    47.012 -  56.344:  101        |
|      1:     9.682 -  19.014: 1109   |   6:    56.344 -  65.676:   86        |
|      2:    19.014 -  28.347:  250   |   7:    65.676 -  75.009:   37        |
|      3:    28.347 -  37.679:  119   |   8:    75.009 -  84.341:    7        |
|      4:    37.679 -  47.012:  100   |   9:    84.341 -  93.674:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1321 r_free = 0.1799             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1320 r_free = 0.1796             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1796   ksol= 0.32   Bsol= 44.14   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.19,-1.32,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.276741                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1323   r_free= 0.1792   ksol= 0.32   Bsol= 43.81   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.40,-1.56,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.275399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.082051              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.705  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.862185              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.702  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1323      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1792      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8831 = 4.08 * 0.50 * 5.3036 + 1.00 * 0.0583                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7325 = 4.08 * 0.50 * 5.2235 + 1.00 * 0.0713                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5131 = 0.86 * 1.00 * 5.2235 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4632 = 0.86 * 1.00 * 5.1652 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    103.43  17.47    None  None   None       |
|    all(noH): 2823   0      0.37    103.43  17.47    None  None   None       |
|    Sol.    : 438    0      5.97    92.75   43.15    None  None   None       |
|    Mac.    : 2385   0      0.37    103.43  12.75    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:     0.367 -  10.673: 1251   |   5:    51.898 -  62.205:   87        |
|      1:    10.673 -  20.979:  970   |   6:    62.205 -  72.511:   57        |
|      2:    20.979 -  31.286:  195   |   7:    72.511 -  82.818:   24        |
|      3:    31.286 -  41.592:  123   |   8:    82.818 -  93.124:    7        |
|      4:    41.592 -  51.898:  107   |   9:    93.124 - 103.430:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1612             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1128 r_free = 0.1610             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1610   ksol= 0.32   Bsol= 43.81   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.40,-1.56,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152610                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6578 0.99   1400  158 0.0973 0.1294      5.3548      5.5593|
|  2:  4.6578 -  3.7157 0.99   1350  143 0.0845 0.1203       5.438      5.6827|
|  3:  3.7157 -  3.2515 0.99   1314  147 0.1092 0.1506      5.5114      5.8522|
|  4:  3.2515 -  2.9568 0.99   1329  157 0.1265 0.1656      5.4896       5.657|
|  5:  2.9568 -  2.7462 0.99   1299  139 0.1308 0.1787      5.3137      5.5147|
|  6:  2.7462 -  2.5852 0.99   1296  148 0.1192 0.1581      5.1939      5.3992|
|  7:  2.5852 -  2.4563 0.99   1313  140 0.1245 0.1730      5.1596      5.3637|
|  8:  2.4563 -  2.3498 0.98   1263  144 0.1195 0.1821      5.0616       5.397|
|  9:  2.3498 -  2.2597 0.98   1291  149 0.1171 0.1810      5.0339      5.3334|
| 10:  2.2597 -  2.1819 0.99   1281  137 0.1113 0.1751       4.958      5.1889|
| 11:  2.1819 -  2.1139 0.98   1283  138 0.1170 0.1929      4.9647      5.3445|
| 12:  2.1139 -  2.0536 0.97   1255  143 0.1083 0.1571      4.8835      5.0649|
| 13:  2.0536 -  1.9997 0.99   1274  142 0.1172 0.1906      4.8073      5.1077|
| 14:  1.9997 -  1.9510 0.52    682   74 0.1063 0.1564      4.6782      4.9272|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6578  1400   158  0.94   8.72   0.98     0.96       6608.55|
|  2:  4.6578 -  3.7157  1350   143  0.95   8.19   1.03     1.02       9313.54|
|  3:  3.7157 -  3.2515  1314   147  0.93  11.93   1.05     1.04      11304.71|
|  4:  3.2515 -  2.9568  1329   157  0.91  14.56   1.02     1.00      11007.46|
|  5:  2.9568 -  2.7462  1299   139  0.90  15.67   1.00     0.97       7917.59|
|  6:  2.7462 -  2.5852  1296   148  0.90  15.87   1.00     0.97       6900.53|
|  7:  2.5852 -  2.4563  1313   140  0.91  15.51   1.00     0.98       6202.42|
|  8:  2.4563 -  2.3498  1263   144  0.90  15.91   0.99     0.96       5253.12|
|  9:  2.3498 -  2.2597  1291   149  0.91  15.30   1.01     0.99       5081.62|
| 10:  2.2597 -  2.1819  1281   137  0.90  15.84   1.01     0.98       4503.69|
| 11:  2.1819 -  2.1139  1283   138  0.89  17.19   1.01     0.97       4664.87|
| 12:  2.1139 -  2.0536  1255   143  0.91  15.61   1.02     1.01       4158.01|
| 13:  2.0536 -  1.9997  1274   142  0.90  16.68   1.01     1.00       3478.34|
| 14:  1.9997 -  1.9510   682    74  0.91  15.22   1.00     0.97       2672.76|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2672.76 max =        11304.71 mean =      6528.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.35|
|phase err.(test): min =        0.00 max =           89.68 mean =        13.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1610   ksol= 0.32   Bsol= 43.80   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.39,-1.55,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152617                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1610   ksol= 0.32   Bsol= 43.80   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.39,-1.55,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152617                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6578 0.99   1400  158 0.0973 0.1294      5.3549      5.5593|
|  2:  4.6578 -  3.7157 0.99   1350  143 0.0845 0.1203       5.438      5.6826|
|  3:  3.7157 -  3.2515 0.99   1314  147 0.1092 0.1506      5.5114      5.8521|
|  4:  3.2515 -  2.9568 0.99   1329  157 0.1265 0.1656      5.4896       5.657|
|  5:  2.9568 -  2.7462 0.99   1299  139 0.1308 0.1787      5.3137      5.5147|
|  6:  2.7462 -  2.5852 0.99   1296  148 0.1192 0.1581      5.1939      5.3992|
|  7:  2.5852 -  2.4563 0.99   1313  140 0.1245 0.1730      5.1596      5.3637|
|  8:  2.4563 -  2.3498 0.98   1263  144 0.1195 0.1821      5.0616       5.397|
|  9:  2.3498 -  2.2597 0.98   1291  149 0.1171 0.1810      5.0339      5.3334|
