# Date 2008-01-16 Time 00:39:39 PST -0800 (1200472779.11 s)
#phil __OFF__

Command line arguments: "../106.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31222
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 106

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.8686, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.40, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.95093
Completeness in resolution range: 0.912942
Completeness with d_max=infinity: 0.91027

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9854
                             d_min =   1.9509

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.95093
Completeness in resolution range: 0.912942
Completeness with d_max=infinity: 0.91027

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9858 -  4.1757 [2250/2279]  2021   229  10.2%
  bin  2:  4.1757 -  3.3263 [2170/2193]  1950   220  10.1%
  bin  3:  3.3263 -  2.9093 [2136/2161]  1933   203   9.5%
  bin  4:  2.9093 -  2.6449 [2108/2135]  1895   213  10.1%
  bin  5:  2.6449 -  2.4562 [2095/2128]  1880   215  10.3%
  bin  6:  2.4562 -  2.3119 [2092/2120]  1888   204   9.8%
  bin  7:  2.3119 -  2.1965 [2084/2120]  1881   203   9.7%
  bin  8:  2.1965 -  2.1012 [2088/2130]  1871   217  10.4%
  bin  9:  2.1012 -  2.0205 [1980/2101]  1789   191   9.6%
  bin 10:  2.0205 -  1.9509 [ 586/2090]   522    64  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_106/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.93 -     1.72: 9
        1.72 -     2.52: 50
        2.52 -     3.31: 3816
        3.31 -     4.11: 9406
        4.11 -     4.90: 15110
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  0.928 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.169 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.170 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.458 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.494 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28386 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_106/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_106/model_refine_001.geo

CPU time processing inputs: 9.55


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.8686 87.2539 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5147   r_free= 0.5076   ksol= 0.00   Bsol= 0.00   scale= 0.767    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.309147                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.6579 0.99   1467  161 0.4206 0.4228      6.6506      6.7044|
|  2:  4.6579 -  3.7157 0.99   1409  155 0.4492 0.4696      6.8528      6.8854|
|  3:  3.7157 -  3.2514 0.99   1374  157 0.4981 0.4749       6.712      6.7239|
|  4:  3.2514 -  2.9567 0.98   1374  145 0.5074 0.4950      6.5364      6.5163|
|  5:  2.9567 -  2.7461 0.99   1361  156 0.5548 0.5528      6.3827       6.404|
|  6:  2.7461 -  2.5851 0.99   1366  152 0.5459 0.5329      6.2912      6.2033|
|  7:  2.5851 -  2.4562 0.98   1328  154 0.5297 0.4888      6.2355      6.1687|
|  8:  2.4562 -  2.3497 0.98   1354  143 0.5543 0.5257      6.1753      6.1962|
|  9:  2.3497 -  2.2596 0.99   1343  143 0.5537 0.5393      6.1239      6.1703|
| 10:  2.2596 -  2.1818 0.99   1345  146 0.5577 0.5772      6.0988      6.1197|
| 11:  2.1818 -  2.1138 0.97   1331  158 0.5670 0.5478      6.0125      6.0342|
| 12:  2.1138 -  2.0535 0.98   1318  151 0.5583 0.5476      5.9521      5.9339|
| 13:  2.0535 -  1.9996 0.76   1026  108 0.5565 0.5870      5.8771      5.8155|
| 14:  1.9996 -  1.9509 0.18    234   30 0.5884 0.4503      5.9288      5.7273|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.6579  1467   161  0.62  40.95   0.78     0.64      94322.80|
|  2:  4.6579 -  3.7157  1409   155  0.61  42.69   0.86     0.67     141104.53|
|  3:  3.7157 -  3.2514  1374   157  0.49  52.85   0.79     0.61     147030.90|
|  4:  3.2514 -  2.9567  1374   145  0.40  59.81   0.76     0.50     121907.91|
|  5:  2.9567 -  2.7461  1361   156  0.31  66.66   0.70     0.40      96349.63|
|  6:  2.7461 -  2.5851  1366   152  0.28  68.71   0.69     0.35      81926.73|
|  7:  2.5851 -  2.4562  1328   154  0.26  70.60   0.72     0.31      74531.70|
|  8:  2.4562 -  2.3497  1354   143  0.27  70.07   0.70     0.33      64809.73|
|  9:  2.3497 -  2.2596  1343   143  0.26  70.34   0.69     0.33      61724.23|
| 10:  2.2596 -  2.1818  1345   146  0.25  71.06   0.73     0.32      54451.79|
| 11:  2.1818 -  2.1138  1331   158  0.21  74.46   0.71     0.28      53596.03|
| 12:  2.1138 -  2.0535  1318   151  0.20  75.06   0.72     0.28      49034.54|
| 13:  2.0535 -  1.9996  1026   108  0.18  76.67   0.72     0.25      43029.71|
| 14:  1.9996 -  1.9509   234    30  0.20  74.74   0.73     0.21      31714.26|
|alpha:            min =        0.21 max =            0.67 mean =         0.41|
|beta:             min =    31714.26 max =       147030.90 mean =     83956.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.23|
|phase err.(test): min =        0.00 max =           90.00 mean =        64.46|
|-----------------------------------------------------------------------------|

