# Date 2008-01-16 Time 02:07:56 PST -0800 (1200478076.21 s)
#phil __OFF__

Command line arguments: "../702.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21638
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 702

-------------------------------------------------------------------------------
  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, 47.6339, 88.1178, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00071
Completeness in resolution range: 0.954072
Completeness with d_max=infinity: 0.951107

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   2.0007

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, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00071
Completeness in resolution range: 0.954072
Completeness with d_max=infinity: 0.951107

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0739 -  4.2806 [2166/2193]  1947   219  10.1%
  bin  2:  4.2806 -  3.4106 [2060/2076]  1857   203   9.9%
  bin  3:  3.4106 -  2.9832 [2053/2072]  1847   206  10.0%
  bin  4:  2.9832 -  2.7122 [2024/2054]  1824   200   9.9%
  bin  5:  2.7122 -  2.5188 [2004/2023]  1799   205  10.2%
  bin  6:  2.5188 -  2.3709 [2010/2046]  1811   199   9.9%
  bin  7:  2.3709 -  2.2525 [1989/2022]  1793   196   9.9%
  bin  8:  2.2525 -  2.1548 [1990/2025]  1786   204  10.3%
  bin  9:  2.1548 -  2.0720 [1973/2000]  1779   194   9.8%
  bin 10:  2.0720 -  2.0007 [1320/2021]  1187   133  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_702/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: 0.15 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:
        1.62 -     2.28: 9
        2.28 -     2.93: 1532
        2.93 -     3.59: 4396
        3.59 -     4.24: 9023
        4.24 -     4.90: 12881
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.624 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.889 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.889 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.952 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27836 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_702/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_702/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 47.63395 88.1178 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: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4873   r_free= 0.4762   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.286477                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1402  155 0.3908 0.3758      6.5927       6.554|
|  2:  4.7741 -  3.8095 0.99   1348  152 0.4084 0.4630      6.7988      6.9325|
|  3:  3.8095 -  3.3339 0.99   1318  147 0.4567 0.4275         6.7      6.6492|
|  4:  3.3339 -  3.0318 0.99   1309  137 0.4763 0.4233      6.5358      6.4683|
|  5:  3.0318 -  2.8160 0.99   1307  152 0.5201 0.4796      6.3812      6.3992|
|  6:  2.8160 -  2.6509 0.99   1304  144 0.5157 0.5549      6.2814      6.2027|
|  7:  2.6509 -  2.5188 0.99   1286  146 0.5054 0.4452      6.2382      6.1367|
|  8:  2.5188 -  2.4096 0.98   1302  139 0.5318 0.4648      6.2005      6.1525|
|  9:  2.4096 -  2.3172 0.98   1283  147 0.5276 0.5864      6.1116      6.1841|
| 10:  2.3172 -  2.2375 0.98   1266  138 0.5538 0.4780      6.1281      6.0871|
| 11:  2.2375 -  2.1677 1.00   1279  145 0.5248 0.5366      6.0346      6.0887|
| 12:  2.1677 -  2.1059 0.97   1280  134 0.5384 0.5520      5.9656      6.0135|
| 13:  2.1059 -  2.0506 0.98   1259  146 0.5421 0.5322      5.8948       5.827|
| 14:  2.0506 -  2.0007 0.53    687   77 0.5467 0.5144      5.8735      5.7811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1402   155  0.70  34.62   0.79     0.71      71345.58|
|  2:  4.7741 -  3.8095  1348   152  0.69  35.76   0.87     0.74     109534.78|
|  3:  3.8095 -  3.3339  1318   147  0.59  44.50   0.80     0.69     115385.63|
|  4:  3.3339 -  3.0318  1309   137  0.51  51.07   0.78     0.59      99534.43|
|  5:  3.0318 -  2.8160  1307   152  0.43  57.21   0.72     0.50      79196.87|
|  6:  2.8160 -  2.6509  1304   144  0.40  59.60   0.70     0.47      70005.81|
|  7:  2.6509 -  2.5188  1286   146  0.41  58.98   0.74     0.46      61773.02|
|  8:  2.5188 -  2.4096  1302   139  0.41  59.10   0.72     0.47      55300.74|
|  9:  2.4096 -  2.3172  1283   147  0.38  61.57   0.69     0.45      52534.38|
| 10:  2.3172 -  2.2375  1266   138  0.34  64.55   0.71     0.40      50552.26|
| 11:  2.2375 -  2.1677  1279   145  0.31  66.85   0.73     0.37      48793.11|
| 12:  2.1677 -  2.1059  1280   134  0.29  68.32   0.73     0.36      44684.85|
| 13:  2.1059 -  2.0506  1259   146  0.27  69.92   0.70     0.33      39116.80|
| 14:  2.0506 -  2.0007   687    77  0.24  72.15   0.71     0.26      32601.09|
|alpha:            min =        0.26 max =            0.74 mean =         0.50|
|beta:             min =    32601.09 max =       115385.63 mean =     68005.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.65|
|phase err.(test): min =        0.00 max =           89.95 mean =        56.92|
|-----------------------------------------------------------------------------|