| 10:  2.2597 -  2.1819 0.99   1281  137 0.1113 0.1751       4.958      5.1889|
| 11:  2.1819 -  2.1139 0.98   1283  138 0.1170 0.1929      4.9647      5.3445|
| 12:  2.1139 -  2.0536 0.97   1255  143 0.1083 0.1571      4.8835      5.0649|
| 13:  2.0536 -  1.9997 0.99   1274  142 0.1172 0.1906      4.8073      5.1077|
| 14:  1.9997 -  1.9510 0.52    682   74 0.1063 0.1564      4.6782      4.9272|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6578  1400   158  0.94   8.72   0.98     0.96       6610.25|
|  2:  4.6578 -  3.7157  1350   143  0.95   8.19   1.03     1.02       9313.98|
|  3:  3.7157 -  3.2515  1314   147  0.93  11.93   1.05     1.04      11303.78|
|  4:  3.2515 -  2.9568  1329   157  0.91  14.56   1.02     1.00      11007.16|
|  5:  2.9568 -  2.7462  1299   139  0.90  15.67   1.00     0.97       7917.62|
|  6:  2.7462 -  2.5852  1296   148  0.90  15.87   1.00     0.97       6900.59|
|  7:  2.5852 -  2.4563  1313   140  0.91  15.51   1.00     0.98       6202.54|
|  8:  2.4563 -  2.3498  1263   144  0.90  15.91   0.99     0.96       5253.19|
|  9:  2.3498 -  2.2597  1291   149  0.91  15.30   1.01     0.99       5081.69|
| 10:  2.2597 -  2.1819  1281   137  0.90  15.84   1.01     0.98       4503.73|
| 11:  2.1819 -  2.1139  1283   138  0.89  17.19   1.01     0.97       4664.90|
| 12:  2.1139 -  2.0536  1255   143  0.91  15.61   1.02     1.01       4158.03|
| 13:  2.0536 -  1.9997  1274   142  0.90  16.68   1.01     1.00       3478.35|
| 14:  1.9997 -  1.9510   682    74  0.91  15.22   1.00     0.97       2672.77|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2672.77 max =        11303.78 mean =      6528.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.35|
|phase err.(test): min =        0.00 max =           89.68 mean =        13.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    103.42  17.46    None  None   None       |
|    all(noH): 2823   0      0.36    103.42  17.46    None  None   None       |
|    Sol.    : 438    0      5.96    92.74   43.14    None  None   None       |
|    Mac.    : 2385   0      0.36    103.42  12.74    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:     0.356 -  10.662: 1251   |   5:    51.888 -  62.194:   87        |
|      1:    10.662 -  20.969:  970   |   6:    62.194 -  72.500:   57        |
|      2:    20.969 -  31.275:  195   |   7:    72.500 -  82.807:   24        |
|      3:    31.275 -  41.581:  123   |   8:    82.807 -  93.113:    7        |
|      4:    41.581 -  51.888:  107   |   9:    93.113 - 103.420:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 4.499
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 318 from: 319
   mapped sites are within: 0.732 - 4.499

peak=    6.590 closest distance to " O   HOH Z 278 " =    1.541
peak=    6.429 closest distance to " NE2 GLN A  11 " =    1.370
peak=    6.162 closest distance to " O   HOH Z   7 " =    1.817
peak=    5.795 closest distance to " O   HOH Z 126 " =    1.969
peak=    5.701 closest distance to " O   HOH Z 385 " =    0.980
peak=    5.671 closest distance to " O   HOH Z 214 " =    1.666
peak=    5.450 closest distance to " NH2 ARG A  56 " =    2.008
peak=    5.298 closest distance to " O   HOH Z 144 " =    1.759
peak=    5.218 closest distance to " O   HOH Z 427 " =    2.155
peak=    5.201 closest distance to " CG  PRO A  54 " =    1.166
peak=    5.174 closest distance to " O   HOH Z 427 " =    1.215
peak=    5.139 closest distance to " O   HOH Z  65 " =    0.989
peak=    5.021 closest distance to " CB  GLN A 223 " =    1.521
peak=    4.903 closest distance to " O   HOH Z 193 " =    1.757
peak=    4.892 closest distance to " O   HOH Z  78 " =    1.620
peak=    4.879 closest distance to " O   HOH Z 124 " =    1.584
peak=    4.871 closest distance to " O   HOH Z 287 " =    1.887
peak=    4.857 closest distance to " O   HOH Z  63 " =    1.671
peak=    4.852 closest distance to " O   HOH Z 222 " =    1.017
peak=    4.761 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.749 closest distance to " O   HOH Z 423 " =    1.860
peak=    4.746 closest distance to " O   HOH Z  49 " =    1.317
peak=    4.737 closest distance to " O   HOH Z  11 " =    1.325
peak=    4.721 closest distance to " O   HOH Z  97 " =    1.267
peak=    4.710 closest distance to " O   HOH Z 202 " =    1.633
peak=    4.629 closest distance to " CB  SER A  63 " =    1.265
peak=    4.609 closest distance to " O   SER A  87 " =    2.170
peak=    4.603 closest distance to " O   HOH Z 272 " =    1.848
peak=    4.573 closest distance to " O   HOH Z 236 " =    1.479
peak=    4.526 closest distance to " CB  SER A   3 " =    1.379
peak=    4.506 closest distance to " O   HOH Z 260 " =    1.222
peak=    4.490 closest distance to " O   HOH Z  28 " =    1.454
peak=    4.480 closest distance to " O   HOH Z 298 " =    1.946
peak=    4.462 closest distance to " O   HOH Z 134 " =    1.647
peak=    4.447 closest distance to " O   HOH Z 371 " =    2.186
peak=    4.416 closest distance to " CB  ASN A 148 " =    1.428
peak=    4.413 closest distance to " O   HOH Z 375 " =    0.979
peak=    4.403 closest distance to " O   HOH Z   1 " =    1.812
peak=    4.387 closest distance to " O   HOH Z  10 " =    1.829
peak=    4.376 closest distance to " O   HOH Z 217 " =    2.873
peak=    4.355 closest distance to " O   HOH Z 155 " =    1.963
peak=    4.341 closest distance to " O   HOH Z 425 " =    1.544
peak=    4.332 closest distance to " O   HOH Z 316 " =    2.976
peak=    4.291 closest distance to " O   HOH Z 282 " =    1.784
peak=    4.267 closest distance to " O   HOH Z 232 " =    2.269
peak=    4.263 closest distance to " CB  GLU A 152 " =    1.308
peak=    4.254 closest distance to " O   HOH Z 108 " =    1.844
peak=    4.251 closest distance to " CB  TYR A 169 " =    0.902
peak=    4.231 closest distance to " CB  PRO A  54 " =    0.934
peak=    4.191 closest distance to " O   HOH Z  97 " =    1.565
peak=    4.176 closest distance to " O   HOH Z 132 " =    1.132
peak=    4.171 closest distance to " CB  GLN A 183 " =    1.181
peak=    4.169 closest distance to " O   HOH Z 276 " =    1.393
peak=    4.140 closest distance to " O   HOH Z 313 " =    1.835
peak=    4.130 closest distance to " CB  TRP A 179 " =    1.339
peak=    4.123 closest distance to " CA  GLY A 241 " =    3.631
peak=    4.118 closest distance to " O   HOH Z 211 " =    1.234
peak=    4.113 closest distance to " CA  TYR A  30 " =    0.983
peak=    4.103 closest distance to " O   HOH Z  73 " =    1.849
peak=    4.095 closest distance to " O   HOH Z 380 " =    1.739
peak=    4.092 closest distance to " O   HOH Z   9 " =    2.272
peak=    4.089 closest distance to " CG  PRO A 198 " =    1.234