============================== 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 = 20.633057             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.119423              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.001   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.685 -  1.106:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.106 -  1.528:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.528 -  1.949:       39 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.949 -  2.371:      258 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.371 -  2.792:      982 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.792 -  3.214:     2192 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.214 -  3.635:     3772 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.635 -  4.057:     5366 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.057 -  4.478:     7114 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.478 -  4.900:     8668 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.711 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.685 |       3.283 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     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:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5188   r_free= 0.5095   ksol= 0.00   Bsol= 0.00   scale= 0.739    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.309266                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5081   r_free= 0.5038   ksol= 0.31   Bsol= 0.00   scale= 0.971    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.51,11.16,8.60,0.00,0.00,0.00); trace/3= 9.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.303116                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.928701             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.501   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.107977              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.655   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5081      final r-factor (work) = 0.4506          |
| start r-factor (free) = 0.5038      final r-factor (free) = 0.4682          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 113.4022 = 18.93 * 0.50 * 6.3069 + 1.00 * 53.7111                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 59.4248 = 18.93 * 0.50 * 6.2633 + 1.00 * 0.1467                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4506      final r-factor (work) = 0.4085          |
| start r-factor (free) = 0.4682      final r-factor (free) = 0.4683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.2173 = 2.11 * 1.00 * 6.2633 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1261 = 2.11 * 1.00 * 6.2156 + 1.00 * 0.0238                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.24   17.49    None  None   None       |
|    all(noH): 2823   0      0.00    99.24   17.49    None  None   None       |
|    Sol.    : 438    0      0.00    99.24   27.42    None  None   None       |
|    Mac.    : 2385   0      0.00    78.44   15.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.924: 1040   |   5:    49.620 -  59.544:   60        |
|      1:     9.924 -  19.848:  787   |   6:    59.544 -  69.468:   28        |
|      2:    19.848 -  29.772:  507   |   7:    69.468 -  79.392:   19        |
|      3:    29.772 -  39.696:  252   |   8:    79.392 -  89.316:    4        |
|      4:    39.696 -  49.620:  123   |   9:    89.316 -  99.240:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4085 r_free = 0.4683             target_work(ml) = 6.207         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4081 r_free = 0.4687             target_work(ml) = 6.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4081   r_free= 0.4687   ksol= 0.31   Bsol= 0.00   scale= 1.129    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.51,11.16,8.60,0.00,0.00,0.00); trace/3= 9.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.205992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4062   r_free= 0.4623   ksol= 0.32   Bsol= 29.25   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,6.45,5.05,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.205980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.402918             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.103  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.710676              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.016  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4062      final r-factor (work) = 0.3432          |
| start r-factor (free) = 0.4623      final r-factor (free) = 0.4087          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.4603 = 10.40 * 0.50 * 6.2124 + 1.00 * 0.1467                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0362 = 10.40 * 0.50 * 6.1406 + 1.00 * 0.0961                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3432      final r-factor (work) = 0.3295          |
| start r-factor (free) = 0.4087      final r-factor (free) = 0.3956          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3888 = 0.71 * 1.00 * 6.1406 + 1.00 * 0.0249                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3340 = 0.71 * 1.00 * 6.0689 + 1.00 * 0.0210                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.66   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    94.66   17.30    None  None   None       |
|    Sol.    : 438    0      0.00    94.66   30.03    None  None   None       |
|    Mac.    : 2385   0      0.00    92.72   14.96    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 -   9.466:  941   |   5:    47.331 -  56.797:   46        |
|      1:     9.466 -  18.932:  881   |   6:    56.797 -  66.263:   34        |
|      2:    18.932 -  28.398:  506   |   7:    66.263 -  75.729:   12        |
|      3:    28.398 -  37.865:  286   |   8:    75.729 -  85.195:    6        |
|      4:    37.865 -  47.331:  107   |   9:    85.195 -  94.661:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3295 r_free = 0.3956             target_work(ml) = 6.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3291 r_free = 0.3954             target_work(ml) = 6.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3291   r_free= 0.3954   ksol= 0.32   Bsol= 29.25   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,6.45,5.05,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.054465                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3263   r_free= 0.3925   ksol= 0.32   Bsol= 29.25   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.05,3.64,2.70,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.053454                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.080960              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.901  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330800              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.165  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3263      final r-factor (work) = 0.2530          |
| start r-factor (free) = 0.3925      final r-factor (free) = 0.3095          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6504 = 9.08 * 0.50 * 6.0686 + 1.00 * 0.0962                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.1901 = 9.08 * 0.50 * 5.9658 + 1.00 * 0.1028                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2530      final r-factor (work) = 0.2338          |
| start r-factor (free) = 0.3095      final r-factor (free) = 0.2890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9935 = 0.33 * 1.00 * 5.9658 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9341 = 0.33 * 1.00 * 5.8020 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.69   16.86    None  None   None       |
|    all(noH): 2823   0      0.00    94.69   16.86    None  None   None       |
|    Sol.    : 438    0      3.32    93.13   33.05    None  None   None       |
|    Mac.    : 2385   0      0.00    94.69   13.89    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 -   9.469:  994   |   5:    47.345 -  56.814:   39        |
|      1:     9.469 -  18.938:  921   |   6:    56.814 -  66.283:   27        |
|      2:    18.938 -  28.407:  447   |   7:    66.283 -  75.752:   11        |
|      3:    28.407 -  37.876:  255   |   8:    75.752 -  85.220:    5        |
|      4:    37.876 -  47.345:  120   |   9:    85.220 -  94.689:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2338 r_free = 0.2890             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2334 r_free = 0.2884             target_work(ml) = 5.769         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2334   r_free= 0.2884   ksol= 0.32   Bsol= 29.25   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.05,3.64,2.70,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.768898                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2305   r_free= 0.2865   ksol= 0.32   Bsol= 37.66   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,0.97,0.76,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.767608                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.900897              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.824   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.320340              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.132   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2305      final r-factor (work) = 0.1782          |
| start r-factor (free) = 0.2865      final r-factor (free) = 0.2283          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2325 = 5.90 * 0.50 * 5.8057 + 1.00 * 0.1030                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8077 = 5.90 * 0.50 * 5.6693 + 1.00 * 0.0808                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1782      final r-factor (work) = 0.1545          |
| start r-factor (free) = 0.2283      final r-factor (free) = 0.2024          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8270 = 0.32 * 1.00 * 5.6693 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7905 = 0.32 * 1.00 * 5.4853 + 1.00 * 0.0333                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.35   16.44    None  None   None       |