============================== 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 = 14.602814             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.902   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.365997              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.341   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      669 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1483 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2572 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3837 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4984 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6476 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7642 |
|-----------------------------------------------------------------------------|
|-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 |       54.431 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.758 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    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 = 12.263)------------------------------------------|
|    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: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4934   r_free= 0.4767   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.288542                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4796   r_free= 0.4657   ksol= 0.31   Bsol= 9.45   scale= 0.986    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.38,10.08,11.06,0.00,0.00,0.00); trace/3= 9.17                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.278624                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.124128             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.891   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.244155              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.320   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4796      final r-factor (work) = 0.3969          |
| start r-factor (free) = 0.4657      final r-factor (free) = 0.4173          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.6878 = 13.12 * 0.50 * 6.2871 + 1.00 * 54.4314                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.8039 = 13.12 * 0.50 * 6.1959 + 1.00 * 0.1459                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3969      final r-factor (work) = 0.3523          |
| start r-factor (free) = 0.4173      final r-factor (free) = 0.4028          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7231 = 1.24 * 1.00 * 6.1959 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6219 = 1.24 * 1.00 * 6.1107 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.38   14.05    None  None   None       |
|    all(noH): 2823   0      0.00    99.38   14.05    None  None   None       |
|    Sol.    : 438    0      0.00    99.38   27.31    None  None   None       |
|    Mac.    : 2385   0      0.00    72.57   11.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.938: 1383   |   5:    49.689 -  59.627:   37        |
|      1:     9.938 -  19.876:  730   |   6:    59.627 -  69.564:   17        |
|      2:    19.876 -  29.813:  395   |   7:    69.564 -  79.502:    5        |
|      3:    29.813 -  39.751:  163   |   8:    79.502 -  89.440:    4        |
|      4:    39.751 -  49.689:   87   |   9:    89.440 -  99.378:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3523 r_free = 0.4028             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3516 r_free = 0.4034             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3516   r_free= 0.4034   ksol= 0.31   Bsol= 9.45   scale= 1.100    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.38,10.08,11.06,0.00,0.00,0.00); trace/3= 9.17                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.093932                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3487   r_free= 0.3975   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,6.21,7.01,0.00,0.00,0.00); trace/3= 5.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.094839                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.522547              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.619   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.471187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.378  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3487      final r-factor (work) = 0.2750          |
| start r-factor (free) = 0.3975      final r-factor (free) = 0.3298          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0069 = 5.52 * 0.50 * 6.1062 + 1.00 * 0.1459                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6097 = 5.52 * 0.50 * 5.9858 + 1.00 * 0.0813                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2750      final r-factor (work) = 0.2575          |
| start r-factor (free) = 0.3298      final r-factor (free) = 0.3067          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8430 = 0.47 * 1.00 * 5.9858 + 1.00 * 0.0226                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7852 = 0.47 * 1.00 * 5.8726 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.34  13.30    None  None   None       |