peak=    4.075 closest distance to " O   HOH Z 133 " =    2.416
peak=    4.037 closest distance to " OD2 ASP A 286 " =    2.519
peak=    4.026 closest distance to " O   HOH Z 352 " =    1.646
peak=    3.990 closest distance to " O   HOH Z 166 " =    1.368
peak=    3.966 closest distance to " O   HOH Z 371 " =    1.996
peak=    3.961 closest distance to " O   PRO A 198 " =    1.511
peak=    3.955 closest distance to " OD1 ASN A  69 " =    2.676
peak=    3.955 closest distance to " O   HOH Z 227 " =    1.856
peak=    3.944 closest distance to " CG  GLN A  11 " =    2.150
peak=    3.940 closest distance to " O   HOH Z 234 " =    3.648
peak=    3.939 closest distance to " O   HOH Z 403 " =    1.358
peak=    3.922 closest distance to " O   HOH Z  68 " =    1.650
peak=    3.920 closest distance to " O   HOH Z 145 " =    1.350
peak=    3.910 closest distance to " O   HOH Z 258 " =    2.087
peak=    3.891 closest distance to " O   HOH Z  78 " =    1.897
peak=    3.875 closest distance to " O   HOH Z 171 " =    2.571
peak=    3.870 closest distance to " CG  GLN A  77 " =    2.295
peak=    3.862 closest distance to " O   HOH Z 151 " =    1.675
peak=    3.858 closest distance to " CG2 VAL A 257 " =    0.872
peak=    3.846 closest distance to " O   HOH Z 261 " =    1.838
peak=    3.844 closest distance to " O   HOH Z 106 " =    2.288
peak=    3.843 closest distance to " CG2 THR A 221 " =    1.217
peak=    3.833 closest distance to " NE AARG A 275 " =    1.490
peak=    3.824 closest distance to " O   HOH Z 139 " =    1.362
peak=    3.802 closest distance to " O   HOH Z 302 " =    1.336
peak=    3.800 closest distance to " O   HOH Z 392 " =    1.185
peak=    3.800 closest distance to " NZ  LYS A 117 " =    1.117
peak=    3.799 closest distance to " O   HOH Z 394 " =    1.552
peak=    3.788 closest distance to " CB  ARG A 275 " =    0.911
peak=    3.785 closest distance to " O   HOH Z 133 " =    1.494
peak=    3.782 closest distance to " CG  ARG A  66 " =    2.389
peak=    3.769 closest distance to " O   HOH Z 414 " =    1.268
peak=    3.752 closest distance to " O   HOH Z  88 " =    2.912
peak=    3.748 closest distance to " OG BSER A  99 " =    2.205
peak=    3.743 closest distance to " O   HOH Z 112 " =    2.407
peak=    3.742 closest distance to " O   HOH Z  97 " =    2.081
peak=    3.741 closest distance to " O   HOH Z 334 " =    2.740
peak=    3.736 closest distance to " O   HOH Z  44 " =    1.981
peak=    3.736 closest distance to " O   HOH Z 126 " =    1.495
peak=    3.735 closest distance to " O   HOH Z   6 " =    1.908
peak=    3.732 closest distance to " O   HOH Z 365 " =    2.561
peak=    3.731 closest distance to " O   HOH Z 405 " =    1.321
peak=    3.727 closest distance to " CB  GLU A 128 " =    0.981
peak=    3.717 closest distance to " CB  ARG A 139 " =    1.245
peak=    3.716 closest distance to " O   HOH Z 152 " =    2.282
peak=    3.709 closest distance to " N   PHE A 130 " =    1.290
peak=    3.703 closest distance to " O   HOH Z 389 " =    1.715
peak=    3.700 closest distance to " O   HOH Z 193 " =    2.147
peak=    3.699 closest distance to " O   HOH Z  59 " =    1.502
peak=    3.694 closest distance to " OD1BASN A 224 " =    2.134
peak=    3.692 closest distance to " OG  SER A  62 " =    3.165
peak=    3.684 closest distance to " O   HOH Z  61 " =    1.636
peak=    3.683 closest distance to " O   HOH Z  50 " =    1.600
peak=    3.683 closest distance to " CB  GLU A 277 " =    3.460
peak=    3.676 closest distance to " O   HOH Z 371 " =    2.894
peak=    3.670 closest distance to " O   HOH Z 378 " =    1.000
peak=    3.661 closest distance to " CB  THR A 157 " =    1.010
peak=    3.647 closest distance to " O   HOH Z  40 " =    2.194
peak=    3.639 closest distance to " CG  LEU A 167 " =    1.236
peak=    3.626 closest distance to " O   HOH Z 271 " =    2.232
peak=    3.625 closest distance to " O   HOH Z 132 " =    2.030
peak=    3.624 closest distance to " CB  ASP A 132 " =    3.985
peak=    3.619 closest distance to " ND2 ASN A 187 " =    1.524
peak=    3.618 closest distance to " CD  LYS A 166 " =    1.412
peak=    3.615 closest distance to " CB  LEU A 228 " =    1.070
peak=    3.613 closest distance to " OG BSER A 258 " =    0.732
peak=    3.606 closest distance to " O   HOH Z   2 " =    1.617
peak=    3.598 closest distance to " CB  VAL A 265 " =    1.432
peak=    3.595 closest distance to " NE2 GLN A  73 " =    3.407
peak=    3.593 closest distance to " NH2 ARG A 219 " =    1.802
peak=    3.589 closest distance to " O   HOH Z 119 " =    1.563
peak=    3.588 closest distance to " O   HOH Z  44 " =    3.286
peak=    3.577 closest distance to " O   HOH Z 419 " =    2.442
peak=    3.576 closest distance to " O   HOH Z 135 " =    1.631
peak=    3.570 closest distance to " O   HOH Z 289 " =    1.422
peak=    3.570 closest distance to " O   HOH Z 109 " =    1.331
peak=    3.569 closest distance to " O   HOH Z 193 " =    1.590
peak=    3.568 closest distance to " O   HOH Z  48 " =    1.583
peak=    3.563 closest distance to " O   HOH Z 116 " =    2.646
peak=    3.548 closest distance to " O   HOH Z 125 " =    2.278
peak=    3.547 closest distance to " CG1 ILE A  33 " =    1.145
peak=    3.547 closest distance to " N   GLY A 196 " =    1.056
peak=    3.547 closest distance to " O   HOH Z   1 " =    1.519
peak=    3.544 closest distance to " CG  TRP A 179 " =    2.115
peak=    3.532 closest distance to " CD1 LEU A 228 " =    1.729
peak=    3.531 closest distance to " O   GLY A 302 " =    1.584
peak=    3.531 closest distance to " O   HOH Z 215 " =    1.356
peak=    3.516 closest distance to " O   HOH Z  32 " =    1.931
peak=    3.512 closest distance to " O   HOH Z 245 " =    1.228
peak=    3.510 closest distance to " CA  ALA A  21 " =    1.168
peak=    3.500 closest distance to " O   HOH Z 213 " =    1.909
peak=    3.499 closest distance to " CB  ALA A  21 " =    1.844
peak=    3.499 closest distance to " O   HOH Z 263 " =    2.457
peak=    3.498 closest distance to " O   HOH Z 417 " =    1.283
peak=    3.494 closest distance to " C   ALA A 299 " =    0.971
peak=    3.492 closest distance to " O   HOH Z 180 " =    2.086
peak=    3.489 closest distance to " O   HOH Z 207 " =    1.849
peak=    3.489 closest distance to " O   ASN A 209 " =    1.568
peak=    3.489 closest distance to " O   HOH Z 368 " =    1.930
peak=    3.485 closest distance to " O   HOH Z 409 " =    2.034
peak=    3.479 closest distance to " O   HOH Z 183 " =    1.389
peak=    3.476 closest distance to " O   HOH Z 209 " =    2.470
peak=    3.475 closest distance to " OD1 ASN A 217 " =    1.630