|    all(noH): 2823   0      0.00    84.35   16.44    None  None   None       |
|    Sol.    : 438    0      4.93    79.71   38.44    None  None   None       |
|    Mac.    : 2385   0      0.00    84.35   12.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.435:  859   |   5:    42.176 -  50.611:   98        |
|      1:     8.435 -  16.870: 1164   |   6:    50.611 -  59.046:   78        |
|      2:    16.870 -  25.306:  301   |   7:    59.046 -  67.482:   29        |
|      3:    25.306 -  33.741:  140   |   8:    67.482 -  75.917:   14        |
|      4:    33.741 -  42.176:  135   |   9:    75.917 -  84.352:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1545 r_free = 0.2024             target_work(ml) = 5.418         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1543 r_free = 0.2025             target_work(ml) = 5.418         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1543   r_free= 0.2025   ksol= 0.32   Bsol= 37.66   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,0.97,0.76,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.417937                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1543   r_free= 0.2024   ksol= 0.32   Bsol= 52.05   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-0.18,0.20,-0.00,0.00,0.00); trace/3= -0.71                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.416918                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.338253              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.334  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.114054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.257   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1543      final r-factor (work) = 0.1318          |
| start r-factor (free) = 0.2024      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2436 = 3.34 * 0.50 * 5.4896 + 1.00 * 0.0808                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0073 = 3.34 * 0.50 * 5.3522 + 1.00 * 0.0737                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1289          |
| start r-factor (free) = 0.1796      final r-factor (free) = 0.1737          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6210 = 0.11 * 1.00 * 5.3522 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6107 = 0.11 * 1.00 * 5.2840 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.99   15.98    None  None   None       |
|    all(noH): 2823   0      0.00    82.99   15.98    None  None   None       |
|    Sol.    : 438    0      5.18    76.30   37.17    None  None   None       |
|    Mac.    : 2385   0      0.00    82.99   12.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.299:  801   |   5:    41.496 -  49.795:  107        |
|      1:     8.299 -  16.598: 1255   |   6:    49.795 -  58.095:   67        |
|      2:    16.598 -  24.898:  291   |   7:    58.095 -  66.394:   30        |
|      3:    24.898 -  33.197:  133   |   8:    66.394 -  74.693:   10        |
|      4:    33.197 -  41.496:  125   |   9:    74.693 -  82.992:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1289 r_free = 0.1737             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1287 r_free = 0.1737             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1737   ksol= 0.32   Bsol= 52.05   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-0.18,0.20,-0.00,0.00,0.00); trace/3= -0.71                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.265152                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.6579 0.99   1467  161 0.1024 0.1444      5.4478      5.6548|
|  2:  4.6579 -  3.7157 0.99   1409  155 0.0924 0.1119      5.5119       5.688|
|  3:  3.7157 -  3.2514 0.99   1374  157 0.1228 0.1690      5.5788      5.8963|
|  4:  3.2514 -  2.9567 0.98   1374  145 0.1444 0.1850      5.5577       5.759|
|  5:  2.9567 -  2.7461 0.99   1361  156 0.1581 0.1847      5.4635      5.6102|
|  6:  2.7461 -  2.5851 0.99   1366  152 0.1432 0.2193      5.3258      5.5288|
|  7:  2.5851 -  2.4562 0.98   1328  154 0.1450 0.1753      5.2675      5.4084|
|  8:  2.4562 -  2.3497 0.98   1354  143 0.1399 0.2001      5.1924      5.4325|
|  9:  2.3497 -  2.2596 0.99   1343  143 0.1387 0.1992       5.125      5.3737|
| 10:  2.2596 -  2.1818 0.99   1345  146 0.1329 0.1940      5.0645      5.2712|
| 11:  2.1818 -  2.1138 0.97   1331  158 0.1351 0.1926        5.01      5.3107|
| 12:  2.1138 -  2.0535 0.98   1318  151 0.1363 0.1770      4.9716      5.1819|
| 13:  2.0535 -  1.9996 0.76   1026  108 0.1290 0.1920      4.8681      5.0716|
| 14:  1.9996 -  1.9509 0.18    234   30 0.1142 0.1749       4.778      4.9402|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.6579  1467   161  0.93  10.47   0.98     0.96       8929.06|
|  2:  4.6579 -  3.7157  1409   155  0.94   9.22   1.02     1.01      10739.92|
|  3:  3.7157 -  3.2514  1374   157  0.92  13.07   1.02     1.01      12387.47|
|  4:  3.2514 -  2.9567  1374   145  0.89  16.62   1.01     1.00      12684.26|
|  5:  2.9567 -  2.7461  1361   156  0.88  18.48   1.01     0.97      10794.20|
|  6:  2.7461 -  2.5851  1366   152  0.88  18.89   0.98     0.94       8822.01|
|  7:  2.5851 -  2.4562  1328   154  0.89  17.87   1.00     0.95       7475.46|
|  8:  2.4562 -  2.3497  1354   143  0.88  18.09   1.02     0.98       6787.97|
|  9:  2.3497 -  2.2596  1343   143  0.88  18.19   1.01     0.97       5977.90|
| 10:  2.2596 -  2.1818  1345   146  0.88  18.18   1.01     0.99       5461.60|
| 11:  2.1818 -  2.1138  1331   158  0.88  18.15   1.01     0.97       4977.71|
| 12:  2.1138 -  2.0535  1318   151  0.88  18.52   1.01     1.01       4687.70|
| 13:  2.0535 -  1.9996  1026   108  0.88  18.20   1.00     0.98       3905.34|
| 14:  1.9996 -  1.9509   234    30  0.91  15.06   0.99     0.94       2992.92|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     2992.92 max =        12684.26 mean =      8021.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.33|
|phase err.(test): min =        0.00 max =           89.26 mean =        15.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1737   ksol= 0.32   Bsol= 50.71   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-0.66,-0.01,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.265123                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1737   ksol= 0.32   Bsol= 50.71   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-0.66,-0.01,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.265123                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.6579 0.99   1467  161 0.1027 0.1430      5.4472      5.6514|
|  2:  4.6579 -  3.7157 0.99   1409  155 0.0929 0.1101      5.5125      5.6887|
|  3:  3.7157 -  3.2514 0.99   1374  157 0.1230 0.1694      5.5809      5.8933|
|  4:  3.2514 -  2.9567 0.98   1374  145 0.1446 0.1858      5.5584      5.7633|
|  5:  2.9567 -  2.7461 0.99   1361  156 0.1582 0.1855      5.4648      5.6119|
|  6:  2.7461 -  2.5851 0.99   1366  152 0.1431 0.2195      5.3257      5.5284|
|  7:  2.5851 -  2.4562 0.98   1328  154 0.1446 0.1755      5.2668      5.4089|
|  8:  2.4562 -  2.3497 0.98   1354  143 0.1394 0.2000      5.1914      5.4334|
|  9:  2.3497 -  2.2596 0.99   1343  143 0.1385 0.1983      5.1238      5.3699|
| 10:  2.2596 -  2.1818 0.99   1345  146 0.1327 0.1942      5.0633      5.2731|
| 11:  2.1818 -  2.1138 0.97   1331  158 0.1351 0.1922      5.0091      5.3091|
| 12:  2.1138 -  2.0535 0.98   1318  151 0.1364 0.1773      4.9723      5.1833|
| 13:  2.0535 -  1.9996 0.76   1026  108 0.1290 0.1913       4.868      5.0695|
| 14:  1.9996 -  1.9509 0.18    234   30 0.1140 0.1746      4.7776      4.9411|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.6579  1467   161  0.93  10.55   0.97     0.95       8903.38|
|  2:  4.6579 -  3.7157  1409   155  0.94   9.26   1.01     1.00      10735.96|
|  3:  3.7157 -  3.2514  1374   157  0.92  13.12   1.01     1.01      12452.83|
|  4:  3.2514 -  2.9567  1374   145  0.89  16.63   1.00     0.99      12705.31|
|  5:  2.9567 -  2.7461  1361   156  0.88  18.50   1.00     0.96      10831.74|
|  6:  2.7461 -  2.5851  1366   152  0.88  18.90   0.97     0.94       8842.82|
|  7:  2.5851 -  2.4562  1328   154  0.89  17.88   0.99     0.94       7489.63|
|  8:  2.4562 -  2.3497  1354   143  0.88  18.08   1.00     0.96       6790.26|
|  9:  2.3497 -  2.2596  1343   143  0.88  18.16   0.99     0.96       5968.78|
| 10:  2.2596 -  2.1818  1345   146  0.88  18.14   1.00     0.97       5449.62|
| 11:  2.1818 -  2.1138  1331   158  0.88  18.11   1.00     0.96       4968.95|
| 12:  2.1138 -  2.0535  1318   151  0.88  18.51   1.00     1.00       4689.26|
| 13:  2.0535 -  1.9996  1026   108  0.88  18.18   0.98     0.97       3897.66|
| 14:  1.9996 -  1.9509   234    30  0.91  15.04   0.97     0.93       2982.14|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2982.14 max =        12705.31 mean =      8029.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.83 mean =        16.34|
|phase err.(test): min =        0.00 max =           89.74 mean =        15.69|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.780)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.00   15.99    None  None   None       |
|    all(noH): 2823   0      0.00    83.00   15.99    None  None   None       |
|    Sol.    : 438    0      5.18    76.30   37.17    None  None   None       |
|    Mac.    : 2385   0      0.00    83.00   12.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.302:  801   |   5:    41.499 -  49.798:  107        |
|      1:     8.302 -  16.601: 1255   |   6:    49.798 -  58.097:   67        |
|      2:    16.601 -  24.901:  291   |   7:    58.097 -  66.397:   30        |
|      3:    24.901 -  33.200:  133   |   8:    66.397 -  74.696:   10        |
|      4:    33.200 -  41.499:  125   |   9:    74.696 -  82.995:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.350 - 5.185
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 336
   mapped sites are within: 0.725 - 5.185