|    all(noH): 2823   0      0.00    102.34  13.30    None  None   None       |
|    Sol.    : 438    0      0.00    102.34  31.55    None  None   None       |
|    Mac.    : 2385   0      0.00    67.79   9.94     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:     0.000 -  10.235: 1557   |   5:    51.172 -  61.407:   41        |
|      1:    10.235 -  20.469:  709   |   6:    61.407 -  71.641:   12        |
|      2:    20.469 -  30.703:  272   |   7:    71.641 -  81.876:    5        |
|      3:    30.703 -  40.938:  142   |   8:    81.876 -  92.110:    1        |
|      4:    40.938 -  51.172:   83   |   9:    92.110 - 102.345:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2575 r_free = 0.3067             target_work(ml) = 5.848         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2571 r_free = 0.3072             target_work(ml) = 5.848         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2571   r_free= 0.3072   ksol= 0.32   Bsol= 50.00   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,6.21,7.01,0.00,0.00,0.00); trace/3= 5.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.848040                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2559   r_free= 0.3069   ksol= 0.31   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,3.80,4.54,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.849240                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.925761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.529529              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.574   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2559      final r-factor (work) = 0.1971          |
| start r-factor (free) = 0.3069      final r-factor (free) = 0.2389          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6760 = 2.93 * 0.50 * 5.8752 + 1.00 * 0.0814                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4603 = 2.93 * 0.50 * 5.7399 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1971      final r-factor (work) = 0.1825          |
| start r-factor (free) = 0.2389      final r-factor (free) = 0.2278          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0543 = 0.53 * 1.00 * 5.7399 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9660 = 0.53 * 1.00 * 5.5765 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.75  13.71    None  None   None       |
|    all(noH): 2823   0      0.00    100.75  13.71    None  None   None       |
|    Sol.    : 438    0      1.49    100.75  36.55    None  None   None       |
|    Mac.    : 2385   0      0.00    73.10   9.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.075: 1655   |   5:    50.373 -  60.448:   72        |
|      1:    10.075 -  20.149:  603   |   6:    60.448 -  70.522:   28        |
|      2:    20.149 -  30.224:  191   |   7:    70.522 -  80.597:    8        |
|      3:    30.224 -  40.299:  142   |   8:    80.597 -  90.672:    2        |
|      4:    40.299 -  50.373:  121   |   9:    90.672 - 100.746:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1825 r_free = 0.2278             target_work(ml) = 5.557         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1824 r_free = 0.2279             target_work(ml) = 5.557         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1824   r_free= 0.2279   ksol= 0.31   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,3.80,4.54,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.557144                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1823   r_free= 0.2275   ksol= 0.33   Bsol= 71.05   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.34,2.77,3.74,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.556665                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.944468              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.582  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.325084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.400  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1823      final r-factor (work) = 0.1452          |
| start r-factor (free) = 0.2275      final r-factor (free) = 0.1905          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2758 = 2.94 * 0.50 * 5.5781 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1011 = 2.94 * 0.50 * 5.4575 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1452      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.1905      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7872 = 0.33 * 1.00 * 5.4575 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8189 = 0.33 * 1.00 * 5.3445 + 1.00 * 0.0815                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.89   13.39    None  None   None       |
|    all(noH): 2823   0      0.00    96.89   13.39    None  None   None       |
|    Sol.    : 438    0      1.64    96.89   36.99    None  None   None       |
|    Mac.    : 2385   0      0.00    75.34   9.05     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.689: 1685   |   5:    48.447 -  58.136:   81        |