peak=    3.475 closest distance to " O   HOH Z 327 " =    1.819
peak=    3.474 closest distance to " CE AMET A  47 " =    1.229
peak=    3.473 closest distance to " CG  GLN A  55 " =    1.920
peak=    3.456 closest distance to " O   HOH Z  43 " =    1.795
peak=    3.450 closest distance to " CG  GLN A  89 " =    1.364
peak=    3.445 closest distance to " CG1BVAL A 121 " =    2.135
peak=    3.443 closest distance to " CB  THR A  31 " =    1.597
peak=    3.442 closest distance to " O   HOH Z  61 " =    1.669
peak=    3.441 closest distance to " O   HOH Z  21 " =    1.571
peak=    3.438 closest distance to " CG  GLN A  88 " =    1.052
peak=    3.436 closest distance to " O   HOH Z 269 " =    1.116
peak=    3.431 closest distance to " CA  ASN A 215 " =    1.242
peak=    3.425 closest distance to " N   ARG A 156 " =    1.225
peak=    3.424 closest distance to " O   HOH Z 286 " =    2.400
peak=    3.421 closest distance to " O   HOH Z 128 " =    1.981
peak=    3.420 closest distance to " O   HOH Z 435 " =    1.800
peak=    3.419 closest distance to " ND1 HIS A  81 " =    1.583
peak=    3.418 closest distance to " O   HOH Z 374 " =    2.615
peak=    3.417 closest distance to " CD2 LEU A 255 " =    1.527
peak=    3.411 closest distance to " O   HOH Z 345 " =    1.485
peak=    3.407 closest distance to " O   HOH Z 250 " =    1.473
peak=    3.405 closest distance to " NH2AARG A 190 " =    1.406
peak=    3.404 closest distance to " CB  VAL A 202 " =    1.635
peak=    3.400 closest distance to " O   HOH Z 244 " =    1.623
peak=    3.399 closest distance to " CD  ARG A 138 " =    0.862
peak=    3.393 closest distance to " O   HOH Z 207 " =    1.819
peak=    3.386 closest distance to " CA  PHE A 283 " =    1.395
peak=    3.382 closest distance to " CG  PRO A  90 " =    1.374
peak=    3.381 closest distance to " O   HOH Z  15 " =    1.387
peak=    3.377 closest distance to " O   HOH Z 286 " =    2.358
peak=    3.377 closest distance to " O   HOH Z 195 " =    1.561
peak=    3.377 closest distance to " O   HOH Z 281 " =    2.002
peak=    3.373 closest distance to " CB  ALA A  34 " =    1.123
peak=    3.372 closest distance to " O   HOH Z 220 " =    1.221
peak=    3.365 closest distance to " O   HOH Z 281 " =    4.499
peak=    3.365 closest distance to " O   HOH Z 158 " =    2.810
peak=    3.350 closest distance to " O   HOH Z 247 " =    1.114
peak=    3.349 closest distance to " O   HOH Z 140 " =    1.631
peak=    3.345 closest distance to " O   ALA A   1 " =    1.446
peak=    3.343 closest distance to " O   HOH Z  17 " =    2.277
peak=    3.340 closest distance to " O   HOH Z 188 " =    1.919
peak=    3.331 closest distance to " O   HOH Z 368 " =    3.679
peak=    3.331 closest distance to " OG1 THR A   4 " =    2.651
peak=    3.329 closest distance to " CB  ASN A 187 " =    1.061
peak=    3.327 closest distance to " O   MET A 105 " =    1.777
peak=    3.323 closest distance to " CD BLYS A 290 " =    1.111
peak=    3.320 closest distance to " CG2 THR A 220 " =    0.996
peak=    3.318 closest distance to " O   HOH Z 112 " =    1.060
peak=    3.315 closest distance to " OE2 GLU A  53 " =    2.111
peak=    3.313 closest distance to " O   HOH Z 288 " =    2.030
peak=    3.311 closest distance to " CA  ILE A 234 " =    1.036
peak=    3.308 closest distance to " O   HOH Z 344 " =    1.137
peak=    3.307 closest distance to " CA  VAL A  41 " =    1.052
peak=    3.305 closest distance to " O   HOH Z 375 " =    2.238
peak=    3.299 closest distance to " O   HOH Z 409 " =    3.364
peak=    3.299 closest distance to " CB  ASP A 132 " =    3.836
peak=    3.297 closest distance to " O  BHOH Z  74 " =    1.382
peak=    3.293 closest distance to " N   ASN A  39 " =    1.312
peak=    3.284 closest distance to " CE1 TYR A 186 " =    1.262
peak=    3.278 closest distance to " CG2BVAL A  41 " =    0.903
peak=    3.274 closest distance to " O   HOH Z  93 " =    1.851
peak=    3.272 closest distance to " O   HOH Z 122 " =    1.463
peak=    3.272 closest distance to " O   HOH Z 357 " =    1.935
peak=    3.272 closest distance to " N   GLN A 278 " =    1.053
peak=    3.271 closest distance to " O   HOH Z 287 " =    2.033
peak=    3.270 closest distance to " CB  GLU A 236 " =    1.416
peak=    3.268 closest distance to " CA  ALA A 160 " =    0.780
peak=    3.261 closest distance to " O   HOH Z 130 " =    2.309
peak=    3.260 closest distance to " O   HOH Z 362 " =    2.083
peak=    3.259 closest distance to " CB  MET A 105 " =    1.347
peak=    3.258 closest distance to " CA  MET A  40 " =    1.162
peak=    3.253 closest distance to " CA  THR A 264 " =    0.788
peak=    3.252 closest distance to " N   ALA A   1 " =    1.283
peak=    3.251 closest distance to " CA  VAL A 126 " =    1.225
peak=    3.250 closest distance to " O   HOH Z 227 " =    1.980
peak=    3.250 closest distance to " CB  ARG A 190 " =    1.769
peak=    3.249 closest distance to " CD  PRO A 243 " =    1.768
peak=    3.248 closest distance to " N   CYS A 260 " =    0.788
peak=    3.245 closest distance to " CB  TRP A 266 " =    1.081
peak=    3.240 closest distance to " O   HOH Z 173 " =    1.953
peak=    3.237 closest distance to " O   HOH Z 345 " =    3.383
peak=    3.236 closest distance to " OG  SER A  22 " =    2.882
peak=    3.233 closest distance to " CA  ALA A  51 " =    1.090
peak=    3.232 closest distance to " O   HOH Z 379 " =    2.172
peak=    3.230 closest distance to " O   SER A  26 " =    1.531
peak=    3.230 closest distance to " CB  SER A  26 " =    1.520
peak=    3.228 closest distance to " O   HOH Z 358 " =    1.268
peak=    3.227 closest distance to " O   HOH Z 146 " =    1.659
peak=    3.223 closest distance to " CG  GLU A 277 " =    2.079
peak=    3.222 closest distance to " CB  SER A 216 " =    0.870
peak=    3.217 closest distance to " CB  GLN A  88 " =    1.269
peak=    3.217 closest distance to " NH1AARG A 145 " =    0.989
peak=    3.216 closest distance to " CB  ARG A 138 " =    0.993
peak=    3.215 closest distance to " O   HOH Z  66 " =    2.203
peak=    3.214 closest distance to " CB  ARG A 102 " =    0.821
peak=    3.212 closest distance to " CB  ASN A 170 " =    1.307
peak=    3.209 closest distance to " CD1 ILE A 263 " =    1.347
peak=    3.208 closest distance to " O   HOH Z 141 " =    1.600
peak=    3.204 closest distance to " CA  GLY A 267 " =    1.287
peak=    3.201 closest distance to " OG  SER A  62 " =    2.943
peak=    3.198 closest distance to " CB  ALA A 291 " =    1.496
peak=    3.190 closest distance to " O   HOH Z 422 " =    2.742
peak=    3.189 closest distance to " NH1 ARG A  14 " =    1.038
peak=    3.187 closest distance to " O   HOH Z 373 " =    1.486