peak=    9.914 closest distance to " CB  VAL A 230 " =    1.421
peak=    7.139 closest distance to " CG1 ILE A 234 " =    1.449
peak=    6.056 closest distance to " O   HOH Z 404 " =    1.555
peak=    5.860 closest distance to " O   HOH Z 124 " =    1.558
peak=    5.746 closest distance to " O   HOH Z 248 " =    1.646
peak=    5.724 closest distance to " O   HOH Z 210 " =    1.405
peak=    5.538 closest distance to " CG1 VAL A 296 " =    1.187
peak=    5.289 closest distance to " O   HOH Z 403 " =    2.022
peak=    5.248 closest distance to " CG  LEU A   5 " =    1.422
peak=    5.136 closest distance to " O   HOH Z 128 " =    1.873
peak=    5.089 closest distance to " O   HOH Z 117 " =    1.195
peak=    4.909 closest distance to " O   HOH Z 154 " =    2.085
peak=    4.887 closest distance to " O   HOH Z 193 " =    2.060
peak=    4.834 closest distance to " O   HOH Z 102 " =    1.505
peak=    4.817 closest distance to " CB  ARG A 275 " =    0.858
peak=    4.790 closest distance to " CB  SER A  63 " =    1.176
peak=    4.785 closest distance to " CD2 LEU A   5 " =    1.196
peak=    4.781 closest distance to " CB  VAL A 296 " =    1.461
peak=    4.709 closest distance to " O   HOH Z 130 " =    2.549
peak=    4.690 closest distance to " O   HOH Z  49 " =    1.566
peak=    4.685 closest distance to " NH2 ARG A  56 " =    2.172
peak=    4.633 closest distance to " O   HOH Z  43 " =    2.079
peak=    4.630 closest distance to " O   HOH Z 238 " =    1.693
peak=    4.541 closest distance to " CG  PRO A  54 " =    1.345
peak=    4.539 closest distance to " O   HOH Z  44 " =    1.620
peak=    4.511 closest distance to " O   HOH Z 394 " =    1.830
peak=    4.497 closest distance to " CB  GLN A 223 " =    1.451
peak=    4.486 closest distance to " O   HOH Z 406 " =    1.614
peak=    4.407 closest distance to " NH1AARG A 275 " =    1.106
peak=    4.390 closest distance to " O   HOH Z 425 " =    1.433
peak=    4.387 closest distance to " O   HOH Z  85 " =    1.945
peak=    4.379 closest distance to " NH2 ARG A 156 " =    1.133
peak=    4.374 closest distance to " O   HOH Z  63 " =    2.472
peak=    4.357 closest distance to " CD2 LEU A 228 " =    1.177
peak=    4.351 closest distance to " O   HOH Z  40 " =    2.096
peak=    4.334 closest distance to " CA  TYR A  30 " =    1.025
peak=    4.330 closest distance to " CA  ALA A  51 " =    1.110
peak=    4.326 closest distance to " O   HOH Z 142 " =    2.418
peak=    4.315 closest distance to " O   HOH Z 402 " =    1.636
peak=    4.310 closest distance to " CD2 TRP A 179 " =    1.380
peak=    4.304 closest distance to " O   HOH Z  76 " =    1.307
peak=    4.293 closest distance to " O   SER A  87 " =    2.285
peak=    4.272 closest distance to " CB  SER A  26 " =    1.774
peak=    4.262 closest distance to " CB  VAL A 230 " =    1.257
peak=    4.254 closest distance to " O   HOH Z  80 " =    2.110
peak=    4.245 closest distance to " CG AARG A 275 " =    1.319
peak=    4.228 closest distance to " O   HOH Z 146 " =    1.616
peak=    4.170 closest distance to " O   HOH Z 234 " =    3.555
peak=    4.152 closest distance to " O   HOH Z 346 " =    1.599
peak=    4.147 closest distance to " O   HOH Z 236 " =    1.606
peak=    4.143 closest distance to " CD  LYS A 166 " =    1.511
peak=    4.142 closest distance to " O   HOH Z  97 " =    1.380
peak=    4.133 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.123 closest distance to " O   HOH Z 389 " =    1.974
peak=    4.105 closest distance to " CD  ARG A 159 " =    0.815
peak=    4.099 closest distance to " O   HOH Z 411 " =    3.566
peak=    4.081 closest distance to " O   HOH Z 209 " =    2.330
peak=    4.046 closest distance to " O   HOH Z 403 " =    1.632
peak=    4.042 closest distance to " O   HOH Z 380 " =    1.938
peak=    4.032 closest distance to " O   ALA A 165 " =    1.281
peak=    4.031 closest distance to " O   HOH Z 414 " =    2.496
peak=    4.015 closest distance to " O   HOH Z  67 " =    2.100
peak=    4.011 closest distance to " CG2 VAL A 296 " =    0.997
peak=    4.006 closest distance to " O   HOH Z 132 " =    2.638
peak=    3.990 closest distance to " O   HOH Z 272 " =    1.940
peak=    3.988 closest distance to " CB  PRO A  54 " =    0.981
peak=    3.974 closest distance to " O   HOH Z 359 " =    1.737
peak=    3.969 closest distance to " O   HOH Z 137 " =    1.769
peak=    3.963 closest distance to " O   HOH Z 431 " =    1.478
peak=    3.954 closest distance to " O   PRO A 198 " =    1.579
peak=    3.949 closest distance to " CB  GLU A 152 " =    1.055
peak=    3.942 closest distance to " CG  PRO A 198 " =    1.279
peak=    3.934 closest distance to " O   HOH Z 433 " =    1.553
peak=    3.913 closest distance to " CZ  PHE A 218 " =    1.092
peak=    3.905 closest distance to " O   HOH Z 126 " =    1.587
peak=    3.903 closest distance to " NE2 GLN A  11 " =    1.076
peak=    3.903 closest distance to " O   HOH Z 365 " =    2.310
peak=    3.886 closest distance to " O   GLY A  91 " =    1.344
peak=    3.860 closest distance to " CB  GLU A 277 " =    0.927
peak=    3.842 closest distance to " CB  PRO A 198 " =    1.105
peak=    3.842 closest distance to " O   HOH Z 409 " =    3.411
peak=    3.833 closest distance to " CG1 ILE A  33 " =    1.256
peak=    3.827 closest distance to " O   HOH Z 265 " =    2.020
peak=    3.823 closest distance to " O   HOH Z 247 " =    1.282
peak=    3.821 closest distance to " CG  PRO A 243 " =    1.131
peak=    3.820 closest distance to " CB  TRP A 179 " =    1.290
peak=    3.815 closest distance to " CD  PRO A  54 " =    0.928
peak=    3.805 closest distance to " CB  GLN A  55 " =    0.880
peak=    3.803 closest distance to " CB  ASN A 187 " =    1.472
peak=    3.796 closest distance to " CG2 THR A 220 " =    0.760
peak=    3.792 closest distance to " CG2 ILE A  20 " =    1.259
peak=    3.791 closest distance to " O   HOH Z 383 " =    1.983
peak=    3.788 closest distance to " O   HOH Z 146 " =    1.393
peak=    3.787 closest distance to " O   HOH Z 232 " =    2.353
peak=    3.780 closest distance to " CB  GLU A 175 " =    1.238
peak=    3.778 closest distance to " O   ASP A 124 " =    1.667
peak=    3.778 closest distance to " O   HOH Z 369 " =    1.883
peak=    3.771 closest distance to " CB  ASN A 148 " =    1.219
peak=    3.769 closest distance to " CB  ASN A 285 " =    0.993
peak=    3.769 closest distance to " CG  ARG A  66 " =    0.998
peak=    3.764 closest distance to " O   HOH Z 183 " =    1.879
peak=    3.730 closest distance to " CA  ASP A 162 " =    1.018
peak=    3.725 closest distance to " CB  SER A  62 " =    0.990
peak=    3.724 closest distance to " CD2 LEU A 297 " =    0.985
peak=    3.721 closest distance to " NZ  LYS A 117 " =    2.597
peak=    3.715 closest distance to " O   HOH Z 327 " =    1.648
peak=    3.713 closest distance to " O   HOH Z 357 " =    2.099
peak=    3.703 closest distance to " CE1 TYR A  30 " =    1.112
peak=    3.682 closest distance to " CZ  PHE A  38 " =    1.147
peak=    3.678 closest distance to " CB  SER A 141 " =    1.037