|      1:     9.689 -  19.379:  598   |   6:    58.136 -  67.826:   44        |
|      2:    19.379 -  29.068:  162   |   7:    67.826 -  77.515:   12        |
|      3:    29.068 -  38.758:  121   |   8:    77.515 -  87.204:    2        |
|      4:    38.758 -  48.447:  117   |   9:    87.204 -  96.894:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1399 r_free = 0.1830             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1397 r_free = 0.1830             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1830   ksol= 0.33   Bsol= 71.05   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.34,2.77,3.74,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.326904                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1399   r_free= 0.1835   ksol= 0.34   Bsol= 71.05   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.28,2.30,3.47,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.328368                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.080651              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.320  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.818364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.480   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1835      final r-factor (free) = 0.1706          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6269 = 2.08 * 0.50 * 5.3450 + 1.00 * 0.0664                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5725 = 2.08 * 0.50 * 5.2918 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1706      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.9307 = 2.82 * 1.00 * 5.2918 + 1.00 * 0.0163                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7833 = 2.82 * 1.00 * 5.2396 + 1.00 * 0.0162                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.79  13.85    None  None   None       |
|    all(noH): 2823   0      0.00    101.79  13.85    None  None   None       |
|    Sol.    : 438    0      0.73    101.79  40.26    None  None   None       |
|    Mac.    : 2385   0      0.00    89.66   9.00     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:     0.000 -  10.179: 1768   |   5:    50.893 -  61.071:   79        |
|      1:    10.179 -  20.357:  528   |   6:    61.071 -  71.250:   51        |
|      2:    20.357 -  30.536:  150   |   7:    71.250 -  81.429:   33        |
|      3:    30.536 -  40.714:  114   |   8:    81.429 -  91.607:    7        |
|      4:    40.714 -  50.893:   92   |   9:    91.607 - 101.786:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1247 r_free = 0.1716             target_work(ml) = 5.243         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1247 r_free = 0.1716             target_work(ml) = 5.243         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1716   ksol= 0.34   Bsol= 71.05   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.28,2.30,3.47,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.242523                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1402  155 0.1047 0.1351      5.4418      5.5692|
|  2:  4.7741 -  3.8095 0.99   1348  152 0.0885 0.1063      5.4656      5.6361|
|  3:  3.8095 -  3.3339 0.99   1318  147 0.1156 0.1528      5.5371      5.8809|
|  4:  3.3339 -  3.0318 0.99   1309  137 0.1315 0.1781      5.5259      5.7203|
|  5:  3.0318 -  2.8160 0.99   1307  152 0.1540 0.1736      5.4578      5.5723|
|  6:  2.8160 -  2.6509 0.99   1304  144 0.1449 0.2420      5.3446      5.6545|
|  7:  2.6509 -  2.5188 0.99   1286  146 0.1466 0.1821      5.2998      5.4456|
|  8:  2.5188 -  2.4096 0.98   1302  139 0.1327 0.1887      5.1973      5.4458|
|  9:  2.4096 -  2.3172 0.98   1283  147 0.1367 0.2136      5.1441       5.431|
| 10:  2.3172 -  2.2375 0.98   1266  138 0.1299 0.1595       5.072      5.2063|
| 11:  2.2375 -  2.1677 1.00   1279  145 0.1290 0.2046      5.0312       5.358|
| 12:  2.1677 -  2.1059 0.97   1280  134 0.1243 0.1850      4.9604      5.2667|
| 13:  2.1059 -  2.0506 0.98   1259  146 0.1204 0.1895      4.8729      5.1048|
| 14:  2.0506 -  2.0007 0.53    687   77 0.1145 0.1948      4.7626      5.0617|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1402   155  0.94   9.82   0.96     0.94       8203.21|
|  2:  4.7741 -  3.8095  1348   152  0.95   8.28   1.00     0.98       9320.56|
|  3:  3.8095 -  3.3339  1318   147  0.93  11.53   1.02     1.01      10901.20|
|  4:  3.3339 -  3.0318  1309   137  0.91  14.66   1.00     0.98      11718.53|
|  5:  3.0318 -  2.8160  1307   152  0.88  18.13   0.99     0.97      10574.88|
|  6:  2.8160 -  2.6509  1304   144  0.87  19.07   0.97     0.93       9323.13|
|  7:  2.6509 -  2.5188  1286   146  0.88  18.01   0.98     0.93       7964.38|
|  8:  2.5188 -  2.4096  1302   139  0.89  17.50   0.98     0.94       6983.55|
|  9:  2.4096 -  2.3172  1283   147  0.89  18.01   0.99     0.94       6250.62|
| 10:  2.3172 -  2.2375  1266   138  0.88  17.98   0.98     0.93       5456.16|
| 11:  2.2375 -  2.1677  1279   145  0.89  17.70   0.97     0.92       5098.83|