peak=    3.186 closest distance to " NH1BARG A 145 " =    1.234
peak=    3.186 closest distance to " N   TRP A 150 " =    1.465
peak=    3.185 closest distance to " OG BSER A 164 " =    2.214
peak=    3.183 closest distance to " CB  ARG A  79 " =    1.389
peak=    3.182 closest distance to " O   HOH Z 116 " =    1.595
peak=    3.181 closest distance to " O   HOH Z 411 " =    2.520
peak=    3.178 closest distance to " O   HOH Z  94 " =    1.916
peak=    3.174 closest distance to " O   HOH Z 158 " =    3.187
peak=    3.171 closest distance to " O   HOH Z   5 " =    1.356
peak=    3.171 closest distance to " CA  SER A  32 " =    1.624
peak=    3.169 closest distance to " CA  SER A  87 " =    0.953
peak=    3.167 closest distance to " O   HOH Z  30 " =    1.567
peak=    3.165 closest distance to " N   SER A  97 " =    0.850
peak=    3.163 closest distance to " CB  SER A 276 " =    1.034
peak=    3.158 closest distance to " O   HOH Z 383 " =    3.185
peak=    3.156 closest distance to " O   HOH Z 172 " =    2.979
peak=    3.156 closest distance to " O   HOH Z 326 " =    1.417
peak=    3.154 closest distance to " O   HOH Z 437 " =    2.148
peak=    3.153 closest distance to " O   HOH Z 203 " =    1.637
peak=    3.150 closest distance to " O   HOH Z 423 " =    1.788
peak=    3.145 closest distance to " O   HOH Z 181 " =    2.155
peak=    3.145 closest distance to " CG1BVAL A  72 " =    1.191
peak=    3.137 closest distance to " N   HIS A  86 " =    1.809
peak=    3.134 closest distance to " C   PRO A 163 " =    1.475
peak=    3.134 closest distance to " O   HOH Z 217 " =    1.517
peak=    3.125 closest distance to " O   HOH Z 216 " =    1.931
peak=    3.123 closest distance to " OE1 GLU A  37 " =    1.133
peak=    3.122 closest distance to " CB  ILE A 120 " =    1.336
peak=    3.120 closest distance to " CB  VAL A 265 " =    2.038
peak=    3.112 closest distance to " CB  MET A  47 " =    1.078
peak=    3.111 closest distance to " CE  LYS A 166 " =    1.810
peak=    3.110 closest distance to " CB  LYS A 117 " =    1.197
peak=    3.110 closest distance to " O   HOH Z 355 " =    1.526
peak=    3.108 closest distance to " O   HOH Z 291 " =    1.556
peak=    3.105 closest distance to " O   HOH Z 154 " =    1.963
peak=    3.104 closest distance to " O   GLY A  57 " =    2.515
peak=    3.101 closest distance to " N   GLU A   2 " =    1.237
peak=    3.100 closest distance to " O   ALA A 165 " =    1.326
peak=    3.095 closest distance to " NZ  LYS A  76 " =    1.353
peak=    3.082 closest distance to " O   HOH Z 115 " =    1.628
peak=    3.081 closest distance to " CA  PHE A 208 " =    0.895
peak=    3.081 closest distance to " NE2 GLN A  58 " =    3.286
peak=    3.075 closest distance to " O   HOH Z 108 " =    1.814
peak=    3.073 closest distance to " N   TYR A  15 " =    1.044
peak=    3.072 closest distance to " O   HOH Z 426 " =    1.731
peak=    3.071 closest distance to " O   HOH Z 115 " =    2.199
peak=    3.048 closest distance to " NE2 GLN A 278 " =    3.609
peak=    3.039 closest distance to " O   HOH Z 425 " =    1.909
peak=    3.028 closest distance to " O   HOH Z  80 " =    2.033

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.754 - 5.506
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 194
   mapped sites are within: 0.754 - 5.506

peak=   -4.766 closest distance to " CD  ARG A  14 " =    3.214
peak=   -4.676 closest distance to " O   HOH Z 377 " =    1.890
peak=   -4.326 closest distance to " O   HOH Z 409 " =    3.273
peak=   -4.267 closest distance to " O   PRO A 198 " =    1.448
peak=   -4.210 closest distance to " O   HOH Z 198 " =    2.197
peak=   -4.151 closest distance to " C   ASN A 285 " =    2.221
peak=   -4.149 closest distance to " CB  TYR A  15 " =    2.073
peak=   -4.137 closest distance to " N   HIS A 115 " =    1.835
peak=   -4.071 closest distance to " CA  GLY A  98 " =    1.956
peak=   -4.069 closest distance to " CG  MET A 105 " =    0.939
peak=   -4.059 closest distance to " C   HIS A 108 " =    1.159
peak=   -4.043 closest distance to " CD  GLN A  88 " =    0.836
peak=   -4.026 closest distance to " O   HOH Z 166 " =    1.273
peak=   -4.019 closest distance to " O   HOH Z  13 " =    1.271
peak=   -4.013 closest distance to " CZ  PHE A  59 " =    1.556
peak=   -4.010 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.993 closest distance to " O   HOH Z 385 " =    1.359
peak=   -3.943 closest distance to " O   HOH Z  65 " =    0.904
peak=   -3.941 closest distance to " N   GLN A  58 " =    1.659
peak=   -3.938 closest distance to " O   ALA A  51 " =    1.348
peak=   -3.922 closest distance to " CD1 LEU A 101 " =    2.264
peak=   -3.915 closest distance to " CB  ALA A 248 " =    1.881
peak=   -3.909 closest distance to " O   HOH Z  28 " =    1.905
peak=   -3.904 closest distance to " CD  ARG A 156 " =    1.927
peak=   -3.873 closest distance to " O   HOH Z  60 " =    1.845
peak=   -3.869 closest distance to " O   HOH Z  43 " =    1.852
peak=   -3.861 closest distance to " CB  CYS A 201 " =    2.311
peak=   -3.860 closest distance to " CB  PRO A 243 " =    2.475
peak=   -3.857 closest distance to " O   HOH Z  52 " =    1.372
peak=   -3.839 closest distance to " OG ASER A 134 " =    1.089
peak=   -3.834 closest distance to " O   HOH Z 102 " =    1.860
peak=   -3.808 closest distance to " O   HOH Z 137 " =    1.309
peak=   -3.782 closest distance to " O   HOH Z 385 " =    2.224
peak=   -3.763 closest distance to " O   TRP A  70 " =    1.453
peak=   -3.736 closest distance to " CD2 LEU A 237 " =    2.397
peak=   -3.724 closest distance to " O   HOH Z 388 " =    1.862
peak=   -3.718 closest distance to " O   HOH Z 351 " =    1.571
peak=   -3.713 closest distance to " CB  ALA A 291 " =    2.180
peak=   -3.713 closest distance to " OE1 GLN A  77 " =    1.692
peak=   -3.707 closest distance to " O   ALA A 161 " =    1.798
peak=   -3.700 closest distance to " O   HOH Z 231 " =    1.816
peak=   -3.692 closest distance to " OD1 ASN A 148 " =    1.601
peak=   -3.686 closest distance to " O   HOH Z 290 " =    1.242
peak=   -3.681 closest distance to " O   PRO A 198 " =    1.223
peak=   -3.681 closest distance to " O   HOH Z 438 " =    1.003
peak=   -3.680 closest distance to " ND2 ASN A  45 " =    1.082
peak=   -3.675 closest distance to " O   HOH Z  93 " =    1.916
peak=   -3.670 closest distance to " CB  ASP A  27 " =    2.388
peak=   -3.669 closest distance to " OG  SER A  97 " =    2.046
peak=   -3.667 closest distance to " CB  ALA A  43 " =    2.180
peak=   -3.665 closest distance to " CG  PHE A 283 " =    2.527
peak=   -3.657 closest distance to " O   HOH Z 410 " =    2.222