peak=    3.675 closest distance to " O   HOH Z   4 " =    1.669
peak=    3.675 closest distance to " OE1 GLN A  11 " =    1.892
peak=    3.672 closest distance to " CB BVAL A  41 " =    1.186
peak=    3.672 closest distance to " OG BSER A 212 " =    2.159
peak=    3.665 closest distance to " O   HOH Z 381 " =    1.444
peak=    3.652 closest distance to " O   HOH Z  11 " =    1.371
peak=    3.649 closest distance to " CG  LEU A 228 " =    1.268
peak=    3.648 closest distance to " O   HOH Z 257 " =    2.254
peak=    3.639 closest distance to " O   GLU A   2 " =    1.715
peak=    3.636 closest distance to " O   ASP A 200 " =    1.618
peak=    3.635 closest distance to " O   HOH Z 151 " =    1.973
peak=    3.631 closest distance to " O   HOH Z 120 " =    0.936
peak=    3.631 closest distance to " CD2 TRP A 179 " =    2.351
peak=    3.627 closest distance to " CG2AVAL A  72 " =    1.723
peak=    3.623 closest distance to " O   HOH Z 423 " =    1.703
peak=    3.619 closest distance to " O   HOH Z 227 " =    1.707
peak=    3.612 closest distance to " O   HOH Z 111 " =    1.676
peak=    3.612 closest distance to " O   HOH Z 214 " =    1.444
peak=    3.608 closest distance to " O   HOH Z 142 " =    1.774
peak=    3.607 closest distance to " O   HOH Z 423 " =    2.151
peak=    3.603 closest distance to " CE1 HIS A 108 " =    1.202
peak=    3.601 closest distance to " CB  THR A 235 " =    1.219
peak=    3.601 closest distance to " CB  ASN A 142 " =    1.086
peak=    3.598 closest distance to " CD  LYS A  76 " =    1.764
peak=    3.596 closest distance to " O   HOH Z 126 " =    1.693
peak=    3.594 closest distance to " CD1 LEU A   5 " =    1.527
peak=    3.586 closest distance to " CE1 TYR A 186 " =    1.236
peak=    3.583 closest distance to " OG  SER A  97 " =    2.961
peak=    3.582 closest distance to " OE1 GLU A   2 " =    1.754
peak=    3.578 closest distance to " CG2 THR A  29 " =    1.359
peak=    3.578 closest distance to " CZ3 TRP A 266 " =    1.049
peak=    3.577 closest distance to " O   HOH Z 134 " =    1.804
peak=    3.572 closest distance to " N   ALA A   1 " =    1.277
peak=    3.572 closest distance to " O   HOH Z 130 " =    1.170
peak=    3.569 closest distance to " CB  ARG A  79 " =    1.410
peak=    3.559 closest distance to " O   HOH Z 255 " =    1.381
peak=    3.548 closest distance to " O   HOH Z 412 " =    3.518
peak=    3.545 closest distance to " CA  VAL A  41 " =    0.850
peak=    3.545 closest distance to " CA  ASP A 191 " =    1.066
peak=    3.544 closest distance to " O   HOH Z 173 " =    2.532
peak=    3.542 closest distance to " O   HOH Z 313 " =    1.778
peak=    3.540 closest distance to " CB  SER A   3 " =    1.289
peak=    3.530 closest distance to " NZ  LYS A 117 " =    1.663
peak=    3.528 closest distance to " CB  ALA A   1 " =    1.273
peak=    3.513 closest distance to " O   HOH Z 277 " =    1.303
peak=    3.511 closest distance to " OG BSER A 212 " =    2.574
peak=    3.504 closest distance to " CG1 ILE A  20 " =    1.370
peak=    3.502 closest distance to " O   HOH Z 371 " =    2.987
peak=    3.502 closest distance to " O   HOH Z 422 " =    2.683
peak=    3.498 closest distance to " O   HOH Z 203 " =    1.638
peak=    3.493 closest distance to " O  BHOH Z 338 " =    2.133
peak=    3.487 closest distance to " ND2 ASN A 187 " =    1.737
peak=    3.487 closest distance to " N   ASN A  39 " =    1.375
peak=    3.485 closest distance to " OG1 THR A 294 " =    2.256
peak=    3.474 closest distance to " CB  ARG A  79 " =    0.804
peak=    3.469 closest distance to " O   HOH Z  42 " =    2.326
peak=    3.463 closest distance to " O   HOH Z  78 " =    1.558
peak=    3.460 closest distance to " O   HOH Z 299 " =    3.929
peak=    3.459 closest distance to " O   THR A 182 " =    1.513
peak=    3.455 closest distance to " O   HOH Z 214 " =    2.510
peak=    3.452 closest distance to " O   HOH Z 298 " =    4.214
peak=    3.448 closest distance to " NH2BARG A 145 " =    2.393
peak=    3.448 closest distance to " O  BHOH Z  74 " =    1.357
peak=    3.446 closest distance to " CB  VAL A 202 " =    1.348
peak=    3.445 closest distance to " CG  PHE A 204 " =    1.083
peak=    3.445 closest distance to " CG2 ILE A 234 " =    1.233
peak=    3.443 closest distance to " O   HOH Z 213 " =    1.452
peak=    3.432 closest distance to " CA  TRP A  85 " =    1.075
peak=    3.428 closest distance to " CG2 THR A 221 " =    1.122
peak=    3.428 closest distance to " OG  SER A  62 " =    2.636
peak=    3.424 closest distance to " CG  LYS A 119 " =    1.039
peak=    3.415 closest distance to " O   HOH Z  46 " =    1.328
peak=    3.415 closest distance to " CD  ARG A 195 " =    0.928
peak=    3.410 closest distance to " CD1 ILE A 199 " =    1.168
peak=    3.409 closest distance to " O   HOH Z 358 " =    2.307
peak=    3.407 closest distance to " O   HOH Z 315 " =    1.824
peak=    3.407 closest distance to " O   HOH Z  59 " =    1.885
peak=    3.406 closest distance to " CB  THR A  31 " =    1.335
peak=    3.405 closest distance to " CA  ALA A 295 " =    0.965
peak=    3.402 closest distance to " O   HOH Z 287 " =    1.923
peak=    3.399 closest distance to " O   HOH Z 234 " =    1.995
peak=    3.390 closest distance to " O   ALA A 158 " =    1.071
peak=    3.388 closest distance to " O   HOH Z  61 " =    1.575
peak=    3.385 closest distance to " NZ  LYS A  76 " =    0.888
peak=    3.384 closest distance to " CB  ALA A   9 " =    1.829
peak=    3.380 closest distance to " O   HOH Z 419 " =    1.877
peak=    3.373 closest distance to " NE1 TRP A  92 " =    1.457
peak=    3.372 closest distance to " CB  SER A  62 " =    3.692
peak=    3.371 closest distance to " CD  LYS A 119 " =    1.899
peak=    3.370 closest distance to " O   HOH Z 427 " =    2.496
peak=    3.369 closest distance to " CG2 VAL A 197 " =    1.151
peak=    3.366 closest distance to " O   HOH Z 147 " =    1.688
peak=    3.366 closest distance to " N   GLU A  44 " =    1.608
peak=    3.363 closest distance to " CD1 LEU A  96 " =    1.055
peak=    3.360 closest distance to " O   HOH Z 116 " =    2.464
peak=    3.359 closest distance to " O   HOH Z 298 " =    5.185
peak=    3.359 closest distance to " CA  ALA A 100 " =    1.198
peak=    3.357 closest distance to " O   HOH Z  51 " =    1.957
peak=    3.347 closest distance to " CB  GLU A  46 " =    1.049
peak=    3.340 closest distance to " N   GLN A 194 " =    1.614
peak=    3.338 closest distance to " N   THR A  42 " =    1.531
peak=    3.329 closest distance to " O   HOH Z 223 " =    1.664
peak=    3.328 closest distance to " O   HOH Z 199 " =    1.624
peak=    3.327 closest distance to " CG2 THR A 294 " =    1.282
peak=    3.326 closest distance to " CB  ASN A  45 " =    1.200
peak=    3.321 closest distance to " O   HOH Z   9 " =    2.366
peak=    3.320 closest distance to " CG  ARG A 269 " =    1.900
peak=    3.316 closest distance to " CG2 ILE A 120 " =    1.393
peak=    3.314 closest distance to " CB  LYS A 289 " =    1.174
peak=    3.311 closest distance to " CG1 ILE A  49 " =    1.434