| 12:  2.1677 -  2.1059  1280   134  0.89  17.22   0.99     0.97       4732.43|
| 13:  2.1059 -  2.0506  1259   146  0.89  17.94   0.97     0.94       4046.35|
| 14:  2.0506 -  2.0007   687    77  0.90  16.18   0.94     0.89       3009.62|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     3009.62 max =        11718.53 mean =      7586.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.77|
|phase err.(test): min =        0.00 max =           88.42 mean =        15.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1714   ksol= 0.34   Bsol= 73.61   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,-0.13,1.07,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.242591                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1714   ksol= 0.34   Bsol= 73.61   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,-0.13,1.07,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.242591                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1402  155 0.1047 0.1352      5.4427      5.5708|
|  2:  4.7741 -  3.8095 0.99   1348  152 0.0885 0.1063      5.4666      5.6365|
|  3:  3.8095 -  3.3339 0.99   1318  147 0.1156 0.1530      5.5377      5.8823|
|  4:  3.3339 -  3.0318 0.99   1309  137 0.1315 0.1780      5.5259      5.7204|
|  5:  3.0318 -  2.8160 0.99   1307  152 0.1540 0.1735      5.4576      5.5719|
|  6:  2.8160 -  2.6509 0.99   1304  144 0.1448 0.2419      5.3443      5.6541|
|  7:  2.6509 -  2.5188 0.99   1286  146 0.1466 0.1825      5.2998      5.4462|
|  8:  2.5188 -  2.4096 0.98   1302  139 0.1327 0.1887      5.1976       5.446|
|  9:  2.4096 -  2.3172 0.98   1283  147 0.1367 0.2136      5.1441      5.4313|
| 10:  2.3172 -  2.2375 0.98   1266  138 0.1298 0.1597      5.0718      5.2066|
| 11:  2.2375 -  2.1677 1.00   1279  145 0.1290 0.2041      5.0307      5.3568|
| 12:  2.1677 -  2.1059 0.97   1280  134 0.1243 0.1844        4.96      5.2654|
| 13:  2.1059 -  2.0506 0.98   1259  146 0.1203 0.1898      4.8724      5.1051|
| 14:  2.0506 -  2.0007 0.53    687   77 0.1147 0.1945      4.7631      5.0606|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1402   155  0.94   9.84   0.96     0.94       8225.31|
|  2:  4.7741 -  3.8095  1348   152  0.95   8.30   1.00     0.98       9340.34|
|  3:  3.8095 -  3.3339  1318   147  0.93  11.55   1.02     1.02      10924.42|
|  4:  3.3339 -  3.0318  1309   137  0.91  14.67   1.01     0.99      11724.49|
|  5:  3.0318 -  2.8160  1307   152  0.88  18.12   1.00     0.98      10571.32|
|  6:  2.8160 -  2.6509  1304   144  0.87  19.07   0.98     0.94       9315.47|
|  7:  2.6509 -  2.5188  1286   146  0.88  18.01   0.98     0.94       7966.22|
|  8:  2.5188 -  2.4096  1302   139  0.89  17.51   0.99     0.95       6986.34|
|  9:  2.4096 -  2.3172  1283   147  0.89  18.02   1.00     0.95       6256.36|
| 10:  2.3172 -  2.2375  1266   138  0.88  17.97   0.99     0.94       5449.57|
| 11:  2.2375 -  2.1677  1279   145  0.89  17.68   0.98     0.93       5092.02|
| 12:  2.1677 -  2.1059  1280   134  0.89  17.20   1.00     0.98       4725.88|
| 13:  2.1059 -  2.0506  1259   146  0.89  17.92   0.98     0.96       4040.81|
| 14:  2.0506 -  2.0007   687    77  0.90  16.17   0.95     0.90       3003.95|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3003.95 max =        11724.49 mean =      7590.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.77|
|phase err.(test): min =        0.00 max =           88.42 mean =        15.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.56    104.35  16.41    None  None   None       |
|    all(noH): 2823   0      2.56    104.35  16.41    None  None   None       |
|    Sol.    : 438    0      3.30    104.35  42.82    None  None   None       |
|    Mac.    : 2385   0      2.56    92.22   11.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.562 -  12.740: 1768   |   5:    53.454 -  63.633:   79        |
|      1:    12.740 -  22.919:  528   |   6:    63.633 -  73.812:   51        |
|      2:    22.919 -  33.097:  150   |   7:    73.812 -  83.990:   33        |
|      3:    33.097 -  43.276:  114   |   8:    83.990 -  94.169:    7        |
|      4:    43.276 -  53.454:   92   |   9:    94.169 - 104.347:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.268 - 5.588
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 330
   mapped sites are within: 0.732 - 5.588

peak=    9.881 closest distance to " CB  VAL A 230 " =    1.434
peak=    6.135 closest distance to " O   HOH Z 210 " =    1.316
peak=    5.949 closest distance to " CG1 VAL A 296 " =    1.214
peak=    5.644 closest distance to " NH2 ARG A  56 " =    2.216
peak=    5.561 closest distance to " CG  LEU A   5 " =    1.181
peak=    5.487 closest distance to " CD1AILE A 234 " =    1.122
peak=    5.360 closest distance to " CB  GLN A 223 " =    1.450
peak=    5.337 closest distance to " NH1 ARG A 138 " =    0.980
peak=    5.162 closest distance to " CG  ARG A 138 " =    1.072
peak=    5.010 closest distance to " CG  PRO A 280 " =    0.945
peak=    4.897 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.835 closest distance to " CG  PRO A  54 " =    1.376