peak=   -3.654 closest distance to " O   PRO A 243 " =    2.374
peak=   -3.650 closest distance to " O   MET A  40 " =    2.741
peak=   -3.643 closest distance to " O   HOH Z 185 " =    1.892
peak=   -3.638 closest distance to " N   GLN A 122 " =    1.430
peak=   -3.630 closest distance to " OG  SER A  87 " =    1.188
peak=   -3.621 closest distance to " CG  ARG A 219 " =    2.264
peak=   -3.611 closest distance to " O   HOH Z 103 " =    1.582
peak=   -3.611 closest distance to " O   VAL A  67 " =    2.669
peak=   -3.611 closest distance to " N   MET A 188 " =    1.806
peak=   -3.608 closest distance to " CE2 TYR A 116 " =    2.984
peak=   -3.600 closest distance to " N   GLN A  88 " =    1.885
peak=   -3.597 closest distance to " O   HOH Z 250 " =    1.407
peak=   -3.594 closest distance to " CA  VAL A 153 " =    2.330
peak=   -3.590 closest distance to " O   VAL A 197 " =    1.343
peak=   -3.585 closest distance to " O   HOH Z 234 " =    4.093
peak=   -3.582 closest distance to " CE3 TRP A 274 " =    2.418
peak=   -3.582 closest distance to " C   ALA A 158 " =    1.279
peak=   -3.553 closest distance to " O   SER A 135 " =    1.475
peak=   -3.548 closest distance to " CB  ALA A   7 " =    1.962
peak=   -3.545 closest distance to " O   HOH Z 415 " =    1.667
peak=   -3.543 closest distance to " CG  ASN A 301 " =    2.096
peak=   -3.520 closest distance to " O   SER A  22 " =    2.593
peak=   -3.517 closest distance to " O   HOH Z 266 " =    4.415
peak=   -3.512 closest distance to " CG  PRO A 163 " =    2.483
peak=   -3.510 closest distance to " CZ3 TRP A 123 " =    1.700
peak=   -3.498 closest distance to " CZ  ARG A  66 " =    0.797
peak=   -3.497 closest distance to " O   HOH Z 298 " =    1.257
peak=   -3.497 closest distance to " CA  GLY A 133 " =    1.908
peak=   -3.481 closest distance to " OG  SER A   3 " =    1.607
peak=   -3.481 closest distance to " O   HOH Z  88 " =    2.040
peak=   -3.474 closest distance to " OG BSER A 134 " =    1.505
peak=   -3.466 closest distance to " ND2 ASN A  39 " =    1.874
peak=   -3.463 closest distance to " CG1BVAL A  41 " =    2.840
peak=   -3.460 closest distance to " O   HOH Z 426 " =    2.167
peak=   -3.444 closest distance to " OG BSER A 134 " =    1.380
peak=   -3.442 closest distance to " CZ  TYR A 214 " =    1.296
peak=   -3.439 closest distance to " O   HOH Z 385 " =    0.775
peak=   -3.438 closest distance to " OG  SER A  26 " =    1.067
peak=   -3.434 closest distance to " CG  ASP A 231 " =    0.754
peak=   -3.426 closest distance to " CB  ALA A 227 " =    2.349
peak=   -3.424 closest distance to " O   HOH Z 111 " =    1.011
peak=   -3.423 closest distance to " O   HOH Z  24 " =    1.218
peak=   -3.421 closest distance to " CB  ASP A 132 " =    2.252
peak=   -3.420 closest distance to " CG  GLN A  58 " =    1.482
peak=   -3.410 closest distance to " CB  ALA A 100 " =    1.978
peak=   -3.403 closest distance to " O   HOH Z  97 " =    2.202
peak=   -3.402 closest distance to " O   GLY A  98 " =    1.974
peak=   -3.388 closest distance to " O   HOH Z 372 " =    2.278
peak=   -3.385 closest distance to " O   SER A 216 " =    1.805
peak=   -3.383 closest distance to " O   ASP A 191 " =    1.924
peak=   -3.378 closest distance to " O   HOH Z 384 " =    3.057
peak=   -3.374 closest distance to " CG  GLU A 152 " =    1.650
peak=   -3.368 closest distance to " OG  SER A 245 " =    1.297
peak=   -3.368 closest distance to " CA  GLY A 241 " =    2.103
peak=   -3.367 closest distance to " O   HOH Z 385 " =    1.193
peak=   -3.359 closest distance to " O   HOH Z 211 " =    1.023
peak=   -3.355 closest distance to " OD1 ASP A 200 " =    1.084
peak=   -3.351 closest distance to " O   HOH Z 252 " =    4.849
peak=   -3.350 closest distance to " OXT GLY A 302 " =    2.962
peak=   -3.349 closest distance to " N   VAL A  72 " =    1.451
peak=   -3.346 closest distance to " O   LEU A 282 " =    2.227
peak=   -3.336 closest distance to " O   SER A 146 " =    1.015
peak=   -3.332 closest distance to " C   LEU A 143 " =    1.320
peak=   -3.330 closest distance to " NE  ARG A  36 " =    1.829
peak=   -3.318 closest distance to " N   LYS A 166 " =    1.867
peak=   -3.318 closest distance to " O   VAL A 189 " =    2.460
peak=   -3.315 closest distance to " OD2 ASP A  65 " =    1.456
peak=   -3.313 closest distance to " O   ARG A 145 " =    1.474
peak=   -3.313 closest distance to " ND2 ASN A  60 " =    1.322
peak=   -3.302 closest distance to " NH1 ARG A  56 " =    2.335
peak=   -3.299 closest distance to " CD2 TYR A 293 " =    1.951
peak=   -3.292 closest distance to " CD  LYS A 166 " =    2.372
peak=   -3.290 closest distance to " N   GLN A  58 " =    1.367
peak=   -3.289 closest distance to " N   ALA A   9 " =    1.394
peak=   -3.289 closest distance to " O   HOH Z 139 " =    2.877
peak=   -3.285 closest distance to " O   HOH Z 427 " =    1.655
peak=   -3.285 closest distance to " CB  PRO A 163 " =    2.431
peak=   -3.281 closest distance to " OD2 ASP A  50 " =    1.407
peak=   -3.280 closest distance to " O   HOH Z 124 " =    1.423
peak=   -3.279 closest distance to " O   VAL A  67 " =    2.774
peak=   -3.277 closest distance to " NH2AARG A 275 " =    5.473
peak=   -3.276 closest distance to " NH2 ARG A  79 " =    1.930
peak=   -3.275 closest distance to " CE  MET A  93 " =    1.251
peak=   -3.274 closest distance to " O   ALA A   7 " =    1.579
peak=   -3.274 closest distance to " CG1 ILE A  20 " =    2.468
peak=   -3.269 closest distance to " OE2 GLU A 152 " =    1.060
peak=   -3.262 closest distance to " O   HOH Z  64 " =    1.345
peak=   -3.262 closest distance to " O   HOH Z 313 " =    2.029
peak=   -3.261 closest distance to " O   HOH Z 426 " =    1.604
peak=   -3.254 closest distance to " O   ARG A  56 " =    1.550
peak=   -3.252 closest distance to " O   HOH Z 210 " =    2.032
peak=   -3.246 closest distance to " O   HOH Z 263 " =    3.065
peak=   -3.243 closest distance to " CE3 TRP A 150 " =    2.071
peak=   -3.243 closest distance to " O   HOH Z 222 " =    1.243
peak=   -3.235 closest distance to " O   ALA A   1 " =    1.096
peak=   -3.232 closest distance to " SG ACYS A 201 " =    1.799
peak=   -3.230 closest distance to " O   HOH Z 147 " =    1.465
peak=   -3.221 closest distance to " O   HOH Z 275 " =    1.578
peak=   -3.219 closest distance to " O   HOH Z 143 " =    2.193
peak=   -3.218 closest distance to " CE2 PHE A 204 " =    1.938
peak=   -3.218 closest distance to " N   ALA A 114 " =    2.380
peak=   -3.215 closest distance to " O   HOH Z  90 " =    2.503
peak=   -3.210 closest distance to " OD1AASN A 224 " =    1.768