peak=    3.303 closest distance to " O   HOH Z 345 " =    1.822
peak=    3.303 closest distance to " NZ  LYS A 193 " =    1.141
peak=    3.303 closest distance to " CB  ARG A 190 " =    1.894
peak=    3.302 closest distance to " O   HOH Z 417 " =    3.168
peak=    3.301 closest distance to " O   HOH Z  83 " =    1.562
peak=    3.298 closest distance to " CD2 TYR A 186 " =    0.999
peak=    3.292 closest distance to " O   HOH Z 162 " =    2.270
peak=    3.292 closest distance to " O   HOH Z 259 " =    1.993
peak=    3.292 closest distance to " CA  SER A  32 " =    1.717
peak=    3.292 closest distance to " NH2AARG A 145 " =    0.938
peak=    3.289 closest distance to " O   HOH Z 214 " =    2.991
peak=    3.288 closest distance to " O   HOH Z 109 " =    1.928
peak=    3.286 closest distance to " NE2 GLN A  77 " =    3.190
peak=    3.285 closest distance to " CG  MET A 185 " =    1.166
peak=    3.282 closest distance to " CZ2 TRP A 274 " =    1.242
peak=    3.282 closest distance to " O   HOH Z  44 " =    2.417
peak=    3.280 closest distance to " O   HOH Z 361 " =    2.883
peak=    3.278 closest distance to " CB  PRO A 213 " =    1.265
peak=    3.277 closest distance to " CA  SER A  12 " =    1.479
peak=    3.273 closest distance to " O   HOH Z 214 " =    2.192
peak=    3.273 closest distance to " CA  ASP A 149 " =    1.188
peak=    3.273 closest distance to " O   HOH Z  56 " =    1.774
peak=    3.269 closest distance to " OG  SER A 245 " =    1.436
peak=    3.267 closest distance to " O   HOH Z  54 " =    1.625
peak=    3.264 closest distance to " O   HOH Z  88 " =    3.154
peak=    3.263 closest distance to " O   HOH Z 117 " =    1.756
peak=    3.262 closest distance to " O   HOH Z 250 " =    1.453
peak=    3.260 closest distance to " OD1 ASN A 301 " =    1.019
peak=    3.260 closest distance to " CZ3 TRP A  85 " =    0.957
peak=    3.256 closest distance to " CD AARG A 190 " =    1.487
peak=    3.251 closest distance to " O   HOH Z 316 " =    2.960
peak=    3.246 closest distance to " O   PRO A 213 " =    1.210
peak=    3.245 closest distance to " CG2AVAL A 121 " =    1.975
peak=    3.245 closest distance to " CB  PHE A  16 " =    1.219
peak=    3.244 closest distance to " CB  ASN A 209 " =    1.008
peak=    3.244 closest distance to " O   HOH Z 162 " =    2.018
peak=    3.240 closest distance to " CB  PHE A 204 " =    0.847
peak=    3.239 closest distance to " CB  SER A  99 " =    1.474
peak=    3.232 closest distance to " O   HOH Z 245 " =    1.504
peak=    3.228 closest distance to " OG BSER A 164 " =    2.193
peak=    3.225 closest distance to " CB  ALA A  71 " =    1.293
peak=    3.222 closest distance to " O   CYS A 168 " =    1.556
peak=    3.220 closest distance to " O   HOH Z  99 " =    1.990
peak=    3.220 closest distance to " O   HOH Z  95 " =    1.503
peak=    3.220 closest distance to " O   HOH Z 435 " =    1.688
peak=    3.217 closest distance to " O   HOH Z 126 " =    1.774
peak=    3.215 closest distance to " O   HOH Z 251 " =    1.772
peak=    3.214 closest distance to " NH1 ARG A  14 " =    1.072
peak=    3.211 closest distance to " O   HOH Z 345 " =    2.748
peak=    3.210 closest distance to " N   SER A 164 " =    0.865
peak=    3.210 closest distance to " O   HOH Z 132 " =    2.819
peak=    3.209 closest distance to " CB  ALA A 248 " =    1.334
peak=    3.208 closest distance to " CB  VAL A 265 " =    1.244
peak=    3.206 closest distance to " O   HOH Z 285 " =    1.592
peak=    3.204 closest distance to " O   HOH Z 154 " =    2.124
peak=    3.204 closest distance to " CG  GLU A  37 " =    0.984
peak=    3.204 closest distance to " CB  TRP A 266 " =    1.066
peak=    3.203 closest distance to " N   PHE A 130 " =    1.351
peak=    3.197 closest distance to " O   CYS A 168 " =    1.867
peak=    3.196 closest distance to " O   HOH Z 322 " =    2.394
peak=    3.193 closest distance to " O   HOH Z 336 " =    1.761
peak=    3.192 closest distance to " CE  LYS A 119 " =    1.025
peak=    3.188 closest distance to " CG  LEU A 167 " =    1.116
peak=    3.184 closest distance to " OH  TYR A 116 " =    1.117
peak=    3.183 closest distance to " N   CYS A 260 " =    0.813
peak=    3.182 closest distance to " CA  SER A  87 " =    0.892
peak=    3.181 closest distance to " CB  ASP A 140 " =    0.733
peak=    3.178 closest distance to " CA  THR A 294 " =    1.818
peak=    3.178 closest distance to " CG  LYS A 289 " =    1.322
peak=    3.177 closest distance to " O   HOH Z 193 " =    1.724
peak=    3.174 closest distance to " CB  ALA A 100 " =    1.196
peak=    3.168 closest distance to " NH2 ARG A  79 " =    1.222
peak=    3.168 closest distance to " O   HOH Z  39 " =    1.198
peak=    3.167 closest distance to " OD1 ASN A 217 " =    1.766
peak=    3.166 closest distance to " N   TYR A 247 " =    1.622
peak=    3.163 closest distance to " O   PHE A  61 " =    1.431
peak=    3.162 closest distance to " O   HOH Z 350 " =    1.919
peak=    3.160 closest distance to " O   HOH Z 426 " =    1.401
peak=    3.154 closest distance to " CB  SER A 271 " =    1.168
peak=    3.152 closest distance to " O   HOH Z 145 " =    2.179
peak=    3.152 closest distance to " O   HOH Z 197 " =    1.987
peak=    3.150 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.150 closest distance to " CG1 VAL A 153 " =    1.064
peak=    3.150 closest distance to " O   HOH Z 158 " =    3.035
peak=    3.148 closest distance to " CA  ARG A 139 " =    1.300
peak=    3.147 closest distance to " O   HOH Z 139 " =    4.520
peak=    3.145 closest distance to " CZ2 TRP A 150 " =    0.995
peak=    3.145 closest distance to " O   HOH Z 408 " =    1.923
peak=    3.137 closest distance to " CD  ARG A  79 " =    1.924
peak=    3.135 closest distance to " OD2 ASP A 298 " =    3.430
peak=    3.132 closest distance to " NH2AARG A 275 " =    3.644
peak=    3.129 closest distance to " O   HOH Z 298 " =    1.809
peak=    3.126 closest distance to " O   HOH Z 438 " =    1.773
peak=    3.122 closest distance to " O   HOH Z  94 " =    1.546
peak=    3.118 closest distance to " O   HOH Z 336 " =    4.309
peak=    3.114 closest distance to " O   HOH Z 141 " =    1.620
peak=    3.114 closest distance to " CG ALYS A 290 " =    1.119
peak=    3.113 closest distance to " N   TYR A  15 " =    0.725
peak=    3.112 closest distance to " O   HOH Z 435 " =    1.947
peak=    3.100 closest distance to " CA  ALA A 129 " =    1.020
peak=    3.095 closest distance to " CA  ARG A  36 " =    1.002
peak=    3.092 closest distance to " O   HOH Z  96 " =    1.897
peak=    3.088 closest distance to " O   HOH Z 123 " =    2.251
peak=    3.084 closest distance to " CA  LYS A 117 " =    1.213
peak=    3.080 closest distance to " CB  SER A 210 " =    0.842
peak=    3.077 closest distance to " CZ  ARG A  14 " =    1.368
peak=    3.060 closest distance to " O   HOH Z 366 " =    2.186
peak=    3.057 closest distance to " OD1 ASP A 231 " =    1.999
peak=    3.054 closest distance to " CA  ASN A 217 " =    1.288
peak=    3.037 closest distance to " CA  ARG A 195 " =    1.240