peak=    4.738 closest distance to " O   HOH Z 128 " =    1.596
peak=    4.684 closest distance to " CG  LEU A 228 " =    1.226
peak=    4.668 closest distance to " O   HOH Z 248 " =    1.437
peak=    4.641 closest distance to " CD2 LEU A 228 " =    1.349
peak=    4.566 closest distance to " O   HOH Z 232 " =    2.257
peak=    4.523 closest distance to " CA  TYR A  30 " =    0.961
peak=    4.486 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.469 closest distance to " O   HOH Z 403 " =    1.824
peak=    4.453 closest distance to " CB  VAL A 296 " =    1.124
peak=    4.433 closest distance to " O   HOH Z 412 " =    3.774
peak=    4.431 closest distance to " CB  SER A  63 " =    1.181
peak=    4.423 closest distance to " CA  ALA A  51 " =    0.996
peak=    4.389 closest distance to " CG2 VAL A 296 " =    1.000
peak=    4.371 closest distance to " O   HOH Z 142 " =    1.673
peak=    4.356 closest distance to " CA  VAL A 230 " =    1.208
peak=    4.341 closest distance to " CD2 LEU A   5 " =    1.101
peak=    4.332 closest distance to " O   HOH Z  49 " =    1.434
peak=    4.328 closest distance to " O   PRO A 198 " =    1.504
peak=    4.317 closest distance to " CG  PRO A 243 " =    1.162
peak=    4.306 closest distance to " CB  PRO A  54 " =    0.960
peak=    4.297 closest distance to " O   HOH Z 261 " =    2.300
peak=    4.259 closest distance to " CZ  PHE A 218 " =    1.106
peak=    4.244 closest distance to " CB  GLN A 183 " =    1.230
peak=    4.232 closest distance to " NE2 GLN A  11 " =    1.057
peak=    4.206 closest distance to " CB  ARG A 190 " =    1.683
peak=    4.189 closest distance to " CZ3 TRP A 266 " =    1.141
peak=    4.177 closest distance to " O   HOH Z 402 " =    1.516
peak=    4.176 closest distance to " O   HOH Z 130 " =    2.527
peak=    4.172 closest distance to " O   HOH Z 251 " =    1.667
peak=    4.152 closest distance to " O   HOH Z 265 " =    2.015
peak=    4.135 closest distance to " O  BHOH Z  74 " =    1.185
peak=    4.119 closest distance to " O   HOH Z 130 " =    1.124
peak=    4.084 closest distance to " O   HOH Z 425 " =    1.541
peak=    4.083 closest distance to " O   HOH Z   4 " =    1.604
peak=    4.061 closest distance to " CA  ALA A 295 " =    1.012
peak=    4.050 closest distance to " CD1 LEU A  96 " =    0.780
peak=    4.044 closest distance to " O   HOH Z 234 " =    3.621
peak=    4.027 closest distance to " CB  TRP A 179 " =    1.302
peak=    4.026 closest distance to " CB  ASN A 142 " =    1.120
peak=    4.021 closest distance to " O   ASP A 200 " =    1.628
peak=    4.006 closest distance to " O   HOH Z  63 " =    1.968
peak=    3.993 closest distance to " O   HOH Z 359 " =    1.687
peak=    3.992 closest distance to " O   HOH Z 394 " =    1.535
peak=    3.991 closest distance to " CB  GLU A 128 " =    1.166
peak=    3.979 closest distance to " CB  ASN A 148 " =    1.433
peak=    3.976 closest distance to " CD2 TRP A 179 " =    1.295
peak=    3.970 closest distance to " O   HOH Z 369 " =    2.038
peak=    3.968 closest distance to " OG BSER A 164 " =    2.160
peak=    3.967 closest distance to " CB  ARG A  79 " =    1.381
peak=    3.961 closest distance to " CG2 ILE A 234 " =    1.037
peak=    3.960 closest distance to " CB  GLU A 277 " =    3.801
peak=    3.959 closest distance to " CD  LYS A 166 " =    1.362
peak=    3.958 closest distance to " O   HOH Z 214 " =    1.355
peak=    3.955 closest distance to " CZ3 TRP A  85 " =    0.888
peak=    3.944 closest distance to " N   SER A 164 " =    0.964
peak=    3.917 closest distance to " CE1 TYR A 186 " =    1.252
peak=    3.910 closest distance to " O   HOH Z 433 " =    1.610
peak=    3.904 closest distance to " CG AARG A 275 " =    1.239
peak=    3.903 closest distance to " O   HOH Z  76 " =    1.124
peak=    3.901 closest distance to " CA  ARG A 195 " =    1.161
peak=    3.894 closest distance to " O   HOH Z 431 " =    1.188
peak=    3.893 closest distance to " O   HOH Z  40 " =    1.899
peak=    3.883 closest distance to " O   SER A  87 " =    2.367
peak=    3.882 closest distance to " O   HOH Z 365 " =    2.473
peak=    3.880 closest distance to " O   HOH Z 126 " =    1.603
peak=    3.859 closest distance to " CD  ARG A 159 " =    0.789
peak=    3.859 closest distance to " O   HOH Z 287 " =    1.786
peak=    3.847 closest distance to " CE  LYS A  76 " =    0.877
peak=    3.846 closest distance to " CA  ARG A  36 " =    1.008
peak=    3.845 closest distance to " O   HOH Z  48 " =    1.724
peak=    3.845 closest distance to " O   ASP A 124 " =    1.159
peak=    3.832 closest distance to " CB  TRP A 266 " =    1.064
peak=    3.822 closest distance to " CG  PRO A 213 " =    1.186
peak=    3.820 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.814 closest distance to " O   HOH Z 188 " =    3.076
peak=    3.808 closest distance to " NH2 ARG A 156 " =    1.179
peak=    3.793 closest distance to " O   HOH Z 346 " =    1.499
peak=    3.792 closest distance to " O   HOH Z  43 " =    2.073
peak=    3.790 closest distance to " O   HOH Z 214 " =    3.019
peak=    3.779 closest distance to " CB  VAL A 202 " =    1.438