peak=   -3.209 closest distance to " O   HOH Z 348 " =    1.775
peak=   -3.206 closest distance to " O   ILE A  49 " =    1.542
peak=   -3.204 closest distance to " O   HOH Z 368 " =    2.214
peak=   -3.201 closest distance to " O   PHE A 218 " =    1.319
peak=   -3.190 closest distance to " CE1 TYR A 169 " =    2.512
peak=   -3.183 closest distance to " O   HOH Z 207 " =    1.878
peak=   -3.181 closest distance to " O   LEU A 143 " =    1.662
peak=   -3.180 closest distance to " ND2 ASN A 249 " =    2.279
peak=   -3.178 closest distance to " O   SER A   3 " =    1.039
peak=   -3.178 closest distance to " C   THR A 264 " =    1.438
peak=   -3.172 closest distance to " CD1 LEU A 255 " =    2.834
peak=   -3.171 closest distance to " CA  SER A 146 " =    2.291
peak=   -3.168 closest distance to " CB  ILE A  33 " =    2.842
peak=   -3.168 closest distance to " O   HOH Z 409 " =    5.506
peak=   -3.167 closest distance to " O   HOH Z 389 " =    1.761
peak=   -3.165 closest distance to " O   HOH Z 131 " =    3.972
peak=   -3.164 closest distance to " O   ALA A 180 " =    1.133
peak=   -3.161 closest distance to " O   HOH Z 364 " =    2.025
peak=   -3.155 closest distance to " OE1 GLN A  88 " =    1.036
peak=   -3.154 closest distance to " CD1 PHE A  59 " =    1.953
peak=   -3.151 closest distance to " CB  PHE A 192 " =    1.607
peak=   -3.148 closest distance to " NH1 ARG A 195 " =    2.331
peak=   -3.142 closest distance to " O   HOH Z  39 " =    1.641
peak=   -3.128 closest distance to " O   ALA A  84 " =    1.800
peak=   -3.121 closest distance to " CD2 LEU A 237 " =    2.616
peak=   -3.121 closest distance to " O   MET A 113 " =    2.421
peak=   -3.117 closest distance to " OG ASER A 216 " =    1.145
peak=   -3.115 closest distance to " N   ALA A   1 " =    3.091
peak=   -3.096 closest distance to " CE2 PHE A 218 " =    2.428
peak=   -3.090 closest distance to " CB  SER A 245 " =    2.472
peak=   -3.088 closest distance to " NH2 ARG A  66 " =    4.447
peak=   -3.088 closest distance to " OG  SER A 206 " =    1.902
peak=   -3.083 closest distance to " N   ASP A 171 " =    2.472
peak=   -3.080 closest distance to " O   SER A  62 " =    2.308
peak=   -3.053 closest distance to " O   HOH Z 377 " =    1.109
peak=   -3.052 closest distance to " N   ASN A 127 " =    2.070
peak=   -3.050 closest distance to " O   ILE A 109 " =    2.526
peak=   -3.048 closest distance to " O   HOH Z 346 " =    1.763
peak=   -3.029 closest distance to " CG2 THR A 178 " =    2.100

================= 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    :  0.4740 0.4792   6.284179e+00   6.282670e+00
   1_bss:  0.4644 0.4693   6.280952e+00   6.271248e+00
   1_xyz:  0.3720 0.4045   6.131573e+00   6.187756e+00
   1_adp:  0.3376 0.4111   6.083901e+00   6.198694e+00
   1_occ:  0.3370 0.4110   6.083400e+00   6.198043e+00
   2_bss:  0.3362 0.4102   6.083591e+00   6.196752e+00
   2_xyz:  0.2644 0.3348   5.885429e+00   6.047335e+00
   2_adp:  0.2406 0.3147   5.818262e+00   5.997476e+00
   2_occ:  0.2402 0.3146   5.817501e+00   5.997355e+00
   3_bss:  0.2399 0.3132   5.814389e+00   5.995395e+00
   3_xyz:  0.1912 0.2492   5.610708e+00   5.808020e+00
   3_adp:  0.1773 0.2349   5.550389e+00   5.759143e+00
   3_occ:  0.1771 0.2345   5.548900e+00   5.756863e+00
   4_bss:  0.1772 0.2339   5.548521e+00   5.755038e+00
   4_xyz:  0.1413 0.1897   5.332615e+00   5.556171e+00
   4_adp:  0.1321 0.1799   5.277682e+00   5.504939e+00
   4_occ:  0.1320 0.1796   5.276741e+00   5.503945e+00
   5_bss:  0.1323 0.1792   5.275399e+00   5.502288e+00
   5_xyz:  0.1161 0.1648   5.176302e+00   5.427232e+00
   5_adp:  0.1129 0.1612   5.153156e+00   5.406525e+00
   5_occ:  0.1128 0.1610   5.152610e+00   5.406028e+00
   5_bss:  0.1128 0.1610   5.152617e+00   5.406029e+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:  0.374  50.000  -2.971   1.463   1.778   0.000   0.000   0.000
   1_xyz:  0.374  50.000  -2.971   1.463   1.778   0.000   0.000   0.000
   1_adp:  0.374  50.000  -2.971   1.463   1.778   0.000   0.000   0.000
   1_occ:  0.374  50.000  -2.971   1.463   1.778   0.000   0.000   0.000
   2_bss:  0.348  53.701  -1.491  -0.099   0.376  -0.000   0.000   0.000
   2_xyz:  0.348  53.701  -1.491  -0.099   0.376  -0.000   0.000   0.000
   2_adp:  0.348  53.701  -1.491  -0.099   0.376  -0.000   0.000   0.000
   2_occ:  0.348  53.701  -1.491  -0.099   0.376  -0.000   0.000   0.000
   3_bss:  0.348  53.701  -1.472  -1.367  -0.534  -0.000  -0.000  -0.000
   3_xyz:  0.348  53.701  -1.472  -1.367  -0.534  -0.000  -0.000  -0.000
   3_adp:  0.348  53.701  -1.472  -1.367  -0.534  -0.000  -0.000  -0.000
   3_occ:  0.348  53.701  -1.472  -1.367  -0.534  -0.000  -0.000  -0.000
   4_bss:  0.324  44.143  -1.938  -2.193  -1.323  -0.000  -0.000  -0.000
   4_xyz:  0.324  44.143  -1.938  -2.193  -1.323  -0.000  -0.000  -0.000
   4_adp:  0.324  44.143  -1.938  -2.193  -1.323  -0.000  -0.000  -0.000
   4_occ:  0.324  44.143  -1.938  -2.193  -1.323  -0.000  -0.000  -0.000
   5_bss:  0.316  43.810  -2.084  -2.402  -1.558  -0.000  -0.000  -0.000
   5_xyz:  0.316  43.810  -2.084  -2.402  -1.558  -0.000  -0.000  -0.000
   5_adp:  0.316  43.810  -2.084  -2.402  -1.558  -0.000  -0.000  -0.000
   5_occ:  0.316  43.810  -2.084  -2.402  -1.558  -0.000  -0.000  -0.000
   5_bss:  0.317  43.799  -2.073  -2.391  -1.547  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.448 0.4006  0.5531    74081.472
   1_bss:  57.736 0.4210  0.5874    69652.068
   1_xyz:  45.208 0.5797  0.7871    48017.510
   1_adp:  46.168 0.5670  0.7777    49002.705
   1_occ:  46.192 0.5667  0.7769    48988.544
   2_bss:  46.006 0.5690  0.7684    48793.305
   2_xyz:  35.563 0.6938  0.9203    30272.959
   2_adp:  32.133 0.7341  0.9432    26198.135
   2_occ:  32.118 0.7343  0.9427    26176.480
   3_bss:  31.938 0.7359  0.9202    25821.968
   3_xyz:  24.678 0.8148  0.9822    16102.628
   3_adp:  22.814 0.8346  0.9856    14352.841
   3_occ:  22.755 0.8352  0.9857    14272.415
   4_bss:  22.721 0.8354  0.9607    14201.130
   4_xyz:  17.747 0.8825  0.9913     9041.564
   4_adp:  16.523 0.8939  0.9910     8238.277
   4_occ:  16.488 0.8943  0.9910     8203.005
   5_bss:  16.446 0.8945  0.9838     8145.970
   5_xyz:  14.825 0.9078  0.9908     6800.207
   5_adp:  14.324 0.9123  0.9877     6540.880
   5_occ:  14.308 0.9124  0.9877     6530.144
   5_bss:  14.308 0.9124  0.9877     6530.255
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8751e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8751e-01
   1_xyz:   1.583  0.012  0.103 16.172  0.006  4.103   1.3505e-01
   1_adp:   1.583  0.012  0.103 16.172  0.006  4.103   1.3505e-01
