# Date 2008-01-16 Time 01:58:51 PST -0800 (1200477531.17 s)
#phil __OFF__

Command line arguments: "../652.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32710
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 652

-------------------------------------------------------------------------------
  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: (70.25, 46.6953, 85.5261, 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: 3.36, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98101
Completeness in resolution range: 0.97269
Completeness with d_max=infinity: 0.969608

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9810

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98101
Completeness in resolution range: 0.97269
Completeness with d_max=infinity: 0.969608

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2386 [2104/2128]  1894   210  10.0%
  bin  2:  4.2386 -  3.3770 [2038/2057]  1834   204  10.0%
  bin  3:  3.3770 -  2.9539 [2009/2028]  1805   204  10.2%
  bin  4:  2.9539 -  2.6855 [1988/2018]  1794   194   9.8%
  bin  5:  2.6855 -  2.4940 [1978/1997]  1780   198  10.0%
  bin  6:  2.4940 -  2.3475 [1945/1970]  1751   194  10.0%
  bin  7:  2.3475 -  2.2304 [1968/1996]  1767   201  10.2%
  bin  8:  2.2304 -  2.1336 [1946/1982]  1755   191   9.8%
  bin  9:  2.1336 -  2.0516 [1940/1982]  1748   192   9.9%
  bin 10:  2.0516 -  1.9810 [1673/1981]  1502   171  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_652/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2211
        3.04 -     3.66: 4729
        3.66 -     4.28: 9099
        4.28 -     4.90: 12435
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.245 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.249 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.304 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28484 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_652/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_652/model_refine_001.geo

CPU time processing inputs: 8.91


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 85.5261 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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4233   r_free= 0.4089   ksol= 0.00   Bsol= 0.00   scale= 0.832    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.213419                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7274 0.99   1376  153 0.3616 0.3512      6.5088      6.4672|
|  2:  4.7274 -  3.7721 0.99   1322  146 0.3199 0.3201      6.6201      6.6197|
|  3:  3.7721 -  3.3011 0.99   1297  145 0.3616 0.3368      6.5358       6.567|
|  4:  3.3011 -  3.0020 0.99   1280  144 0.3952 0.3648      6.4354      6.3526|
|  5:  3.0020 -  2.7883 0.99   1282  143 0.4363 0.4439      6.2943      6.3078|
|  6:  2.7883 -  2.6248 0.99   1279  137 0.4416 0.5131       6.223      6.2408|
|  7:  2.6248 -  2.4940 0.99   1271  142 0.4697 0.4251      6.2056      6.1483|
|  8:  2.4940 -  2.3859 0.98   1260  146 0.4740 0.4298      6.1444      6.1204|
|  9:  2.3859 -  2.2944 0.98   1260  136 0.4667 0.4497      6.0852      6.0478|
| 10:  2.2944 -  2.2154 0.99   1240  141 0.4740 0.4678      6.0902      6.0799|
| 11:  2.2154 -  2.1464 0.98   1264  135 0.4898 0.4019      6.0368      5.9308|
| 12:  2.1464 -  2.0852 0.97   1237  139 0.4767 0.4635      5.9617      5.9948|
| 13:  2.0852 -  2.0304 1.00   1250  144 0.4913 0.5054      5.8771      5.8637|
| 14:  2.0304 -  1.9810 0.78   1012  108 0.5037 0.5119      5.8222      5.7533|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7274  1376   153  0.73  31.87   0.82     0.76      60973.90|
|  2:  4.7274 -  3.7721  1322   146  0.78  28.00   0.92     0.84      71982.30|
|  3:  3.7721 -  3.3011  1297   145  0.72  33.83   0.89     0.82      73296.57|
|  4:  3.3011 -  3.0020  1280   144  0.66  38.65   0.85     0.74      66264.84|
|  5:  3.0020 -  2.7883  1282   143  0.56  47.00   0.78     0.64      60313.73|
|  6:  2.7883 -  2.6248  1279   137  0.54  49.12   0.77     0.60      55055.78|
|  7:  2.6248 -  2.4940  1271   142  0.53  49.95   0.76     0.60      50549.58|
|  8:  2.4940 -  2.3859  1260   146  0.53  49.68   0.77     0.61      44676.27|
|  9:  2.3859 -  2.2944  1260   136  0.56  47.74   0.76     0.62      38113.75|
| 10:  2.2944 -  2.2154  1240   141  0.56  47.56   0.79     0.63      33840.31|
| 11:  2.2154 -  2.1464  1264   135  0.54  49.06   0.78     0.62      31980.47|
| 12:  2.1464 -  2.0852  1237   139  0.49  53.28   0.79     0.58      33708.82|
| 13:  2.0852 -  2.0304  1250   144  0.42  58.70   0.78     0.50      31985.88|
| 14:  2.0304 -  1.9810  1012   108  0.38  61.25   0.74     0.42      27666.65|
|alpha:            min =        0.42 max =            0.84 mean =         0.65|
|beta:             min =    27666.65 max =        73296.57 mean =     49195.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.70|
|phase err.(test): min =        0.00 max =           89.96 mean =        45.81|
|-----------------------------------------------------------------------------|