peak=    3.777 closest distance to " O   HOH Z 427 " =    3.078
peak=    3.777 closest distance to " CB  ASP A 124 " =    0.754
peak=    3.775 closest distance to " O   HOH Z 154 " =    1.424
peak=    3.773 closest distance to " CB  TYR A 169 " =    0.732
peak=    3.760 closest distance to " O   ASN A  74 " =    1.549
peak=    3.751 closest distance to " O   HOH Z 420 " =    5.588
peak=    3.748 closest distance to " O   HOH Z 422 " =    2.630
peak=    3.740 closest distance to " OG  SER A 245 " =    1.534
peak=    3.739 closest distance to " O   HOH Z 280 " =    2.975
peak=    3.738 closest distance to " O   HOH Z 423 " =    1.746
peak=    3.738 closest distance to " CB  GLN A  88 " =    1.212
peak=    3.734 closest distance to " O   HOH Z 102 " =    1.365
peak=    3.721 closest distance to " CB  SER A  26 " =    1.788
peak=    3.720 closest distance to " CA  TYR A 116 " =    1.378
peak=    3.719 closest distance to " O   HOH Z 298 " =    1.915
peak=    3.717 closest distance to " O   HOH Z 316 " =    3.082
peak=    3.708 closest distance to " O   HOH Z 313 " =    1.714
peak=    3.706 closest distance to " CA  ALA A 160 " =    0.969
peak=    3.703 closest distance to " O   HOH Z 303 " =    2.287
peak=    3.684 closest distance to " CB AVAL A  41 " =    1.206
peak=    3.681 closest distance to " O   HOH Z  44 " =    2.046
peak=    3.673 closest distance to " O   HOH Z  78 " =    1.725
peak=    3.671 closest distance to " OG  SER A 276 " =    1.575
peak=    3.652 closest distance to " CD2 LEU A 297 " =    0.854
peak=    3.649 closest distance to " NH2AARG A 145 " =    1.108
peak=    3.649 closest distance to " O   HOH Z  80 " =    2.000
peak=    3.641 closest distance to " CB  SER A 273 " =    0.923
peak=    3.639 closest distance to " O   HOH Z 285 " =    2.333
peak=    3.638 closest distance to " O   HOH Z   3 " =    1.870
peak=    3.637 closest distance to " CG2 VAL A 197 " =    1.125
peak=    3.634 closest distance to " O   HOH Z 131 " =    2.305
peak=    3.632 closest distance to " O   HOH Z 437 " =    1.774
peak=    3.628 closest distance to " CG  MET A 185 " =    1.247
peak=    3.623 closest distance to " O   HOH Z 272 " =    1.880
peak=    3.619 closest distance to " O   HOH Z 126 " =    1.916
peak=    3.608 closest distance to " OD2 ASP A 298 " =    3.754
peak=    3.608 closest distance to " O   HOH Z 124 " =    1.107
peak=    3.602 closest distance to " O   HOH Z  19 " =    1.839
peak=    3.601 closest distance to " O   HOH Z 406 " =    1.493
peak=    3.599 closest distance to " CG  PHE A 204 " =    0.921
peak=    3.592 closest distance to " O   HOH Z 247 " =    1.478
peak=    3.590 closest distance to " OE1 GLU A   2 " =    1.715
peak=    3.589 closest distance to " O   THR A 220 " =    1.227
peak=    3.584 closest distance to " CG2 THR A 221 " =    1.116
peak=    3.582 closest distance to " O   HOH Z 203 " =    1.802
peak=    3.574 closest distance to " N   ASN A  39 " =    1.252
peak=    3.560 closest distance to " CB  VAL A 265 " =    1.167
peak=    3.559 closest distance to " CB  GLU A  46 " =    0.980
peak=    3.557 closest distance to " CA  SER A  12 " =    1.357
peak=    3.556 closest distance to " CG1 VAL A 153 " =    1.023
peak=    3.556 closest distance to " O   HOH Z 117 " =    1.113
peak=    3.554 closest distance to " CA  ALA A 291 " =    0.901
peak=    3.545 closest distance to " NH1AARG A 145 " =    1.258
peak=    3.545 closest distance to " CD  ARG A 138 " =    1.258
peak=    3.542 closest distance to " CA  LYS A 117 " =    1.258
peak=    3.539 closest distance to " O   HOH Z 365 " =    2.804
peak=    3.534 closest distance to " O   HOH Z 199 " =    1.546
peak=    3.532 closest distance to " CE3 TRP A  85 " =    1.078
peak=    3.528 closest distance to " OE1 GLN A  55 " =    1.358
peak=    3.524 closest distance to " O   HOH Z 391 " =    2.892
peak=    3.515 closest distance to " O   HOH Z 193 " =    1.858
peak=    3.508 closest distance to " CA  ALA A  21 " =    1.244
peak=    3.504 closest distance to " CG  LEU A 167 " =    1.101
peak=    3.503 closest distance to " CA  SER A  87 " =    1.025
peak=    3.499 closest distance to " CA  ILE A 106 " =    0.774
peak=    3.499 closest distance to " O   HOH Z 146 " =    1.641
peak=    3.499 closest distance to " NE2 GLN A  77 " =    3.270
peak=    3.499 closest distance to " OH  TYR A 116 " =    1.061
peak=    3.497 closest distance to " CA  VAL A 125 " =    1.360
peak=    3.497 closest distance to " O   HOH Z  56 " =    1.683
peak=    3.497 closest distance to " CB  GLN A  89 " =    1.169
peak=    3.489 closest distance to " O   ALA A 165 " =    1.486
peak=    3.487 closest distance to " CB  THR A  52 " =    0.822
peak=    3.467 closest distance to " CB  SER A  62 " =    0.863
peak=    3.465 closest distance to " CD  ARG A 269 " =    1.025
peak=    3.452 closest distance to " O   HOH Z 327 " =    2.348
peak=    3.446 closest distance to " CB  ASN A 215 " =    1.279
peak=    3.446 closest distance to " CB  SER A 288 " =    1.528
peak=    3.443 closest distance to " CB  GLU A 152 " =    1.057
peak=    3.439 closest distance to " CD1 LEU A 300 " =    1.100