   1_occ:   1.583  0.012  0.103 16.172  0.006  4.103   1.3505e-01
   2_bss:   1.583  0.012  0.103 16.172  0.006  4.103   1.3505e-01
   2_xyz:   1.335  0.009  0.090 15.017  0.005  4.108   9.3964e-02
   2_adp:   1.335  0.009  0.090 15.017  0.005  4.108   9.3964e-02
   2_occ:   1.335  0.009  0.090 15.017  0.005  4.108   9.3964e-02
   3_bss:   1.335  0.009  0.090 15.017  0.005  4.108   9.3964e-02
   3_xyz:   0.938  0.006  0.060 14.282  0.004  4.105   5.3720e-02
   3_adp:   0.938  0.006  0.060 14.282  0.004  4.105   5.3720e-02
   3_occ:   0.938  0.006  0.060 14.282  0.004  4.105   5.3720e-02
   4_bss:   0.938  0.006  0.060 14.282  0.004  4.105   5.3720e-02
   4_xyz:   1.022  0.006  0.070 14.395  0.004  4.109   5.8309e-02
   4_adp:   1.022  0.006  0.070 14.395  0.004  4.109   5.8309e-02
   4_occ:   1.022  0.006  0.070 14.395  0.004  4.109   5.8309e-02
   5_bss:   1.022  0.006  0.070 14.395  0.004  4.109   5.8309e-02
   5_xyz:   1.125  0.008  0.077 14.900  0.004  4.106   7.1264e-02
   5_adp:   1.125  0.008  0.077 14.900  0.004  4.106   7.1264e-02
   5_occ:   1.125  0.008  0.077 14.900  0.004  4.106   7.1264e-02
   5_bss:   1.125  0.008  0.077 14.900  0.004  4.106   7.1264e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.514   2.3812e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.514   2.3812e-01
   1_xyz:  10.484  0.087  0.423 88.591  0.027  1.906   1.0753e-01
   1_adp:  10.484  0.087  0.423 88.591  0.027  1.906   1.0753e-01
   1_occ:  10.484  0.087  0.423 88.591  0.027  1.906   1.0753e-01
   2_bss:  10.484  0.087  0.423 88.591  0.027  1.906   1.0753e-01
   2_xyz:   8.773  0.061  0.303 89.459  0.043  2.279   9.2796e-02
   2_adp:   8.773  0.061  0.303 89.459  0.043  2.279   9.2796e-02
   2_occ:   8.773  0.061  0.303 89.459  0.043  2.279   9.2796e-02
   3_bss:   8.773  0.061  0.303 89.459  0.043  2.279   9.2796e-02
   3_xyz:   6.962  0.040  0.221 80.662  0.030  2.323   3.8405e-02
   3_adp:   6.962  0.040  0.221 80.662  0.030  2.323   3.8405e-02
   3_occ:   6.962  0.040  0.221 80.662  0.030  2.323   3.8405e-02
   4_bss:   6.962  0.040  0.221 80.662  0.030  2.323   3.8405e-02
   4_xyz:   6.503  0.036  0.247 82.427  0.033  2.323   4.3257e-02
   4_adp:   6.503  0.036  0.247 82.427  0.033  2.323   4.3257e-02
   4_occ:   6.503  0.036  0.247 82.427  0.033  2.323   4.3257e-02
   5_bss:   6.503  0.036  0.247 82.427  0.033  2.323   4.3257e-02
   5_xyz:   7.188  0.058  0.271 84.576  0.030  2.230   6.5281e-02
   5_adp:   7.188  0.058  0.271 84.576  0.030  2.230   6.5281e-02
   5_occ:   7.188  0.058  0.271 84.576  0.030  2.230   6.5281e-02
   5_bss:   7.188  0.058  0.271 84.576  0.030  2.230   6.5281e-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:  95.42   0.00  19.29  88.75   0.00  16.01  95.42   0.00  37.14
   1_occ:  95.42   0.00  19.29  88.75   0.00  16.01  95.42   0.00  37.14
   2_bss:  95.42   0.00  19.29  88.75   0.00  16.01  95.42   0.00  37.14
   2_xyz:  95.42   0.00  19.29  88.75   0.00  16.01  95.42   0.00  37.14
   2_adp:  92.85   0.00  17.91  91.72   0.00  14.14  92.85   2.21  38.43
   2_occ:  92.85   0.00  17.91  91.72   0.00  14.14  92.85   2.21  38.43
   3_bss:  92.85   0.00  17.91  91.72   0.00  14.14  92.85   2.21  38.43
   3_xyz:  92.85   0.00  17.91  91.72   0.00  14.14  92.85   2.21  38.43
   3_adp:  89.67   1.11  17.55  89.67   1.11  13.26  87.39   4.79  40.89
   3_occ:  89.67   1.11  17.55  89.67   1.11  13.26  87.39   4.79  40.89
   4_bss:  89.67   1.11  17.55  89.67   1.11  13.26  87.39   4.79  40.89
   4_xyz:  89.67   1.11  17.55  89.67   1.11  13.26  87.39   4.79  40.89
   4_adp:  93.67   0.35  17.61  93.67   0.35  12.88  86.00   6.09  43.38
   4_occ:  93.67   0.35  17.61  93.67   0.35  12.88  86.00   6.09  43.38
   5_bss:  93.67   0.35  17.61  93.67   0.35  12.88  86.00   6.09  43.38
   5_xyz:  93.67   0.35  17.61  93.67   0.35  12.88  86.00   6.09  43.38
   5_adp: 103.43   0.37  17.47 103.43   0.37  12.75  92.75   5.97  43.15
   5_occ: 103.43   0.37  17.47 103.43   0.37  12.75  92.75   5.97  43.15
   5_bss: 103.42   0.36  17.46 103.42   0.36  12.74  92.74   5.96  43.14
------------------------------------------------------------------------
 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:    1.920    0.007    0.353
   1_adp:    1.920    0.007    0.353
   1_occ:    1.920    0.007    0.353
   2_bss:    1.920    0.007    0.353
   2_xyz:    1.517    0.052    0.588
   2_adp:    1.517    0.052    0.588
   2_occ:    1.517    0.052    0.588
   3_bss:    1.517    0.052    0.588
   3_xyz:    1.453    0.032    0.688
   3_adp:    1.453    0.032    0.688
   3_occ:    1.453    0.032    0.688
   4_bss:    1.453    0.032    0.688
   4_xyz:    1.575    0.049    0.778
   4_adp:    1.575    0.049    0.778
   4_occ:    1.575    0.049    0.778
   5_bss:    1.575    0.049    0.778
   5_xyz:    1.572    0.048    0.808
   5_adp:    1.572    0.048    0.808
   5_occ:    1.572    0.048    0.808
   5_bss:    1.572    0.048    0.808
------------------------------------------------------------------------

CPU time actual refinement: 292.44


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_737/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_737/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_737/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_737/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_737/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 292.30 
  Macro-tasks:
    bulk solvent and scale       = 33.20  
    individual site refinement   = 121.50 
    weights calculation          = 25.23  
    collect and process          = 5.41   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 185.43 
  Micro-tasks:
    mask                            = 2.08   
    f_calc                          = 96.67  
    alpha_beta                      = 6.90   
    target                          = 0.93   
    gradients_wrt_atomic_parameters = 101.95 
    fmodel                         = 5.53   
    r_factors                      = 0.14   
    phase_errors                   = 8.62   
    foms                           = 0.16   
    TOTAL for micro-tasks          = 222.98 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.201 micro seconds
Total CPU time: 5.07 minutes
from_scatterers_fft:    625 calls, 96.36 s
gradients_fft:          570 calls, 91.06 s

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

# Date 2008-01-16 Time 05:31:18 PST -0800 (1200490278.66 s)
Start R-work = 0.4740, R-free = 0.4792 (no bulk solvent and anisotropic scale)
Final R-work = 0.1363, R-free = 0.1819 (no bulk solvent and anisotropic scale)

Start R-work = 0.4644, R-free = 0.4693
Final R-work = 0.1128, R-free = 0.1610