============================== 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 = 7.034825              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.142   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.597471              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.906   (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 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1524 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2659 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3940 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5119 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6598 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7782 |
|-----------------------------------------------------------------------------|
|-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 |       53.455 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.712 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    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 = 11.748)------------------------------------------|
|    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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4320   r_free= 0.4182   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.220459                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4137   r_free= 0.4001   ksol= 0.36   Bsol= 12.95   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,8.58,8.58,0.00,0.00,0.00); trace/3= 8.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.209149                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.377037              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.048   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.589769              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.153   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4137      final r-factor (work) = 0.3065          |
| start r-factor (free) = 0.4001      final r-factor (free) = 0.3299          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.3162 = 6.38 * 0.50 * 6.2291 + 1.00 * 53.4546                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3976 = 6.38 * 0.50 * 6.0482 + 1.00 * 0.1127                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3065      final r-factor (work) = 0.2390          |
| start r-factor (free) = 0.3299      final r-factor (free) = 0.2757          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5817 = 0.59 * 1.00 * 6.0482 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4596 = 0.59 * 1.00 * 5.8467 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.18   10.52    None  None   None       |
|    all(noH): 2823   0      0.00    63.18   10.52    None  None   None       |
|    Sol.    : 438    0      0.00    59.71   27.69    None  None   None       |
|    Mac.    : 2385   0      0.00    63.18   7.36     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 -   6.318: 1362   |   5:    31.590 -  37.908:  116        |
|      1:     6.318 -  12.636:  746   |   6:    37.908 -  44.226:   63        |
|      2:    12.636 -  18.954:  216   |   7:    44.226 -  50.544:   23        |
|      3:    18.954 -  25.272:  157   |   8:    50.544 -  56.862:    6        |
|      4:    25.272 -  31.590:  128   |   9:    56.862 -  63.180:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2390 r_free = 0.2757             target_work(ml) = 5.767         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2384 r_free = 0.2760             target_work(ml) = 5.766         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2384   r_free= 0.2760   ksol= 0.36   Bsol= 12.95   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,8.58,8.58,0.00,0.00,0.00); trace/3= 8.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.766307                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2323   r_free= 0.2687   ksol= 0.34   Bsol= 31.90   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.71,4.46,5.42,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.762477                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.330349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.271   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.293462              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.403  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2323      final r-factor (work) = 0.1554          |
| start r-factor (free) = 0.2687      final r-factor (free) = 0.1969          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8710 = 3.33 * 0.50 * 5.8606 + 1.00 * 0.1122                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3541 = 3.33 * 0.50 * 5.5810 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1554      final r-factor (work) = 0.1411          |
| start r-factor (free) = 0.1969      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6490 = 0.29 * 1.00 * 5.5810 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5830 = 0.29 * 1.00 * 5.3603 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.41   10.93    None  None   None       |
|    all(noH): 2823   0      0.00    66.41   10.93    None  None   None       |
|    Sol.    : 438    0      1.16    58.49   31.28    None  None   None       |
|    Mac.    : 2385   0      0.00    66.41   7.19     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.641: 1519   |   5:    33.204 -  39.844:  116        |
|      1:     6.641 -  13.282:  635   |   6:    39.844 -  46.485:   94        |
|      2:    13.282 -  19.922:  198   |   7:    46.485 -  53.126:   40        |
|      3:    19.922 -  26.563:   93   |   8:    53.126 -  59.767:    8        |
|      4:    26.563 -  33.204:  117   |   9:    59.767 -  66.407:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1411 r_free = 0.1829             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1410 r_free = 0.1826             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1410   r_free= 0.1826   ksol= 0.34   Bsol= 31.90   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.71,4.46,5.42,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.324023                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1824   ksol= 0.32   Bsol= 31.90   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,3.49,4.40,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.323552                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.563084              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.554  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.921604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.533  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1409      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1824      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9370 = 2.56 * 0.50 * 5.3656 + 1.00 * 0.0608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7873 = 2.56 * 0.50 * 5.2452 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0891 = 1.92 * 1.00 * 5.2452 + 1.00 * 0.0098                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9178 = 1.92 * 1.00 * 5.1543 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.29   11.59    None  None   None       |
|    all(noH): 2823   0      0.00    80.29   11.59    None  None   None       |
|    Sol.    : 438    0      0.91    73.56   34.54    None  None   None       |
|    Mac.    : 2385   0      0.00    80.29   7.38     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 -   8.030: 1712   |   5:    40.147 -  48.177:   92        |
|      1:     8.030 -  16.059:  542   |   6:    48.177 -  56.206:   71        |
|      2:    16.059 -  24.088:  146   |   7:    56.206 -  64.236:   27        |
|      3:    24.088 -  32.118:  107   |   8:    64.236 -  72.265:   11        |
|      4:    32.118 -  40.147:  111   |   9:    72.265 -  80.295:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1574             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1574             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1574   ksol= 0.32   Bsol= 31.90   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.11,3.49,4.40,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149689                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1568   ksol= 0.32   Bsol= 38.45   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,3.31,4.19,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148712                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.375734              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.142  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.143473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.823  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6103 = 1.38 * 0.50 * 5.1539 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5940 = 1.38 * 0.50 * 5.1492 + 1.00 * 0.0520                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7519 = 0.14 * 1.00 * 5.1492 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7499 = 0.14 * 1.00 * 5.1568 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.79   11.39    None  None   None       |
|    all(noH): 2823   0      0.00    79.79   11.39    None  None   None       |
|    Sol.    : 438    0      1.12    70.68   33.44    None  None   None       |