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.489 - 5.944
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 200
   mapped sites are within: 0.716 - 5.944

peak=   -4.624 closest distance to " O   HOH Z 290 " =    0.751
peak=   -4.503 closest distance to " CG  GLN A  58 " =    1.015
peak=   -4.437 closest distance to " CD2 TYR A  30 " =    2.756
peak=   -4.416 closest distance to " CB  ALA A 248 " =    2.176
peak=   -4.342 closest distance to " O   HOH Z 422 " =    1.151
peak=   -4.243 closest distance to " CD2 LEU A 237 " =    2.499
peak=   -4.218 closest distance to " CG1 VAL A 296 " =    0.958
peak=   -4.161 closest distance to " O   HOH Z 166 " =    1.550
peak=   -4.067 closest distance to " C   THR A 279 " =    1.150
peak=   -4.063 closest distance to " CD  ARG A  14 " =    3.155
peak=   -4.024 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.993 closest distance to " CD  ARG A 156 " =    1.955
peak=   -3.975 closest distance to " CG  PRO A 243 " =    1.595
peak=   -3.967 closest distance to " O   HOH Z 411 " =    5.443
peak=   -3.960 closest distance to " O   HOH Z 351 " =    1.623
peak=   -3.957 closest distance to " CD1 PHE A  59 " =    1.922
peak=   -3.954 closest distance to " O   HOH Z 174 " =    1.986
peak=   -3.936 closest distance to " O   GLY A 241 " =    2.333
peak=   -3.907 closest distance to " O   GLN A  11 " =    0.988
peak=   -3.893 closest distance to " CD  GLN A 223 " =    0.801
peak=   -3.863 closest distance to " N   ALA A   1 " =    2.366
peak=   -3.857 closest distance to " CG2 THR A 182 " =    2.240
peak=   -3.818 closest distance to " SG  CYS A 260 " =    2.049
peak=   -3.813 closest distance to " O   HOH Z 155 " =    1.787
peak=   -3.803 closest distance to " O   HOH Z 151 " =    0.871
peak=   -3.801 closest distance to " CA  VAL A  67 " =    2.904
peak=   -3.791 closest distance to " O   HOH Z 340 " =    0.820
peak=   -3.791 closest distance to " O   HOH Z 164 " =    5.944
peak=   -3.787 closest distance to " C   LYS A  76 " =    1.596
peak=   -3.783 closest distance to " O   HOH Z 423 " =    2.398
peak=   -3.781 closest distance to " O   PRO A 198 " =    1.202
peak=   -3.781 closest distance to " O   HOH Z 109 " =    2.792
peak=   -3.772 closest distance to " OG  SER A  97 " =    2.413
peak=   -3.737 closest distance to " O   PRO A 163 " =    2.142
peak=   -3.720 closest distance to " CD1 LEU A 101 " =    2.378
peak=   -3.699 closest distance to " CH2 TRP A 179 " =    1.282
peak=   -3.685 closest distance to " O   HOH Z 166 " =    1.271
peak=   -3.682 closest distance to " O   HOH Z 110 " =    1.386
peak=   -3.673 closest distance to " O   HOH Z   6 " =    1.881
peak=   -3.672 closest distance to " O  BHOH Z 338 " =    1.187
peak=   -3.656 closest distance to " C   HIS A 108 " =    1.191
peak=   -3.656 closest distance to " O   HOH Z 432 " =    0.872
peak=   -3.647 closest distance to " CB  PHE A 208 " =    2.378
peak=   -3.623 closest distance to " CE1 TYR A 247 " =    2.584
peak=   -3.614 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.612 closest distance to " CB  ALA A 161 " =    2.321
peak=   -3.606 closest distance to " OG  SER A  63 " =    0.862
peak=   -3.591 closest distance to " O   TRP A  92 " =    2.227
peak=   -3.579 closest distance to " O   HOH Z 193 " =    1.274
peak=   -3.571 closest distance to " CB  SER A 210 " =    1.256
peak=   -3.569 closest distance to " CA  ASP A 298 " =    1.117
peak=   -3.568 closest distance to " O   HOH Z 120 " =    0.988
peak=   -3.555 closest distance to " O   HOH Z 165 " =    1.891
peak=   -3.552 closest distance to " O   HOH Z 411 " =    1.475
peak=   -3.547 closest distance to " O   HOH Z 246 " =    0.931
peak=   -3.545 closest distance to " OXT GLY A 302 " =    2.818
peak=   -3.527 closest distance to " CG  GLN A 103 " =    2.433
peak=   -3.527 closest distance to " O   GLN A  94 " =    2.347
peak=   -3.514 closest distance to " OD1 ASN A 301 " =    0.896
peak=   -3.514 closest distance to " OD1 ASN A 173 " =    1.649
peak=   -3.511 closest distance to " OG BSER A 134 " =    1.481
peak=   -3.498 closest distance to " O   HOH Z 428 " =    2.508
peak=   -3.495 closest distance to " O   HOH Z  64 " =    0.906
peak=   -3.494 closest distance to " CZ2 TRP A  92 " =    2.727
peak=   -3.491 closest distance to " O   TYR A  15 " =    1.839
peak=   -3.491 closest distance to " NE2 GLN A  11 " =    1.213
peak=   -3.483 closest distance to " CB  TRP A  85 " =    2.782
peak=   -3.483 closest distance to " CD2 TYR A 293 " =    1.839
peak=   -3.478 closest distance to " O   HOH Z 124 " =    1.362
peak=   -3.478 closest distance to " O   HOH Z 312 " =    1.681
peak=   -3.468 closest distance to " OD2 ASP A 140 " =    0.947
peak=   -3.463 closest distance to " NE2 GLN A  88 " =    0.921
peak=   -3.459 closest distance to " O   HOH Z 205 " =    0.891
peak=   -3.455 closest distance to " NZ  LYS A 119 " =    1.156
peak=   -3.454 closest distance to " O   SER A 271 " =    2.199
peak=   -3.453 closest distance to " N   GLN A 122 " =    1.610
peak=   -3.451 closest distance to " O   HOH Z 169 " =    0.834
peak=   -3.449 closest distance to " CG  ASP A 231 " =    0.716
peak=   -3.449 closest distance to " CD2 PHE A 192 " =    2.126
peak=   -3.436 closest distance to " CG2BVAL A  41 " =    2.586
peak=   -3.434 closest distance to " O   HOH Z 171 " =    2.376
peak=   -3.433 closest distance to " C   VAL A 265 " =    0.879
peak=   -3.430 closest distance to " O   SER A 273 " =    1.112
peak=   -3.429 closest distance to " CD2 TYR A 172 " =    2.098
peak=   -3.427 closest distance to " CZ  TYR A 172 " =    1.876
peak=   -3.425 closest distance to " O   HOH Z 433 " =    0.957
peak=   -3.420 closest distance to " CZ  TYR A 169 " =    1.707
peak=   -3.413 closest distance to " O   HOH Z  15 " =    1.468
peak=   -3.412 closest distance to " CG  LEU A  83 " =    1.957
peak=   -3.404 closest distance to " O   HOH Z 174 " =    3.713
peak=   -3.399 closest distance to " O   HOH Z 285 " =    1.351
peak=   -3.398 closest distance to " O   HOH Z 425 " =    1.059
peak=   -3.396 closest distance to " O   SER A  95 " =    1.674
peak=   -3.392 closest distance to " O   HOH Z 265 " =    1.038
peak=   -3.386 closest distance to " N   ALA A 248 " =    2.687
peak=   -3.384 closest distance to " OD2 ASP A 298 " =    0.906
peak=   -3.375 closest distance to " N   SER A 276 " =    1.490
peak=   -3.373 closest distance to " O   HOH Z 394 " =    5.256
peak=   -3.372 closest distance to " CG2 VAL A 202 " =    2.725
peak=   -3.369 closest distance to " O   HOH Z 423 " =    3.898
peak=   -3.357 closest distance to " O   HOH Z 384 " =    1.864
peak=   -3.356 closest distance to " NE2 GLN A 278 " =    1.937
peak=   -3.353 closest distance to " CG  ARG A 139 " =    0.889
peak=   -3.351 closest distance to " CE1 HIS A  81 " =    1.286
peak=   -3.342 closest distance to " O   HOH Z  10 " =    1.563
peak=   -3.342 closest distance to " O   HOH Z  56 " =    1.132
peak=   -3.335 closest distance to " N   ALA A 226 " =    1.985
peak=   -3.334 closest distance to " CG  LEU A   5 " =    0.735
peak=   -3.331 closest distance to " C   ILE A 239 " =    2.119
peak=   -3.329 closest distance to " O   HOH Z 109 " =    0.778
peak=   -3.328 closest distance to " CA  TRP A 274 " =    1.133
peak=   -3.326 closest distance to " ND2 ASN A  45 " =    1.183
peak=   -3.325 closest distance to " O   HOH Z  44 " =    1.514
peak=   -3.310 closest distance to " NH1 ARG A 195 " =    2.514
peak=   -3.309 closest distance to " O   HOH Z  78 " =    1.792
peak=   -3.309 closest distance to " C   SER A 206 " =    1.576
peak=   -3.308 closest distance to " O   HOH Z 216 " =    0.862
peak=   -3.307 closest distance to " O   HOH Z 250 " =    1.737
peak=   -3.307 closest distance to " CD2 PHE A  61 " =    2.611
peak=   -3.305 closest distance to " O   HOH Z 109 " =    3.619
peak=   -3.305 closest distance to " O   HOH Z  60 " =    2.292
peak=   -3.299 closest distance to " CD2 PHE A 225 " =    1.009
peak=   -3.290 closest distance to " O   HOH Z 183 " =    1.493
peak=   -3.282 closest distance to " O   HOH Z 131 " =    4.097
peak=   -3.273 closest distance to " O   GLY A 196 " =    1.045
peak=   -3.267 closest distance to " CG2 VAL A 296 " =    1.197
peak=   -3.266 closest distance to " O   HOH Z  92 " =    1.373
peak=   -3.263 closest distance to " CG  PHE A  59 " =    1.979
peak=   -3.257 closest distance to " CD  LYS A 289 " =    2.445
peak=   -3.250 closest distance to " ND2 ASN A 301 " =    1.828
peak=   -3.246 closest distance to " ND2 ASN A  39 " =    1.198
peak=   -3.245 closest distance to " CB  ALA A  43 " =    2.607
peak=   -3.243 closest distance to " CH2 TRP A 150 " =    1.007
peak=   -3.242 closest distance to " O   HOH Z 388 " =    2.176
peak=   -3.239 closest distance to " CD2 LEU A 237 " =    2.816
peak=   -3.239 closest distance to " O   HOH Z  28 " =    2.327
peak=   -3.238 closest distance to " CZ  ARG A 259 " =    0.828
peak=   -3.235 closest distance to " N   ARG A  66 " =    1.829
peak=   -3.234 closest distance to " O   ALA A  34 " =    1.986
peak=   -3.234 closest distance to " CE  LYS A  76 " =    2.605
peak=   -3.232 closest distance to " CD2 LEU A 143 " =    2.388
peak=   -3.225 closest distance to " O   HOH Z 157 " =    3.418
peak=   -3.224 closest distance to " O   HOH Z 368 " =    1.925
peak=   -3.220 closest distance to " O   ALA A 227 " =    1.198
peak=   -3.218 closest distance to " CD  PRO A 243 " =    1.861
peak=   -3.216 closest distance to " CD  GLN A 223 " =    1.755
peak=   -3.215 closest distance to " CD1 LEU A 167 " =    2.138
peak=   -3.213 closest distance to " O   HOH Z 231 " =    2.099
peak=   -3.211 closest distance to " O   HOH Z 219 " =    2.484
peak=   -3.208 closest distance to " CA  GLY A 133 " =    2.097
peak=   -3.206 closest distance to " O   HOH Z 227 " =    0.810
peak=   -3.203 closest distance to " OD1 ASN A 148 " =    1.351
peak=   -3.202 closest distance to " O   ASN A  45 " =    1.863
peak=   -3.200 closest distance to " CD  ARG A 195 " =    5.140
peak=   -3.198 closest distance to " OD1 ASP A 298 " =    2.128
peak=   -3.196 closest distance to " O   HOH Z   7 " =    1.551
peak=   -3.192 closest distance to " O   HOH Z  31 " =    2.237
peak=   -3.187 closest distance to " N   ALA A 295 " =    1.023
peak=   -3.186 closest distance to " O   HOH Z 345 " =    2.821
peak=   -3.180 closest distance to " SD  MET A 188 " =    1.153
peak=   -3.179 closest distance to " CB  ASP A 286 " =    1.564
peak=   -3.174 closest distance to " NH2 ARG A  79 " =    2.069
peak=   -3.173 closest distance to " O   HOH Z 154 " =    1.108
peak=   -3.170 closest distance to " O   HOH Z 249 " =    1.081
peak=   -3.167 closest distance to " CG2 VAL A 189 " =    2.049
peak=   -3.164 closest distance to " CD1 TRP A  70 " =    1.785
peak=   -3.164 closest distance to " O   LYS A 289 " =    0.983
peak=   -3.154 closest distance to " OXT GLY A 302 " =    3.524
peak=   -3.153 closest distance to " CG  ARG A 219 " =    2.306
peak=   -3.144 closest distance to " O   HOH Z 394 " =    1.747
peak=   -3.140 closest distance to " OD2 ASP A 272 " =    1.597
peak=   -3.138 closest distance to " CG2 THR A  18 " =    2.880
peak=   -3.137 closest distance to " OE2 GLU A 277 " =    2.667
peak=   -3.136 closest distance to " CZ  PHE A  38 " =    2.356
peak=   -3.132 closest distance to " O   HOH Z 221 " =    1.091
peak=   -3.131 closest distance to " CZ  ARG A  79 " =    1.802
peak=   -3.130 closest distance to " O   HOH Z 377 " =    1.880
peak=   -3.123 closest distance to " CD1 TRP A 179 " =    1.154
peak=   -3.122 closest distance to " O   PHE A 218 " =    1.378
peak=   -3.122 closest distance to " C   VAL A 174 " =    1.757
peak=   -3.121 closest distance to " ND2 ASN A 249 " =    1.144
peak=   -3.113 closest distance to " O   ALA A   1 " =    1.669
peak=   -3.110 closest distance to " CG  GLU A 277 " =    1.456
peak=   -3.109 closest distance to " O   HOH Z 231 " =    0.818
peak=   -3.106 closest distance to " NH1 ARG A 195 " =    2.384
peak=   -3.102 closest distance to " O   HOH Z 329 " =    0.873
peak=   -3.088 closest distance to " O   HOH Z 322 " =    0.744
peak=   -3.084 closest distance to " O   HOH Z  67 " =    2.922
peak=   -3.083 closest distance to " O   HOH Z 191 " =    5.685
peak=   -3.072 closest distance to " CD1 PHE A 130 " =    2.234
peak=   -3.071 closest distance to " OG1 THR A  82 " =    1.375
peak=   -3.062 closest distance to " O   HOH Z 397 " =    1.174
peak=   -3.059 closest distance to " O   HOH Z 193 " =    1.995
peak=   -3.019 closest distance to " O   HOH Z 105 " =    2.267