|    Mac.    : 2385   0      0.00    79.79   7.34     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 -   7.979: 1737   |   5:    39.894 -  47.872:   92        |
|      1:     7.979 -  15.957:  535   |   6:    47.872 -  55.851:   69        |
|      2:    15.957 -  23.936:  139   |   7:    55.851 -  63.830:   22        |
|      3:    23.936 -  31.915:  114   |   8:    63.830 -  71.808:   11        |
|      4:    31.915 -  39.894:  101   |   9:    71.808 -  79.787:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1542             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1541             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1541   ksol= 0.32   Bsol= 38.45   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,3.31,4.19,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145279                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1541   ksol= 0.32   Bsol= 38.45   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,3.31,4.19,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145279                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.115448              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.912  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.290555              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.089  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5063 = 2.12 * 0.50 * 5.1566 + 1.00 * 0.0520                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4841 = 2.12 * 0.50 * 5.1253 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.0006 = 4.29 * 1.00 * 5.1253 + 1.00 * 0.0100                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.9315 = 4.29 * 1.00 * 5.1085 + 1.00 * 0.0134                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.87   11.58    None  None   None       |
|    all(noH): 2823   0      0.00    87.87   11.58    None  None   None       |
|    Sol.    : 438    0      1.14    79.50   34.34    None  None   None       |
|    Mac.    : 2385   0      0.00    87.87   7.40     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 -   8.787: 1811   |   5:    43.935 -  52.722:   89        |
|      1:     8.787 -  17.574:  480   |   6:    52.722 -  61.510:   45        |
|      2:    17.574 -  26.361:  140   |   7:    61.510 -  70.297:   20        |
|      3:    26.361 -  35.148:  123   |   8:    70.297 -  79.084:    4        |
|      4:    35.148 -  43.935:  107   |   9:    79.084 -  87.871:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1547             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1548             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1548   ksol= 0.32   Bsol= 38.45   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,3.31,4.19,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120131                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7274 0.99   1376  153 0.0974 0.1276      5.3675      5.5128|
|  2:  4.7274 -  3.7721 0.99   1322  146 0.0849 0.1089      5.4227      5.6033|
|  3:  3.7721 -  3.3011 0.99   1297  145 0.1029 0.1506      5.4538      5.8457|
|  4:  3.3011 -  3.0020 0.99   1280  144 0.1178 0.1517      5.4386      5.5778|
|  5:  3.0020 -  2.7883 0.99   1282  143 0.1248 0.1730      5.2943       5.535|
|  6:  2.7883 -  2.6248 0.99   1279  137 0.1137 0.1692      5.1738      5.3836|
|  7:  2.6248 -  2.4940 0.99   1271  142 0.1228 0.1589      5.1413      5.3786|
|  8:  2.4940 -  2.3859 0.98   1260  146 0.1132 0.1748      5.0594      5.3467|
|  9:  2.3859 -  2.2944 0.98   1260  136 0.1146 0.1760      5.0278      5.2767|
| 10:  2.2944 -  2.2154 0.99   1240  141 0.1038 0.1665      4.9305      5.2072|
| 11:  2.2154 -  2.1464 0.98   1264  135 0.1091 0.1697      4.9194      5.2516|
| 12:  2.1464 -  2.0852 0.97   1237  139 0.1080 0.1670      4.8557      5.2076|
| 13:  2.0852 -  2.0304 1.00   1250  144 0.1088 0.1675      4.7835      5.0492|
| 14:  2.0304 -  1.9810 0.78   1012  108 0.1023 0.1789      4.6559      4.9222|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7274  1376   153  0.94   8.75   0.98     0.96       6889.03|
|  2:  4.7274 -  3.7721  1322   146  0.95   7.67   1.02     1.01       8714.75|
|  3:  3.7721 -  3.3011  1297   145  0.94  10.86   1.03     1.02       9932.96|
|  4:  3.3011 -  3.0020  1280   144  0.92  13.00   1.01     1.00       9932.07|
|  5:  3.0020 -  2.7883  1282   143  0.91  15.22   1.00     0.96       7779.56|
|  6:  2.7883 -  2.6248  1279   137  0.91  15.11   0.99     0.96       6708.09|
|  7:  2.6248 -  2.4940  1271   142  0.91  15.36   0.99     0.96       5933.43|
|  8:  2.4940 -  2.3859  1260   146  0.91  14.81   1.00     0.97       5211.88|
|  9:  2.3859 -  2.2944  1260   136  0.91  15.06   1.01     0.99       4992.79|
| 10:  2.2944 -  2.2154  1240   141  0.91  14.89   1.01     0.97       4178.68|
| 11:  2.2154 -  2.1464  1264   135  0.90  16.15   1.00     0.97       4294.04|
| 12:  2.1464 -  2.0852  1237   139  0.92  14.36   1.01     0.99       3725.61|
| 13:  2.0852 -  2.0304  1250   144  0.91  15.72   1.02     1.01       3358.56|
| 14:  2.0304 -  1.9810  1012   108  0.92  14.43   0.99     0.95       2539.10|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2539.10 max =         9932.96 mean =      6099.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.60|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.21|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1547   ksol= 0.32   Bsol= 41.99   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.23,0.66,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1547   ksol= 0.32   Bsol= 41.99   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.23,0.66,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120094                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7274 0.99   1376  153 0.0974 0.1277      5.3677      5.5131|
|  2:  4.7274 -  3.7721 0.99   1322  146 0.0849 0.1089      5.4229      5.6036|
|  3:  3.7721 -  3.3011 0.99   1297  145 0.1029 0.1506       5.454       5.846|
|  4:  3.3011 -  3.0020 0.99   1280  144 0.1178 0.1517      5.4385      5.5778|
|  5:  3.0020 -  2.7883 0.99   1282  143 0.1248 0.1729      5.2941      5.5347|
|  6:  2.7883 -  2.6248 0.99   1279  137 0.1137 0.1693      5.1736      5.3834|
|  7:  2.6248 -  2.4940 0.99   1271  142 0.1228 0.1590      5.1414      5.3793|
|  8:  2.4940 -  2.3859 0.98   1260  146 0.1133 0.1748      5.0595      5.3464|
|  9:  2.3859 -  2.2944 0.98   1260  136 0.1146 0.1760      5.0277      5.2768|
| 10:  2.2944 -  2.2154 0.99   1240  141 0.1038 0.1666      4.9304      5.2075|
| 11:  2.2154 -  2.1464 0.98   1264  135 0.1091 0.1695      4.9193      5.2513|
| 12:  2.1464 -  2.0852 0.97   1237  139 0.1079 0.1669      4.8554      5.2073|
| 13:  2.0852 -  2.0304 1.00   1250  144 0.1088 0.1674      4.7832      5.0488|
| 14:  2.0304 -  1.9810 0.78   1012  108 0.1023 0.1789      4.6556      4.9219|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7274  1376   153  0.94   8.75   0.98     0.96       6892.76|
|  2:  4.7274 -  3.7721  1322   146  0.95   7.68   1.02     1.01       8719.94|
|  3:  3.7721 -  3.3011  1297   145  0.94  10.86   1.03     1.02       9939.97|
|  4:  3.3011 -  3.0020  1280   144  0.92  13.00   1.01     1.00       9931.34|
|  5:  3.0020 -  2.7883  1282   143  0.91  15.22   1.00     0.96       7778.03|
|  6:  2.7883 -  2.6248  1279   137  0.91  15.11   0.99     0.97       6706.82|
|  7:  2.6248 -  2.4940  1271   142  0.91  15.36   0.99     0.96       5935.01|
|  8:  2.4940 -  2.3859  1260   146  0.91  14.81   1.00     0.97       5211.60|
|  9:  2.3859 -  2.2944  1260   136  0.91  15.06   1.01     0.99       4994.51|
| 10:  2.2944 -  2.2154  1240   141  0.91  14.89   1.01     0.97       4176.81|
| 11:  2.2154 -  2.1464  1264   135  0.90  16.14   1.01     0.97       4293.16|
| 12:  2.1464 -  2.0852  1237   139  0.92  14.36   1.01     0.99       3723.73|
| 13:  2.0852 -  2.0304  1250   144  0.91  15.72   1.02     1.01       3356.47|
| 14:  2.0304 -  1.9810  1012   108  0.92  14.42   0.99     0.95       2536.29|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2536.29 max =         9939.97 mean =      6100.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.60|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.21|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.54    91.41   15.12    None  None   None       |
|    all(noH): 2823   0      3.54    91.41   15.12    None  None   None       |
|    Sol.    : 438    0      4.68    83.04   37.89    None  None   None       |
|    Mac.    : 2385   0      3.54    91.41   10.94    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:     3.542 -  12.330: 1811   |   5:    47.478 -  56.265:   89        |
|      1:    12.330 -  21.117:  480   |   6:    56.265 -  65.052:   45        |
|      2:    21.117 -  29.904:  140   |   7:    65.052 -  73.839:   20        |
|      3:    29.904 -  38.691:  123   |   8:    73.839 -  82.626:    4        |
|      4:    38.691 -  47.478:  107   |   9:    82.626 -  91.413:    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)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.360 - 5.801
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 299
   mapped sites are within: 0.730 - 5.801