================= 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    :  0.5147 0.5076   6.309147e+00   6.304391e+00
   1_bss:  0.5081 0.5038   6.303116e+00   6.304026e+00
   1_xyz:  0.4506 0.4682   6.251885e+00   6.273923e+00
   1_adp:  0.4085 0.4683   6.206561e+00   6.269882e+00
   1_occ:  0.4081 0.4687   6.205992e+00   6.270497e+00
   2_bss:  0.4062 0.4623   6.205980e+00   6.269726e+00
   2_xyz:  0.3432 0.4087   6.084691e+00   6.197648e+00
   2_adp:  0.3295 0.3956   6.054707e+00   6.176756e+00
   2_occ:  0.3291 0.3954   6.054465e+00   6.177019e+00
   3_bss:  0.3263 0.3925   6.053454e+00   6.176407e+00
   3_xyz:  0.2530 0.3095   5.837455e+00   5.998429e+00
   3_adp:  0.2338 0.2890   5.769715e+00   5.941344e+00
   3_occ:  0.2334 0.2884   5.768898e+00   5.941003e+00
   4_bss:  0.2305 0.2865   5.767608e+00   5.938934e+00
   4_xyz:  0.1782 0.2283   5.545953e+00   5.751168e+00
   4_adp:  0.1545 0.2024   5.418272e+00   5.626942e+00
   4_occ:  0.1543 0.2025   5.417937e+00   5.626975e+00
   5_bss:  0.1543 0.2024   5.416918e+00   5.625110e+00
   5_xyz:  0.1318 0.1796   5.289816e+00   5.514299e+00
   5_adp:  0.1289 0.1737   5.265647e+00   5.479451e+00
   5_occ:  0.1287 0.1737   5.265152e+00   5.479157e+00
   5_bss:  0.1287 0.1737   5.265123e+00   5.478957e+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:  0.306   0.000   7.514  11.157   8.604   0.000   0.000   0.000
   1_xyz:  0.306   0.000   7.514  11.157   8.604   0.000   0.000   0.000
   1_adp:  0.306   0.000   7.514  11.157   8.604   0.000   0.000   0.000
   1_occ:  0.306   0.000   7.514  11.157   8.604   0.000   0.000   0.000
   2_bss:  0.320  29.255   3.557   6.448   5.049   0.000   0.000   0.000
   2_xyz:  0.320  29.255   3.557   6.448   5.049   0.000   0.000   0.000
   2_adp:  0.320  29.255   3.557   6.448   5.049   0.000   0.000   0.000
   2_occ:  0.320  29.255   3.557   6.448   5.049   0.000   0.000   0.000
   3_bss:  0.320  29.255   1.053   3.636   2.701   0.000   0.000   0.000
   3_xyz:  0.320  29.255   1.053   3.636   2.701   0.000   0.000   0.000
   3_adp:  0.320  29.255   1.053   3.636   2.701   0.000   0.000   0.000
   3_occ:  0.320  29.255   1.053   3.636   2.701   0.000   0.000   0.000
   4_bss:  0.319  37.657  -1.306   0.969   0.757   0.000   0.000   0.000
   4_xyz:  0.319  37.657  -1.306   0.969   0.757   0.000   0.000   0.000
   4_adp:  0.319  37.657  -1.306   0.969   0.757   0.000   0.000   0.000
   4_occ:  0.319  37.657  -1.306   0.969   0.757   0.000   0.000   0.000
   5_bss:  0.325  52.046  -2.159  -0.184   0.201  -0.000   0.000   0.000
   5_xyz:  0.325  52.046  -2.159  -0.184   0.201  -0.000   0.000   0.000
   5_adp:  0.325  52.046  -2.159  -0.184   0.201  -0.000   0.000   0.000
   5_occ:  0.325  52.046  -2.159  -0.184   0.201  -0.000   0.000   0.000
   5_bss:  0.325  50.714  -2.391  -0.661  -0.011  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.257 0.3390  0.4084    83947.371
   1_bss:  65.782 0.3177  0.4909    84638.108
   1_xyz:  58.704 0.4084  0.6205    70363.348
   1_adp:  56.363 0.4387  0.7495    67943.204
   1_occ:  56.359 0.4388  0.7486    67977.519
   2_bss:  55.684 0.4475  0.6730    67062.283
   2_xyz:  46.492 0.5633  0.8466    50209.107
   2_adp:  44.310 0.5905  0.9049    46667.038
   2_occ:  44.329 0.5903  0.9044    46719.539
   3_bss:  44.060 0.5934  0.8305    46233.103
   3_xyz:  33.282 0.7194  0.9675    26612.281
   3_adp:  30.420 0.7522  1.0086    22938.141
   3_occ:  30.375 0.7527  1.0087    22862.625
   4_bss:  30.204 0.7548  0.9317    22721.722
   4_xyz:  23.128 0.8297  0.9855    13848.586
   4_adp:  19.672 0.8647  0.9998    10783.302
   4_occ:  19.673 0.8647  0.9998    10794.098
   5_bss:  19.594 0.8655  0.9709    10744.538
   5_xyz:  17.104 0.8882  0.9801     8477.216
   5_adp:  16.277 0.8961  0.9800     8017.689
   5_occ:  16.270 0.8962  0.9799     8020.644
   5_bss:  16.275 0.8961  0.9696     8027.959
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3711e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3711e+01
   1_xyz:   1.692  0.013  0.106 18.441  0.007  4.106   1.4669e-01
   1_adp:   1.692  0.013  0.106 18.441  0.007  4.106   1.4669e-01
   1_occ:   1.692  0.013  0.106 18.441  0.007  4.106   1.4669e-01
   2_bss:   1.692  0.013  0.106 18.441  0.007  4.106   1.4669e-01
   2_xyz:   1.299  0.009  0.080 16.575  0.005  4.126   9.6111e-02
   2_adp:   1.299  0.009  0.080 16.575  0.005  4.126   9.6111e-02
   2_occ:   1.299  0.009  0.080 16.575  0.005  4.126   9.6111e-02
   3_bss:   1.299  0.009  0.080 16.575  0.005  4.126   9.6111e-02
   3_xyz:   1.338  0.010  0.094 16.532  0.005  4.127   1.0275e-01
   3_adp:   1.338  0.010  0.094 16.532  0.005  4.127   1.0275e-01
   3_occ:   1.338  0.010  0.094 16.532  0.005  4.127   1.0275e-01
   4_bss:   1.338  0.010  0.094 16.532  0.005  4.127   1.0275e-01
   4_xyz:   1.157  0.009  0.083 15.650  0.005  4.124   8.0759e-02
   4_adp:   1.157  0.009  0.083 15.650  0.005  4.124   8.0759e-02
   4_occ:   1.157  0.009  0.083 15.650  0.005  4.124   8.0759e-02
   5_bss:   1.157  0.009  0.083 15.650  0.005  4.124   8.0759e-02
   5_xyz:   1.141  0.009  0.087 15.425  0.004  4.114   7.3733e-02
   5_adp:   1.141  0.009  0.087 15.425  0.004  4.114   7.3733e-02
   5_occ:   1.141  0.009  0.087 15.425  0.004  4.114   7.3733e-02
   5_bss:   1.141  0.009  0.087 15.425  0.004  4.114   7.3733e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.685   6.9512e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.685   6.9512e+00
   1_xyz:  15.299  0.164  0.469 86.434  0.047  2.217   9.9046e-02
   1_adp:  15.299  0.164  0.469 86.434  0.047  2.217   9.9046e-02
   1_occ:  15.299  0.164  0.469 86.434  0.047  2.217   9.9046e-02
   2_bss:  15.299  0.164  0.469 86.434  0.047  2.217   9.9046e-02
   2_xyz:   7.395  0.096  0.270 83.046  0.032  2.151   6.5491e-02
   2_adp:   7.395  0.096  0.270 83.046  0.032  2.151   6.5491e-02
   2_occ:   7.395  0.096  0.270 83.046  0.032  2.151   6.5491e-02
   3_bss:   7.395  0.096  0.270 83.046  0.032  2.151   6.5491e-02
   3_xyz:   9.051  0.060  0.334 80.060  0.036  2.238   1.5148e-01
   3_adp:   9.051  0.060  0.334 80.060  0.036  2.238   1.5148e-01
   3_occ:   9.051  0.060  0.334 80.060  0.036  2.238   1.5148e-01
   4_bss:   9.051  0.060  0.334 80.060  0.036  2.238   1.5148e-01
   4_xyz:   7.715  0.055  0.327 79.470  0.041  2.083   7.1211e-02
   4_adp:   7.715  0.055  0.327 79.470  0.041  2.083   7.1211e-02
   4_occ:   7.715  0.055  0.327 79.470  0.041  2.083   7.1211e-02
   5_bss:   7.715  0.055  0.327 79.470  0.041  2.083   7.1211e-02
   5_xyz:   7.455  0.050  0.492 83.176  0.042  2.134   4.7539e-02
   5_adp:   7.455  0.050  0.492 83.176  0.042  2.134   4.7539e-02
   5_occ:   7.455  0.050  0.492 83.176  0.042  2.134   4.7539e-02
   5_bss:   7.455  0.050  0.492 83.176  0.042  2.134   4.7539e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  99.24   0.00  17.49  78.44   0.00  15.66  99.24   0.00  27.42
   1_occ:  99.24   0.00  17.49  78.44   0.00  15.66  99.24   0.00  27.42
   2_bss:  99.24   0.00  17.49  78.44   0.00  15.66  99.24   0.00  27.42
   2_xyz:  99.24   0.00  17.49  78.44   0.00  15.66  99.24   0.00  27.42
   2_adp:  94.66   0.00  17.30  92.72   0.00  14.96  94.66   0.00  30.03
   2_occ:  94.66   0.00  17.30  92.72   0.00  14.96  94.66   0.00  30.03
   3_bss:  94.66   0.00  17.30  92.72   0.00  14.96  94.66   0.00  30.03
   3_xyz:  94.66   0.00  17.30  92.72   0.00  14.96  94.66   0.00  30.03
   3_adp:  94.69   0.00  16.86  94.69   0.00  13.89  93.13   3.32  33.05
   3_occ:  94.69   0.00  16.86  94.69   0.00  13.89  93.13   3.32  33.05
   4_bss:  94.69   0.00  16.86  94.69   0.00  13.89  93.13   3.32  33.05
   4_xyz:  94.69   0.00  16.86  94.69   0.00  13.89  93.13   3.32  33.05
   4_adp:  84.35   0.00  16.44  84.35   0.00  12.40  79.71   4.93  38.44
   4_occ:  84.35   0.00  16.44  84.35   0.00  12.40  79.71   4.93  38.44
   5_bss:  84.35   0.00  16.44  84.35   0.00  12.40  79.71   4.93  38.44
   5_xyz:  84.35   0.00  16.44  84.35   0.00  12.40  79.71   4.93  38.44
   5_adp:  82.99   0.00  15.98  82.99   0.00  12.09  76.30   5.18  37.17
   5_occ:  82.99   0.00  15.98  82.99   0.00  12.09  76.30   5.18  37.17
   5_bss:  83.00   0.00  15.99  83.00   0.00  12.09  76.30   5.18  37.17
------------------------------------------------------------------------
 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:    1.244    0.013    0.408
   1_adp:    1.244    0.013    0.408
   1_occ:    1.244    0.013    0.408
   2_bss:    1.244    0.013    0.408
   2_xyz:    1.885    0.027    0.582
   2_adp:    1.885    0.027    0.582
   2_occ:    1.885    0.027    0.582
   3_bss:    1.885    0.027    0.582
   3_xyz:    1.974    0.031    0.744
   3_adp:    1.974    0.031    0.744
   3_occ:    1.974    0.031    0.744
   4_bss:    1.974    0.031    0.744
   4_xyz:    2.182    0.054    0.849
   4_adp:    2.182    0.054    0.849
   4_occ:    2.182    0.054    0.849
   5_bss:    2.182    0.054    0.849
   5_xyz:    2.197    0.037    0.892
   5_adp:    2.197    0.037    0.892
   5_occ:    2.197    0.037    0.892
   5_bss:    2.197    0.037    0.892
------------------------------------------------------------------------

CPU time actual refinement: 368.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_106/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/trial/run_106/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_106/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_106/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_106/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 368.00 
  Macro-tasks:
    bulk solvent and scale       = 41.01  
    individual site refinement   = 155.16 
    weights calculation          = 33.11  
    collect and process          = 6.35   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 235.75 
  Micro-tasks:
    mask                            = 3.25   
    f_calc                          = 119.52 
    alpha_beta                      = 8.47   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 129.37 
    fmodel                         = 7.36   
    r_factors                      = 0.29   
    phase_errors                   = 9.68   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 279.33 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.115 micro seconds
Total CPU time: 6.37 minutes
from_scatterers_fft:    679 calls, 119.11 s
gradients_fft:          623 calls, 115.75 s

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

# Date 2008-01-16 Time 00:46:00 PST -0800 (1200473160.13 s)
Start R-work = 0.5147, R-free = 0.5076 (no bulk solvent and anisotropic scale)
Final R-work = 0.1504, R-free = 0.1904 (no bulk solvent and anisotropic scale)

Start R-work = 0.5081, R-free = 0.5038
Final R-work = 0.1287, R-free = 0.1737