peak=   11.505 closest distance to " CB  VAL A 230 " =    1.445
peak=    7.186 closest distance to " CG2 VAL A 296 " =    1.125
peak=    6.254 closest distance to " CG  LEU A   5 " =    1.148
peak=    5.749 closest distance to " NE2 GLN A  11 " =    1.158
peak=    5.707 closest distance to " CG  LEU A 228 " =    1.109
peak=    5.675 closest distance to " CD2 LEU A   5 " =    1.192
peak=    5.608 closest distance to " NH2 ARG A  56 " =    2.170
peak=    5.331 closest distance to " CB  VAL A 296 " =    1.058
peak=    5.321 closest distance to " CB  GLN A 183 " =    1.271
peak=    5.294 closest distance to " CB  GLN A 223 " =    1.504
peak=    5.079 closest distance to " O   HOH Z 144 " =    1.722
peak=    5.027 closest distance to " O   HOH Z 126 " =    1.964
peak=    4.909 closest distance to " CB  SER A  63 " =    1.275
peak=    4.722 closest distance to " CB  VAL A 230 " =    1.115
peak=    4.716 closest distance to " O   HOH Z 193 " =    1.706
peak=    4.657 closest distance to " CB  ARG A 275 " =    0.883
peak=    4.653 closest distance to " O   HOH Z 427 " =    2.928
peak=    4.638 closest distance to " O   HOH Z 232 " =    2.358
peak=    4.613 closest distance to " CG  PRO A 213 " =    1.205
peak=    4.604 closest distance to " O   HOH Z 209 " =    2.292
peak=    4.560 closest distance to " C   PRO A 198 " =    1.484
peak=    4.530 closest distance to " CB  GLU A 152 " =    1.224
peak=    4.517 closest distance to " O   HOH Z 203 " =    1.684
peak=    4.485 closest distance to " O   HOH Z 272 " =    1.866
peak=    4.471 closest distance to " OD1 ASN A  69 " =    2.647
peak=    4.462 closest distance to " O   HOH Z 316 " =    3.061
peak=    4.431 closest distance to " O   HOH Z 298 " =    1.784
peak=    4.402 closest distance to " CD2 LEU A 228 " =    1.116
peak=    4.353 closest distance to " CB  SER A   3 " =    1.290
peak=    4.315 closest distance to " CB  TYR A 169 " =    0.791
peak=    4.302 closest distance to " O   HOH Z 158 " =    3.113
peak=    4.299 closest distance to " O   HOH Z  61 " =    1.652
peak=    4.240 closest distance to " CB  ASN A 148 " =    1.373
peak=    4.239 closest distance to " O   HOH Z  43 " =    1.979
peak=    4.223 closest distance to " O   HOH Z  15 " =    2.267
peak=    4.219 closest distance to " O   HOH Z 369 " =    2.155
peak=    4.214 closest distance to " O   HOH Z 236 " =    1.976
peak=    4.214 closest distance to " O   HOH Z 346 " =    1.614
peak=    4.200 closest distance to " CB  VAL A 265 " =    1.328
peak=    4.166 closest distance to " O   HOH Z 368 " =    2.107
peak=    4.162 closest distance to " O   SER A  87 " =    2.344
peak=    4.144 closest distance to " CB  ARG A  79 " =    1.453
peak=    4.129 closest distance to " O   HOH Z 303 " =    2.018
peak=    4.117 closest distance to " O   HOH Z  78 " =    1.714
peak=    4.101 closest distance to " ND2 ASN A 187 " =    1.452
peak=    4.085 closest distance to " CA  TYR A  30 " =    0.966
peak=    4.084 closest distance to " O   HOH Z 263 " =    1.608
peak=    4.079 closest distance to " O   HOH Z 403 " =    1.685
peak=    4.055 closest distance to " CB  GLU A 128 " =    1.034
peak=    4.052 closest distance to " O   HOH Z 265 " =    2.479
peak=    4.037 closest distance to " O   HOH Z 144 " =    2.291
peak=    4.015 closest distance to " O   HOH Z  59 " =    1.928
peak=    4.015 closest distance to " CB  TRP A 266 " =    1.026
peak=    4.000 closest distance to " O   HOH Z 411 " =    3.808
peak=    3.999 closest distance to " OG BSER A 164 " =    2.152
peak=    3.993 closest distance to " CB  ARG A 139 " =    0.954
peak=    3.981 closest distance to " O   HOH Z 124 " =    1.333
peak=    3.962 closest distance to " CB  TRP A 179 " =    1.336
peak=    3.957 closest distance to " CG  PRO A 198 " =    1.142
peak=    3.934 closest distance to " O   HOH Z  66 " =    2.203
peak=    3.907 closest distance to " O   HOH Z  97 " =    1.989
peak=    3.883 closest distance to " O   HOH Z 250 " =    1.331
peak=    3.877 closest distance to " O   HOH Z 280 " =    2.924
peak=    3.855 closest distance to " CA  ALA A 158 " =    1.249
peak=    3.850 closest distance to " CA  ASN A 215 " =    1.199
peak=    3.849 closest distance to " O   HOH Z 423 " =    1.752
peak=    3.833 closest distance to " CG1BVAL A  72 " =    1.599
peak=    3.830 closest distance to " O   HOH Z 248 " =    1.673
peak=    3.820 closest distance to " O   HOH Z 425 " =    1.354
peak=    3.805 closest distance to " O   HOH Z 344 " =    2.950
peak=    3.791 closest distance to " CG  PRO A 243 " =    1.115
peak=    3.790 closest distance to " CB  ASP A 140 " =    0.915
peak=    3.790 closest distance to " O   HOH Z 371 " =    3.066
peak=    3.786 closest distance to " O   HOH Z 128 " =    2.005
peak=    3.784 closest distance to " CB  GLU A 277 " =    3.538
peak=    3.775 closest distance to " CB  SER A 216 " =    0.829
peak=    3.771 closest distance to " O   HOH Z 234 " =    3.544
peak=    3.766 closest distance to " CG2 VAL A 257 " =    0.851
peak=    3.757 closest distance to " CG  ARG A  66 " =    2.682
peak=    3.756 closest distance to " O   HOH Z 392 " =    3.167
peak=    3.747 closest distance to " O   HOH Z 425 " =    2.108
peak=    3.741 closest distance to " NH2 ARG A 156 " =    1.084
peak=    3.737 closest distance to " O   HOH Z 389 " =    1.897
peak=    3.726 closest distance to " N   PHE A 130 " =    1.344
peak=    3.725 closest distance to " O   HOH Z 189 " =    2.628
peak=    3.720 closest distance to " CA  PHE A 283 " =    1.276
peak=    3.713 closest distance to " O   HOH Z  97 " =    2.630
peak=    3.690 closest distance to " O   HOH Z 193 " =    1.703
peak=    3.685 closest distance to " O   HOH Z  44 " =    1.679
peak=    3.679 closest distance to " CB  ARG A 190 " =    1.660
peak=    3.679 closest distance to " CA  VAL A  41 " =    0.822
peak=    3.677 closest distance to " OD2 ASP A 286 " =    2.733
peak=    3.670 closest distance to " CD BLYS A 290 " =    1.115
peak=    3.658 closest distance to " CB  VAL A 202 " =    1.609
peak=    3.649 closest distance to " O   HOH Z 180 " =    2.138
peak=    3.639 closest distance to " O   HOH Z 147 " =    1.684
peak=    3.635 closest distance to " CB  ASN A 148 " =    1.910
peak=    3.629 closest distance to " O   HOH Z 286 " =    2.400
peak=    3.627 closest distance to " O   MET A 105 " =    1.833
peak=    3.619 closest distance to " CA  ALA A  51 " =    0.982
peak=    3.606 closest distance to " CB  LEU A 143 " =    1.189
peak=    3.602 closest distance to " O   HOH Z  88 " =    3.112
peak=    3.598 closest distance to " CE  LYS A  76 " =    0.949
peak=    3.595 closest distance to " O   HOH Z 299 " =    4.264
peak=    3.593 closest distance to " CG2 THR A 221 " =    1.258
peak=    3.592 closest distance to " CB  ASN A  39 " =    0.927
peak=    3.592 closest distance to " CA  ALA A  21 " =    1.158
peak=    3.585 closest distance to " CB  ALA A   9 " =    1.588
peak=    3.583 closest distance to " CB  PRO A  54 " =    0.762
peak=    3.580 closest distance to " O   HOH Z 245 " =    1.357
peak=    3.579 closest distance to " O   HOH Z 290 " =    0.948
peak=    3.573 closest distance to " CB  ALA A 248 " =    1.385
peak=    3.566 closest distance to " CB  THR A 157 " =    1.132
peak=    3.566 closest distance to " CD2 TRP A 179 " =    1.440
peak=    3.565 closest distance to " CZ  PHE A 218 " =    1.096
peak=    3.564 closest distance to " O   HOH Z 112 " =    1.649
peak=    3.564 closest distance to " O   HOH Z 172 " =    3.623
peak=    3.563 closest distance to " O   HOH Z 145 " =    1.989
peak=    3.562 closest distance to " O   HOH Z 133 " =    1.512
peak=    3.556 closest distance to " CB BVAL A  41 " =    1.207
peak=    3.547 closest distance to " O   HOH Z 422 " =    2.586
peak=    3.546 closest distance to " O   HOH Z 128 " =    2.158
peak=    3.538 closest distance to " CB  ALA A 291 " =    1.481
peak=    3.538 closest distance to " CB  THR A  31 " =    1.691
peak=    3.534 closest distance to " O   HOH Z 227 " =    2.194
peak=    3.527 closest distance to " OE1 GLU A   2 " =    2.110
peak=    3.520 closest distance to " O   HOH Z 305 " =    3.495
peak=    3.518 closest distance to " O   HOH Z 407 " =    2.428
peak=    3.516 closest distance to " O   HOH Z 141 " =    1.597
peak=    3.512 closest distance to " CD1 LEU A 228 " =    1.960
peak=    3.502 closest distance to " O   HOH Z 227 " =    1.684
peak=    3.500 closest distance to " CE1 TYR A 186 " =    1.328
peak=    3.498 closest distance to " O   HOH Z  78 " =    2.107
peak=    3.494 closest distance to " CA  LYS A 290 " =    1.263
peak=    3.489 closest distance to " CA  VAL A 126 " =    0.904
peak=    3.488 closest distance to " O   HOH Z 402 " =    1.439
peak=    3.486 closest distance to " O   HOH Z 322 " =    1.923
peak=    3.484 closest distance to " O   HOH Z 132 " =    2.582
peak=    3.483 closest distance to " O   HOH Z 193 " =    1.886
peak=    3.474 closest distance to " NZ  LYS A 117 " =    3.103
peak=    3.472 closest distance to " CB  LEU A 228 " =    1.308
peak=    3.472 closest distance to " O   HOH Z  10 " =    1.776
peak=    3.472 closest distance to " CG1 ILE A  33 " =    1.251
peak=    3.471 closest distance to " CB  THR A  82 " =    1.312
peak=    3.465 closest distance to " CD1 ILE A  33 " =    1.578
peak=    3.462 closest distance to " CA  THR A 264 " =    0.766
peak=    3.459 closest distance to " CB  ASN A 142 " =    1.144
peak=    3.459 closest distance to " CG  LEU A 167 " =    1.171
peak=    3.458 closest distance to " CD  LYS A 119 " =    1.368
peak=    3.456 closest distance to " O   HOH Z 329 " =    3.828
peak=    3.455 closest distance to " CG  GLN A  88 " =    1.031
peak=    3.453 closest distance to " O   HOH Z 273 " =    2.702
peak=    3.450 closest distance to " O   GLN A 278 " =    1.354
peak=    3.448 closest distance to " O   HOH Z  61 " =    1.557
peak=    3.439 closest distance to " CB  ASN A 110 " =    1.189
peak=    3.436 closest distance to " O   HOH Z 207 " =    1.758
peak=    3.435 closest distance to " O   HOH Z 303 " =    1.788
peak=    3.434 closest distance to " O   HOH Z   1 " =    1.788
peak=    3.432 closest distance to " O   HOH Z 437 " =    1.866
peak=    3.430 closest distance to " CA  SER A 146 " =    1.782
peak=    3.429 closest distance to " CB  HIS A 108 " =    0.841
peak=    3.425 closest distance to " O   HOH Z 189 " =    2.735
peak=    3.419 closest distance to " O   HOH Z 214 " =    2.118
peak=    3.418 closest distance to " O   HOH Z   9 " =    1.939
peak=    3.418 closest distance to " N   ASN A  39 " =    1.204
peak=    3.414 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.413 closest distance to " CA  ALA A 291 " =    0.907
peak=    3.410 closest distance to " CG  MET A 185 " =    1.280
peak=    3.409 closest distance to " CG  GLN A  58 " =    2.755
peak=    3.407 closest distance to " CD2 LEU A   5 " =    0.730
peak=    3.405 closest distance to " CG  GLN A  77 " =    2.279
peak=    3.405 closest distance to " O   HOH Z  48 " =    1.743
peak=    3.402 closest distance to " N   ARG A 156 " =    1.329
peak=    3.399 closest distance to " O   HOH Z   3 " =    1.792
peak=    3.398 closest distance to " O   TRP A 274 " =    1.908
peak=    3.397 closest distance to " CB  SER A  26 " =    1.680
peak=    3.397 closest distance to " O   HOH Z 108 " =    2.230
peak=    3.394 closest distance to " O   HOH Z 222 " =    2.497
peak=    3.394 closest distance to " CB  SER A 273 " =    0.861
peak=    3.392 closest distance to " O   HOH Z 163 " =    1.807
peak=    3.392 closest distance to " CB  LEU A 255 " =    0.759
peak=    3.380 closest distance to " CD1 ILE A 106 " =    1.080
peak=    3.380 closest distance to " O   HOH Z 156 " =    3.208
peak=    3.376 closest distance to " O   ASP A 124 " =    1.095
peak=    3.374 closest distance to " CB  ILE A  20 " =    1.458
peak=    3.372 closest distance to " O   HOH Z 426 " =    1.561
peak=    3.371 closest distance to " O   HOH Z 345 " =    3.323
peak=    3.369 closest distance to " O   HOH Z 313 " =    1.806
peak=    3.369 closest distance to " CG2 ILE A 120 " =    1.225
peak=    3.368 closest distance to " CA  LYS A 117 " =    1.225
peak=    3.366 closest distance to " N   VAL A 126 " =    1.241
peak=    3.364 closest distance to " O   HOH Z 417 " =    3.196
peak=    3.354 closest distance to " O   HOH Z 148 " =    3.341
peak=    3.338 closest distance to " CD2 LEU A 255 " =    1.654
peak=    3.337 closest distance to " N   SER A 135 " =    1.363
peak=    3.336 closest distance to " O   HOH Z 128 " =    1.980
peak=    3.335 closest distance to " O   HOH Z 368 " =    3.597
peak=    3.332 closest distance to " O   HOH Z 423 " =    2.846
peak=    3.325 closest distance to " CG1 VAL A 153 " =    0.966
peak=    3.321 closest distance to " O  BHOH Z 338 " =    2.411
peak=    3.320 closest distance to " OG  SER A  97 " =    2.651
peak=    3.319 closest distance to " CB  ALA A 295 " =    1.244
peak=    3.317 closest distance to " OD1BASN A 224 " =    2.211
peak=    3.317 closest distance to " CG  MET A 185 " =    1.099
peak=    3.317 closest distance to " O   HOH Z 374 " =    2.547
peak=    3.316 closest distance to " ND1 HIS A  86 " =    1.668
peak=    3.315 closest distance to " O   HOH Z 116 " =    1.675
peak=    3.313 closest distance to " CE  LYS A  48 " =    1.090
peak=    3.308 closest distance to " OE2 GLU A  53 " =    1.986
peak=    3.307 closest distance to " OG  SER A  22 " =    2.794
peak=    3.307 closest distance to " CA  ARG A  36 " =    0.984
peak=    3.299 closest distance to " O   HOH Z 145 " =    3.633
peak=    3.291 closest distance to " O   HOH Z 366 " =    2.934
peak=    3.290 closest distance to " O   HOH Z  85 " =    1.265
peak=    3.289 closest distance to " CG2 ILE A  20 " =    1.458
peak=    3.286 closest distance to " CA  ARG A 195 " =    1.174
peak=    3.284 closest distance to " O   HOH Z 368 " =    2.629
peak=    3.283 closest distance to " CB  SER A 212 " =    1.118
peak=    3.282 closest distance to " NH2BARG A 145 " =    1.975
peak=    3.282 closest distance to " O   HOH Z 435 " =    1.961
peak=    3.282 closest distance to " O   HOH Z   1 " =    4.688
peak=    3.278 closest distance to " CG AARG A 275 " =    1.081
peak=    3.278 closest distance to " O   LYS A 290 " =    2.392
peak=    3.278 closest distance to " CB  MET A  40 " =    0.872
peak=    3.276 closest distance to " O   ALA A 158 " =    1.429
peak=    3.276 closest distance to " CB  VAL A 268 " =    0.836
peak=    3.275 closest distance to " CA  ASN A 176 " =    1.109
peak=    3.272 closest distance to " O   HOH Z 175 " =    2.106
peak=    3.272 closest distance to " CA  THR A 221 " =    0.944
peak=    3.269 closest distance to " ND1 HIS A  81 " =    1.654
peak=    3.267 closest distance to " O   HOH Z  30 " =    1.214
peak=    3.267 closest distance to " CG1 ILE A  49 " =    1.363
peak=    3.265 closest distance to " O   HOH Z 279 " =    2.171
peak=    3.265 closest distance to " O   HOH Z  40 " =    2.311
peak=    3.260 closest distance to " O   HOH Z 135 " =    1.832
peak=    3.260 closest distance to " CG BARG A 102 " =    1.807
peak=    3.257 closest distance to " O   HOH Z   1 " =    1.651
peak=    3.255 closest distance to " CA  ASP A 162 " =    1.094
peak=    3.249 closest distance to " O   HOH Z  19 " =    2.383
peak=    3.241 closest distance to " OE1 GLU A 236 " =    1.693
peak=    3.237 closest distance to " O   HOH Z  48 " =    1.422
peak=    3.237 closest distance to " O   HOH Z 337 " =    3.610
peak=    3.228 closest distance to " CB  LYS A 117 " =    1.165
peak=    3.223 closest distance to " O   HOH Z 409 " =    3.203
peak=    3.220 closest distance to " CB  SER A  62 " =    1.250
peak=    3.220 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.215 closest distance to " O   HOH Z 130 " =    2.305
peak=    3.213 closest distance to " O   HOH Z 371 " =    1.662
peak=    3.211 closest distance to " O   HOH Z 350 " =    1.577
peak=    3.210 closest distance to " CB  GLN A 278 " =    0.912
peak=    3.202 closest distance to " O   HOH Z 417 " =    2.020
peak=    3.198 closest distance to " N   ASP A 162 " =    1.262
peak=    3.198 closest distance to " O   HOH Z 132 " =    3.100
peak=    3.196 closest distance to " CA  ALA A 233 " =    1.327
peak=    3.193 closest distance to " OG BSER A 134 " =    3.147
peak=    3.193 closest distance to " O   HOH Z 250 " =    1.748
peak=    3.191 closest distance to " O   GLN A  58 " =    1.479
peak=    3.190 closest distance to " O   HOH Z 432 " =    1.397
peak=    3.190 closest distance to " O   HOH Z 341 " =    2.227
peak=    3.186 closest distance to " NE2 GLN A  58 " =    5.801
peak=    3.184 closest distance to " O   HOH Z  21 " =    1.687
peak=    3.182 closest distance to " O   HOH Z 357 " =    1.818
peak=    3.179 closest distance to " O   HOH Z 411 " =    1.698
peak=    3.178 closest distance to " NH1AARG A 145 " =    1.040
peak=    3.177 closest distance to " O   HOH Z 261 " =    1.494
peak=    3.176 closest distance to " CB  TRP A 150 " =    1.408
peak=    3.170 closest distance to " CB  ASN A 215 " =    1.142
peak=    3.164 closest distance to " CA  LEU A 282 " =    1.074
peak=    3.159 closest distance to " CB  GLN A 205 " =    1.136
peak=    3.159 closest distance to " O   HOH Z 353 " =    2.611
peak=    3.153 closest distance to " CG2 THR A 294 " =    1.659
peak=    3.152 closest distance to " O   HOH Z 359 " =    3.630
peak=    3.136 closest distance to " CD  LYS A 166 " =    1.318
peak=    3.136 closest distance to " CG2 VAL A 197 " =    1.007
peak=    3.135 closest distance to " O   HOH Z  71 " =    2.213
peak=    3.126 closest distance to " O   HOH Z 367 " =    3.444
peak=    3.124 closest distance to " O   HOH Z 336 " =    1.796
peak=    3.121 closest distance to " O   HOH Z  80 " =    2.319
peak=    3.116 closest distance to " CA  ASP A 140 " =    1.190
peak=    3.114 closest distance to " O   HOH Z 334 " =    1.306
peak=    3.111 closest distance to " O   HOH Z 433 " =    1.761
peak=    3.110 closest distance to " O   HOH Z 133 " =    2.488
peak=    3.107 closest distance to " CB  ASN A 224 " =    1.034
peak=    3.093 closest distance to " CG  GLN A  89 " =    1.515
peak=    3.092 closest distance to " O   HOH Z 285 " =    3.019
peak=    3.091 closest distance to " O   HOH Z 419 " =    1.831
peak=    3.088 closest distance to " O   HOH Z 271 " =    1.990
peak=    3.087 closest distance to " CA  ALA A 299 " =    0.971
peak=    3.083 closest distance to " O   HOH Z 325 " =    2.193
peak=    3.069 closest distance to " NZ  LYS A  76 " =    1.383
peak=    3.063 closest distance to " CA  ARG A 102 " =    1.121
peak=    3.061 closest distance to " O   HOH Z  85 " =    2.138
peak=    3.056 closest distance to " CD2 TYR A  30 " =    1.046
peak=    3.052 closest distance to " CA  MET A 105 " =    0.988
peak=    3.044 closest distance to " O   THR A  31 " =    1.547

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.763 - 5.435
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.763 - 5.435

peak=   -4.794 closest distance to " CG2 VAL A 230 " =    0.849
peak=   -4.690 closest distance to " CD  ARG A 156 " =    1.994
peak=   -4.645 closest distance to " SG  CYS A 254 " =    3.230
peak=   -4.587 closest distance to " O   HOH Z 266 " =    4.807
peak=   -4.314 closest distance to " CG  GLN A 223 " =    1.939
peak=   -4.252 closest distance to " CB  PRO A 243 " =    2.621
peak=   -4.226 closest distance to " OG BSER A 134 " =    1.212
peak=   -4.149 closest distance to " CG2 VAL A 296 " =    1.299
peak=   -4.127 closest distance to " C   HIS A 108 " =    1.180
peak=   -4.060 closest distance to " CB  ALA A 161 " =    2.534
peak=   -4.027 closest distance to " CE2 TYR A  30 " =    2.794
peak=   -3.982 closest distance to " O   HOH Z 231 " =    1.938
peak=   -3.980 closest distance to " O   HOH Z 435 " =    2.812
peak=   -3.957 closest distance to " O   PRO A 163 " =    2.094
peak=   -3.955 closest distance to " CE2 PHE A 218 " =    2.615
peak=   -3.950 closest distance to " CG2 THR A   4 " =    1.930
peak=   -3.933 closest distance to " CG1 VAL A 112 " =    2.922
peak=   -3.927 closest distance to " CE  MET A 105 " =    2.218
peak=   -3.907 closest distance to " CG2BVAL A  41 " =    2.679
peak=   -3.903 closest distance to " O   HOH Z 290 " =    1.157
peak=   -3.900 closest distance to " CD2 LEU A 300 " =    2.842
peak=   -3.899 closest distance to " N   GLN A  58 " =    1.696
peak=   -3.870 closest distance to " OD1 ASN A 187 " =    1.665
peak=   -3.866 closest distance to " OXT GLY A 302 " =    2.865
peak=   -3.863 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.855 closest distance to " CB  ALA A 248 " =    2.032
peak=   -3.853 closest distance to " O   VAL A  67 " =    2.707
peak=   -3.784 closest distance to " ND2 ASN A  45 " =    1.542
peak=   -3.777 closest distance to " CB  PHE A 192 " =    1.891
peak=   -3.773 closest distance to " CB  PRO A 280 " =    2.072
peak=   -3.760 closest distance to " O   HOH Z 114 " =    2.943
peak=   -3.749 closest distance to " CG  PHE A 283 " =    2.812
peak=   -3.732 closest distance to " O   HOH Z 389 " =    1.893
peak=   -3.704 closest distance to " O   HOH Z 166 " =    1.482
peak=   -3.701 closest distance to " O   HOH Z 198 " =    2.233
peak=   -3.697 closest distance to " CZ  PHE A  59 " =    1.507
peak=   -3.688 closest distance to " CD  LYS A 289 " =    2.554
peak=   -3.680 closest distance to " O   PRO A 198 " =    1.235
peak=   -3.664 closest distance to " O   HOH Z 351 " =    1.591
peak=   -3.651 closest distance to " N   THR A 157 " =    1.454
peak=   -3.641 closest distance to " O   HOH Z 102 " =    1.597
peak=   -3.636 closest distance to " CB  ALA A 291 " =    2.340
peak=   -3.636 closest distance to " CB  ALA A 248 " =    2.393
peak=   -3.620 closest distance to " CB  PRO A 163 " =    2.527
peak=   -3.607 closest distance to " ND2 ASN A 187 " =    1.589
peak=   -3.601 closest distance to " CD1 LEU A 228 " =    2.144
peak=   -3.599 closest distance to " ND2 ASN A  45 " =    1.087
peak=   -3.596 closest distance to " N   ALA A 226 " =    2.025
peak=   -3.590 closest distance to " O   HOH Z 211 " =    1.595
peak=   -3.574 closest distance to " C   ASN A 187 " =    1.842
peak=   -3.574 closest distance to " NZ  LYS A 119 " =    3.473
peak=   -3.571 closest distance to " CB  TYR A  15 " =    2.183
peak=   -3.568 closest distance to " NH2 ARG A  79 " =    1.932
peak=   -3.564 closest distance to " O   HOH Z 407 " =    3.021
peak=   -3.557 closest distance to " O   HOH Z 196 " =    2.269
peak=   -3.557 closest distance to " CD  ARG A 139 " =    1.577
peak=   -3.539 closest distance to " NH2AARG A 275 " =    5.172
peak=   -3.534 closest distance to " CZ  TYR A 169 " =    1.630
peak=   -3.533 closest distance to " O   HOH Z  13 " =    1.480
peak=   -3.532 closest distance to " CB  ASP A 132 " =    2.309
peak=   -3.529 closest distance to " O   HOH Z 103 " =    1.824
peak=   -3.528 closest distance to " N   THR A 235 " =    1.317
peak=   -3.526 closest distance to " N   ALA A 248 " =    1.570
peak=   -3.517 closest distance to " CA  ASP A 298 " =    1.040
peak=   -3.501 closest distance to " O   HOH Z  43 " =    1.831
peak=   -3.501 closest distance to " CG  LEU A 228 " =    1.070
peak=   -3.499 closest distance to " NE2 GLN A  88 " =    1.935
peak=   -3.496 closest distance to " CD  GLN A  58 " =    1.168
peak=   -3.488 closest distance to " O   HOH Z 388 " =    2.102
peak=   -3.486 closest distance to " CG1 VAL A 296 " =    1.303
peak=   -3.484 closest distance to " O   HOH Z 198 " =    1.511
peak=   -3.480 closest distance to " CG1 VAL A 112 " =    2.624
peak=   -3.476 closest distance to " O   SER A  22 " =    2.263
peak=   -3.475 closest distance to " CG  LYS A 193 " =    2.367
peak=   -3.475 closest distance to " O   PRO A 198 " =    1.321
peak=   -3.474 closest distance to " C   ALA A 158 " =    1.238
peak=   -3.470 closest distance to " OG  SER A  87 " =    1.347
peak=   -3.464 closest distance to " O   HOH Z  60 " =    2.047
peak=   -3.460 closest distance to " N   SER A 276 " =    1.279
peak=   -3.457 closest distance to " O   HOH Z  44 " =    2.197
peak=   -3.456 closest distance to " CZ3 TRP A 179 " =    1.230
peak=   -3.456 closest distance to " CB  ALA A 291 " =    2.124
peak=   -3.456 closest distance to " O   HOH Z 166 " =    1.990
peak=   -3.455 closest distance to " O   ARG A 145 " =    1.587
peak=   -3.451 closest distance to " CA  GLY A 203 " =    2.286
peak=   -3.448 closest distance to " CD1 LEU A 101 " =    2.419
peak=   -3.444 closest distance to " O   HOH Z 185 " =    2.240
peak=   -3.439 closest distance to " O   MET A  40 " =    2.675
peak=   -3.439 closest distance to " C   ASP A 231 " =    2.555
peak=   -3.427 closest distance to " CG1 VAL A 250 " =    2.717
peak=   -3.420 closest distance to " CG1 VAL A 230 " =    1.872
peak=   -3.419 closest distance to " OD1 ASN A 148 " =    1.485
peak=   -3.418 closest distance to " CB  ASP A 132 " =    2.304
peak=   -3.411 closest distance to " C   LEU A 143 " =    1.005
peak=   -3.404 closest distance to " O   HOH Z 139 " =    3.010
peak=   -3.404 closest distance to " CA  GLY A  98 " =    1.866
peak=   -3.396 closest distance to " OD2 ASP A 171 " =    2.283
peak=   -3.396 closest distance to " O   HOH Z  90 " =    2.761
peak=   -3.392 closest distance to " N   PHE A  59 " =    2.158
peak=   -3.388 closest distance to " CD1 PHE A  59 " =    1.947
peak=   -3.381 closest distance to " O   HOH Z 389 " =    4.759
peak=   -3.379 closest distance to " O   HOH Z 191 " =    5.435
peak=   -3.376 closest distance to " NH1 ARG A  36 " =    2.014
peak=   -3.367 closest distance to " O   HOH Z  52 " =    1.508
peak=   -3.367 closest distance to " CD1 LEU A 101 " =    2.605
peak=   -3.366 closest distance to " OG ASER A 134 " =    0.963
peak=   -3.364 closest distance to " OH  TYR A 214 " =    1.239
peak=   -3.360 closest distance to " CA  ASP A  27 " =    2.446
peak=   -3.359 closest distance to " OG BSER A 134 " =    1.672
peak=   -3.357 closest distance to " C   MET A 188 " =    1.403
peak=   -3.356 closest distance to " O   HOH Z 165 " =    1.972
peak=   -3.355 closest distance to " O   HOH Z 385 " =    1.898
peak=   -3.354 closest distance to " CG  PRO A 163 " =    2.538
peak=   -3.353 closest distance to " OG  SER A  62 " =    1.680
peak=   -3.351 closest distance to " N   HIS A 115 " =    2.025
peak=   -3.350 closest distance to " O   HOH Z 394 " =    1.547
peak=   -3.350 closest distance to " N   ALA A  43 " =    2.490
peak=   -3.347 closest distance to " O   HOH Z 350 " =    1.685
peak=   -3.334 closest distance to " O   HOH Z 339 " =    1.848
peak=   -3.334 closest distance to " O   LYS A 117 " =    1.671
peak=   -3.321 closest distance to " OD2 ASP A 191 " =    1.402
peak=   -3.321 closest distance to " O   GLY A  80 " =    2.531
peak=   -3.320 closest distance to " O   PHE A 218 " =    1.658
peak=   -3.317 closest distance to " CG  TRP A 266 " =    1.860
peak=   -3.317 closest distance to " O   HOH Z 369 " =    2.063
peak=   -3.314 closest distance to " O   VAL A 189 " =    2.564
peak=   -3.312 closest distance to " O   HOH Z 309 " =    2.483
peak=   -3.300 closest distance to " O   HOH Z 313 " =    1.706
peak=   -3.297 closest distance to " N   SER A 212 " =    2.006
peak=   -3.296 closest distance to " CB  ASN A  39 " =    2.201
peak=   -3.295 closest distance to " OG  SER A  26 " =    1.183
peak=   -3.290 closest distance to " O   ALA A 161 " =    1.582
peak=   -3.282 closest distance to " C   LEU A 222 " =    0.768
peak=   -3.280 closest distance to " O   HOH Z 140 " =    1.672
peak=   -3.279 closest distance to " ND2 ASN A 249 " =    2.374
peak=   -3.277 closest distance to " CA  TYR A  30 " =    2.907
peak=   -3.276 closest distance to " O   HOH Z 417 " =    2.795
peak=   -3.271 closest distance to " C   GLN A 205 " =    1.947
peak=   -3.269 closest distance to " OG1 THR A 178 " =    1.227
peak=   -3.267 closest distance to " O   HOH Z 281 " =    2.747
peak=   -3.267 closest distance to " C   ALA A   8 " =    1.573
peak=   -3.262 closest distance to " CG2 ILE A 263 " =    2.314
peak=   -3.262 closest distance to " O   HOH Z 234 " =    3.976
peak=   -3.258 closest distance to " CD2 LEU A 167 " =    1.704
peak=   -3.258 closest distance to " CD2 LEU A 237 " =    2.747
peak=   -3.258 closest distance to " CB  ALA A   7 " =    2.143
peak=   -3.256 closest distance to " O   ASN A 187 " =    1.532
peak=   -3.256 closest distance to " OG  SER A 206 " =    1.641
peak=   -3.254 closest distance to " CA  GLY A 133 " =    2.213
peak=   -3.249 closest distance to " CA  GLY A 241 " =    3.045
peak=   -3.243 closest distance to " CG  ARG A 269 " =    2.365
peak=   -3.235 closest distance to " O   HOH Z 426 " =    1.660
peak=   -3.234 closest distance to " CD1 TYR A 247 " =    2.526
peak=   -3.231 closest distance to " OG  SER A  97 " =    2.152
peak=   -3.229 closest distance to " O   ALA A  51 " =    1.320
peak=   -3.227 closest distance to " NH2BARG A 275 " =    1.664
peak=   -3.227 closest distance to " O   HOH Z 134 " =    2.828
peak=   -3.225 closest distance to " O   GLY A 196 " =    1.046
peak=   -3.225 closest distance to " N   GLN A  77 " =    1.500
peak=   -3.222 closest distance to " CB  ALA A 131 " =    2.066
peak=   -3.218 closest distance to " O   ALA A 100 " =    2.453
peak=   -3.217 closest distance to " CE3 TRP A 150 " =    1.993
peak=   -3.216 closest distance to " O   HOH Z 411 " =    3.902
peak=   -3.215 closest distance to " CB  GLN A  11 " =    1.962
peak=   -3.213 closest distance to " O   HOH Z 210 " =    1.184
peak=   -3.212 closest distance to " CG  GLN A 278 " =    2.134
peak=   -3.208 closest distance to " O   HOH Z  97 " =    1.624
peak=   -3.206 closest distance to " O   HOH Z 385 " =    2.067
peak=   -3.206 closest distance to " CG  MET A 105 " =    0.907
peak=   -3.201 closest distance to " CG  LEU A 101 " =    2.342
peak=   -3.196 closest distance to " O   TRP A  70 " =    1.499
peak=   -3.193 closest distance to " O   SER A  95 " =    1.557
peak=   -3.191 closest distance to " O   HOH Z 410 " =    2.095
peak=   -3.188 closest distance to " NH1AARG A 275 " =    1.847
peak=   -3.179 closest distance to " NH1 ARG A 195 " =    2.582
peak=   -3.176 closest distance to " O   HOH Z 423 " =    2.093
peak=   -3.173 closest distance to " CG  GLU A   2 " =    2.005
peak=   -3.166 closest distance to " ND2 ASN A  60 " =    1.501
peak=   -3.166 closest distance to " N   ASP A 171 " =    2.308
peak=   -3.165 closest distance to " CD2 TYR A 293 " =    2.087
peak=   -3.165 closest distance to " O   SER A 135 " =    1.495
peak=   -3.164 closest distance to " N   ALA A 248 " =    1.877
peak=   -3.163 closest distance to " ND2 ASN A  69 " =    1.753
peak=   -3.162 closest distance to " O   LEU A 167 " =    1.481
peak=   -3.162 closest distance to " CD2 TYR A 247 " =    2.471
peak=   -3.158 closest distance to " CG  GLU A 277 " =    1.179
peak=   -3.156 closest distance to " CE BMET A  47 " =    1.729
peak=   -3.155 closest distance to " O   VAL A 197 " =    1.317
peak=   -3.154 closest distance to " CD2 LEU A   5 " =    1.199
peak=   -3.152 closest distance to " CA  GLY A 133 " =    1.976
peak=   -3.147 closest distance to " O   HOH Z 123 " =    2.373
peak=   -3.144 closest distance to " CZ2 TRP A 179 " =    2.369
peak=   -3.143 closest distance to " OXT GLY A 302 " =    3.526
peak=   -3.137 closest distance to " O   HOH Z 131 " =    4.065
peak=   -3.136 closest distance to " N   LYS A 289 " =    1.459
peak=   -3.134 closest distance to " O   HOH Z 137 " =    1.501
peak=   -3.121 closest distance to " O   HOH Z 311 " =    3.691
peak=   -3.120 closest distance to " O   HOH Z 436 " =    1.549
peak=   -3.119 closest distance to " CG1 VAL A 197 " =    2.230
peak=   -3.119 closest distance to " O   HOH Z 148 " =    2.957
peak=   -3.113 closest distance to " O   HOH Z 353 " =    2.013
peak=   -3.098 closest distance to " NH2 ARG A  79 " =    1.562
peak=   -3.094 closest distance to " O   HOH Z  63 " =    1.272
peak=   -3.087 closest distance to " CG2 VAL A 189 " =    1.993
peak=   -3.075 closest distance to " CB  VAL A 296 " =    1.332
peak=   -3.070 closest distance to " O   HOH Z 222 " =    1.569
peak=   -3.059 closest distance to " CG  GLU A 152 " =    1.431
peak=   -3.053 closest distance to " O   HOH Z 111 " =    1.198
peak=   -3.051 closest distance to " O   HOH Z 288 " =    1.425
peak=   -3.045 closest distance to " O   HOH Z 193 " =    1.660
peak=   -3.015 closest distance to " OD1 ASP A 200 " =    1.376

================= 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    :  0.4233 0.4089   6.213419e+00   6.189901e+00
   1_bss:  0.4137 0.4001   6.209149e+00   6.175850e+00
   1_xyz:  0.3065 0.3299   5.986740e+00   6.031707e+00
   1_adp:  0.2390 0.2757   5.767487e+00   5.888169e+00
   1_occ:  0.2384 0.2760   5.766307e+00   5.888878e+00
   2_bss:  0.2323 0.2687   5.762477e+00   5.881987e+00
   2_xyz:  0.1554 0.1969   5.407779e+00   5.600078e+00
   2_adp:  0.1411 0.1829   5.324831e+00   5.529062e+00
   2_occ:  0.1410 0.1826   5.324023e+00   5.528029e+00
   3_bss:  0.1409 0.1824   5.323552e+00   5.526413e+00
   3_xyz:  0.1187 0.1592   5.174488e+00   5.400538e+00
   3_adp:  0.1134 0.1574   5.149800e+00   5.391274e+00
   3_occ:  0.1134 0.1574   5.149689e+00   5.391160e+00
   4_bss:  0.1137 0.1568   5.148712e+00   5.388591e+00
   4_xyz:  0.1131 0.1565   5.148355e+00   5.388707e+00
   4_adp:  0.1148 0.1542   5.145432e+00   5.371720e+00
   4_occ:  0.1148 0.1541   5.145279e+00   5.371636e+00
   5_bss:  0.1148 0.1541   5.145279e+00   5.371636e+00
   5_xyz:  0.1101 0.1525   5.117785e+00   5.359028e+00
   5_adp:  0.1082 0.1547   5.120018e+00   5.374573e+00
   5_occ:  0.1082 0.1548   5.120131e+00   5.374771e+00
   5_bss:  0.1082 0.1547   5.120094e+00   5.374768e+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:  0.358  12.954   7.387   8.584   8.576   0.000   0.000   0.000
   1_xyz:  0.358  12.954   7.387   8.584   8.576   0.000   0.000   0.000
   1_adp:  0.358  12.954   7.387   8.584   8.576   0.000   0.000   0.000
   1_occ:  0.358  12.954   7.387   8.584   8.576   0.000   0.000   0.000
   2_bss:  0.338  31.904   3.711   4.463   5.420   0.000   0.000   0.000
   2_xyz:  0.338  31.904   3.711   4.463   5.420   0.000   0.000   0.000
   2_adp:  0.338  31.904   3.711   4.463   5.420   0.000   0.000   0.000
   2_occ:  0.338  31.904   3.711   4.463   5.420   0.000   0.000   0.000
   3_bss:  0.325  31.904   3.110   3.488   4.397   0.000   0.000   0.000
   3_xyz:  0.325  31.904   3.110   3.488   4.397   0.000   0.000   0.000
   3_adp:  0.325  31.904   3.110   3.488   4.397   0.000   0.000   0.000
   3_occ:  0.325  31.904   3.110   3.488   4.397   0.000   0.000   0.000
   4_bss:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   4_xyz:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   4_adp:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   4_occ:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   5_bss:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   5_xyz:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   5_adp:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   5_occ:  0.323  38.448   3.046   3.311   4.188   0.000   0.000   0.000
   5_bss:  0.323  41.990  -0.432  -0.227   0.659   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.716 0.5753  0.6452    49198.050
   1_bss:  45.878 0.5705  0.8137    46539.629
   1_xyz:  34.874 0.7021  0.9781    29107.583
   1_adp:  27.166 0.7894  1.0700    19358.908
   1_occ:  27.180 0.7892  1.0689    19344.345
   2_bss:  26.875 0.7921  0.9391    18904.721
   2_xyz:  18.595 0.8749  1.0002     9679.642
   2_adp:  16.815 0.8915  1.0109     8434.702
   2_occ:  16.795 0.8917  1.0108     8408.495
   3_bss:  16.757 0.8919  0.9795     8375.549
   3_xyz:  14.227 0.9129  0.9891     6459.879
   3_adp:  14.020 0.9148  0.9872     6337.715
   3_occ:  14.020 0.9148  0.9872     6335.291
   4_bss:  13.981 0.9152  0.9817     6305.603
   4_xyz:  13.873 0.9163  0.9814     6273.488
   4_adp:  13.455 0.9197  0.9850     6071.636
   4_occ:  13.456 0.9197  0.9849     6071.824
   5_bss:  13.456 0.9197  0.9849     6071.824
   5_xyz:  13.227 0.9213  0.9858     5925.967
   5_adp:  13.558 0.9188  0.9810     6095.812
   5_occ:  13.563 0.9188  0.9808     6099.834
   5_bss:  13.562 0.9188  0.9819     6100.355
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3455e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3455e+01
   1_xyz:   1.473  0.011  0.099 17.971  0.006  4.119   1.1273e-01
   1_adp:   1.473  0.011  0.099 17.971  0.006  4.119   1.1273e-01
   1_occ:   1.473  0.011  0.099 17.971  0.006  4.119   1.1273e-01
   2_bss:   1.473  0.011  0.099 17.971  0.006  4.119   1.1273e-01
   2_xyz:   0.975  0.006  0.073 16.224  0.004  4.118   6.0807e-02
   2_adp:   0.975  0.006  0.073 16.224  0.004  4.118   6.0807e-02
   2_occ:   0.975  0.006  0.073 16.224  0.004  4.118   6.0807e-02
   3_bss:   0.975  0.006  0.073 16.224  0.004  4.118   6.0807e-02
   3_xyz:   1.010  0.007  0.083 16.012  0.004  4.122   6.5265e-02
   3_adp:   1.010  0.007  0.083 16.012  0.004  4.122   6.5265e-02
   3_occ:   1.010  0.007  0.083 16.012  0.004  4.122   6.5265e-02
   4_bss:   1.010  0.007  0.083 16.012  0.004  4.122   6.5265e-02
   4_xyz:   0.881  0.005  0.072 15.678  0.003  4.112   5.2046e-02
   4_adp:   0.881  0.005  0.072 15.678  0.003  4.112   5.2046e-02
   4_occ:   0.881  0.005  0.072 15.678  0.003  4.112   5.2046e-02
   5_bss:   0.881  0.005  0.072 15.678  0.003  4.112   5.2046e-02
   5_xyz:   1.012  0.007  0.083 15.844  0.004  4.113   6.2948e-02
   5_adp:   1.012  0.007  0.083 15.844  0.004  4.113   6.2948e-02
   5_occ:   1.012  0.007  0.083 15.844  0.004  4.113   6.2948e-02
   5_bss:   1.012  0.007  0.083 15.844  0.004  4.113   6.2948e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9306e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9306e+00
   1_xyz:  12.134  0.135  0.415 89.370  0.029  2.247   8.2244e-02
   1_adp:  12.134  0.135  0.415 89.370  0.029  2.247   8.2244e-02
   1_occ:  12.134  0.135  0.415 89.370  0.029  2.247   8.2244e-02
   2_bss:  12.134  0.135  0.415 89.370  0.029  2.247   8.2244e-02
   2_xyz:   6.936  0.056  0.376 82.958  0.036  2.281   3.9938e-02
   2_adp:   6.936  0.056  0.376 82.958  0.036  2.281   3.9938e-02
   2_occ:   6.936  0.056  0.376 82.958  0.036  2.281   3.9938e-02
   3_bss:   6.936  0.056  0.376 82.958  0.036  2.281   3.9938e-02
   3_xyz:   6.460  0.045  0.570 83.870  0.036  2.285   8.0103e-02
   3_adp:   6.460  0.045  0.570 83.870  0.036  2.285   8.0103e-02
   3_occ:   6.460  0.045  0.570 83.870  0.036  2.285   8.0103e-02
   4_bss:   6.460  0.045  0.570 83.870  0.036  2.285   8.0103e-02
   4_xyz:   6.535  0.036  0.443 83.376  0.033  2.401   3.0786e-02
   4_adp:   6.535  0.036  0.443 83.376  0.033  2.401   3.0786e-02
   4_occ:   6.535  0.036  0.443 83.376  0.033  2.401   3.0786e-02
   5_bss:   6.535  0.036  0.443 83.376  0.033  2.401   3.0786e-02
   5_xyz:   6.507  0.042  0.598 83.952  0.035  2.267   4.2522e-02
   5_adp:   6.507  0.042  0.598 83.952  0.035  2.267   4.2522e-02
   5_occ:   6.507  0.042  0.598 83.952  0.035  2.267   4.2522e-02
   5_bss:   6.507  0.042  0.598 83.952  0.035  2.267   4.2522e-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:  63.18   0.00  10.52  63.18   0.00   7.36  59.71   0.00  27.69
   1_occ:  63.18   0.00  10.52  63.18   0.00   7.36  59.71   0.00  27.69
   2_bss:  63.18   0.00  10.52  63.18   0.00   7.36  59.71   0.00  27.69
   2_xyz:  63.18   0.00  10.52  63.18   0.00   7.36  59.71   0.00  27.69
   2_adp:  66.41   0.00  10.93  66.41   0.00   7.19  58.49   1.16  31.28
   2_occ:  66.41   0.00  10.93  66.41   0.00   7.19  58.49   1.16  31.28
   3_bss:  66.41   0.00  10.93  66.41   0.00   7.19  58.49   1.16  31.28
   3_xyz:  66.41   0.00  10.93  66.41   0.00   7.19  58.49   1.16  31.28
   3_adp:  80.29   0.00  11.59  80.29   0.00   7.38  73.56   0.91  34.54
   3_occ:  80.29   0.00  11.59  80.29   0.00   7.38  73.56   0.91  34.54
   4_bss:  80.29   0.00  11.59  80.29   0.00   7.38  73.56   0.91  34.54
   4_xyz:  80.29   0.00  11.59  80.29   0.00   7.38  73.56   0.91  34.54
   4_adp:  79.79   0.00  11.39  79.79   0.00   7.34  70.68   1.12  33.44
   4_occ:  79.79   0.00  11.39  79.79   0.00   7.34  70.68   1.12  33.44
   5_bss:  79.79   0.00  11.39  79.79   0.00   7.34  70.68   1.12  33.44
   5_xyz:  79.79   0.00  11.39  79.79   0.00   7.34  70.68   1.12  33.44
   5_adp:  87.87   0.00  11.58  87.87   0.00   7.40  79.50   1.14  34.34
   5_occ:  87.87   0.00  11.58  87.87   0.00   7.40  79.50   1.14  34.34
   5_bss:  91.41   3.54  15.12  91.41   3.54  10.94  83.04   4.68  37.89
------------------------------------------------------------------------
 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:    1.158    0.020    0.399
   1_adp:    1.158    0.020    0.399
   1_occ:    1.158    0.020    0.399
   2_bss:    1.158    0.020    0.399
   2_xyz:    1.326    0.014    0.487
   2_adp:    1.326    0.014    0.487
   2_occ:    1.326    0.014    0.487
   3_bss:    1.326    0.014    0.487
   3_xyz:    1.426    0.034    0.523
   3_adp:    1.426    0.034    0.523
   3_occ:    1.426    0.034    0.523
   4_bss:    1.426    0.034    0.523
   4_xyz:    1.520    0.032    0.529
   4_adp:    1.520    0.032    0.529
   4_occ:    1.520    0.032    0.529
   5_bss:    1.520    0.032    0.529
   5_xyz:    1.574    0.018    0.538
   5_adp:    1.574    0.018    0.538
   5_occ:    1.574    0.018    0.538
   5_bss:    1.574    0.018    0.538
------------------------------------------------------------------------

CPU time actual refinement: 317.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_652/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_652/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_652/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_652/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_652/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.84 
  Macro-tasks:
    bulk solvent and scale       = 42.96  
    individual site refinement   = 122.66 
    weights calculation          = 32.84  
    collect and process          = 6.74   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 205.30 
  Micro-tasks:
    mask                            = 1.66   
    f_calc                          = 96.23  
    alpha_beta                      = 8.62   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 100.97 
    fmodel                         = 7.34   
    r_factors                      = 0.23   
    phase_errors                   = 11.80  
    foms                           = 0.16   
    TOTAL for micro-tasks          = 228.22 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.549 micro seconds
Total CPU time: 5.52 minutes
from_scatterers_fft:    625 calls, 95.86 s
gradients_fft:          570 calls, 90.30 s

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

# Date 2008-01-16 Time 02:04:23 PST -0800 (1200477863.76 s)
Start R-work = 0.4233, R-free = 0.4089 (no bulk solvent and anisotropic scale)
Final R-work = 0.1258, R-free = 0.1709 (no bulk solvent and anisotropic scale)

Start R-work = 0.4137, R-free = 0.4001
Final R-work = 0.1082, R-free = 0.1547