peak=    3.438 closest distance to " CD  LYS A 119 " =    1.964
peak=    3.437 closest distance to " O   HOH Z 407 " =    2.587
peak=    3.436 closest distance to " O   HOH Z 174 " =    2.322
peak=    3.432 closest distance to " O   PRO A 213 " =    1.342
peak=    3.428 closest distance to " CA  VAL A  41 " =    0.765
peak=    3.426 closest distance to " O   HOH Z 238 " =    0.939
peak=    3.422 closest distance to " CZ  PHE A  38 " =    1.153
peak=    3.420 closest distance to " CB  MET A  47 " =    1.005
peak=    3.403 closest distance to " O   HOH Z 258 " =    2.066
peak=    3.402 closest distance to " OG  SER A 135 " =    1.303
peak=    3.400 closest distance to " CD1 ILE A  33 " =    1.743
peak=    3.399 closest distance to " CA  ASP A 162 " =    1.051
peak=    3.397 closest distance to " O   HOH Z 393 " =    3.299
peak=    3.396 closest distance to " CG  GLN A  11 " =    1.390
peak=    3.393 closest distance to " O   HOH Z 344 " =    2.971
peak=    3.393 closest distance to " CB  MET A  40 " =    0.827
peak=    3.391 closest distance to " CE1 HIS A 108 " =    1.180
peak=    3.381 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.378 closest distance to " CA  GLU A 152 " =    0.901
peak=    3.376 closest distance to " O   HOH Z 158 " =    3.197
peak=    3.375 closest distance to " O   THR A 251 " =    1.129
peak=    3.372 closest distance to " O   HOH Z 189 " =    2.994
peak=    3.368 closest distance to " CB  PRO A 243 " =    1.479
peak=    3.365 closest distance to " CG1 ILE A  49 " =    1.679
peak=    3.360 closest distance to " O   HOH Z 368 " =    3.397
peak=    3.355 closest distance to " CA  ASN A 217 " =    1.227
peak=    3.354 closest distance to " CA  ALA A 154 " =    1.010
peak=    3.352 closest distance to " CB  ALA A  43 " =    0.913
peak=    3.352 closest distance to " O   HOH Z  47 " =    2.689
peak=    3.347 closest distance to " O   HOH Z 337 " =    1.779
peak=    3.346 closest distance to " O   HOH Z  83 " =    1.497
peak=    3.343 closest distance to " CG  GLN A  58 " =    0.965
peak=    3.343 closest distance to " CB  TRP A 150 " =    1.407
peak=    3.340 closest distance to " O   HOH Z 285 " =    2.143
peak=    3.339 closest distance to " CA  GLY A 267 " =    0.988
peak=    3.338 closest distance to " CA  ASP A 191 " =    1.173
peak=    3.337 closest distance to " O   THR A 182 " =    1.490
peak=    3.336 closest distance to " CG1 ILE A  33 " =    1.222
peak=    3.332 closest distance to " O   HOH Z 134 " =    1.305
peak=    3.331 closest distance to " CZ3 TRP A 274 " =    4.415
peak=    3.330 closest distance to " CB  ALA A   9 " =    1.678
peak=    3.328 closest distance to " CB  ALA A 248 " =    1.263
peak=    3.322 closest distance to " OD1 ASN A  69 " =    2.558
peak=    3.319 closest distance to " O   HOH Z 185 " =    1.701
peak=    3.316 closest distance to " CB  ASP A 140 " =    0.991
peak=    3.314 closest distance to " CG2AVAL A 121 " =    2.094
peak=    3.314 closest distance to " CB  SER A   3 " =    1.307
peak=    3.310 closest distance to " O   HOH Z 290 " =    1.082
peak=    3.308 closest distance to " O   HOH Z 357 " =    2.595
peak=    3.306 closest distance to " O   PRO A  90 " =    1.468
peak=    3.305 closest distance to " CG2 ILE A  20 " =    1.355
peak=    3.304 closest distance to " CA  ARG A 139 " =    1.237
peak=    3.303 closest distance to " O   HOH Z 438 " =    2.711
peak=    3.298 closest distance to " CD1 LEU A   5 " =    1.375
peak=    3.298 closest distance to " O   HOH Z 213 " =    1.640
peak=    3.297 closest distance to " CB  ASN A 173 " =    1.059
peak=    3.296 closest distance to " N   VAL A 126 " =    1.493
peak=    3.295 closest distance to " CZ  PHE A 192 " =    1.127
peak=    3.295 closest distance to " ND2 ASN A 187 " =    1.671
peak=    3.294 closest distance to " CB  ASP A 107 " =    1.222
peak=    3.291 closest distance to " CA  ALA A 100 " =    0.837
peak=    3.284 closest distance to " O   HOH Z 357 " =    2.203
peak=    3.282 closest distance to " O   GLY A  91 " =    1.192
peak=    3.281 closest distance to " CE  LYS A 119 " =    1.051
peak=    3.280 closest distance to " O   HOH Z 132 " =    2.851
peak=    3.279 closest distance to " O   HOH Z 133 " =    2.586
peak=    3.272 closest distance to " O   GLU A   2 " =    1.552
peak=    3.266 closest distance to " O   HOH Z 301 " =    1.846
peak=    3.264 closest distance to " CD  PRO A  54 " =    1.061
peak=    3.264 closest distance to " O   HOH Z 435 " =    2.069
peak=    3.262 closest distance to " O   HOH Z 417 " =    3.038
peak=    3.262 closest distance to " CE1 HIS A 115 " =    1.125
peak=    3.259 closest distance to " CD1 ILE A 199 " =    0.957
peak=    3.258 closest distance to " OE1 GLN A  88 " =    0.880
peak=    3.254 closest distance to " O   ASP A 124 " =    1.786
peak=    3.252 closest distance to " ND2 ASN A 249 " =    1.886
peak=    3.250 closest distance to " CG  MET A 188 " =    0.920
peak=    3.248 closest distance to " O   HOH Z 120 " =    2.683
peak=    3.247 closest distance to " CD  ARG A 195 " =    1.031
peak=    3.245 closest distance to " O   HOH Z 336 " =    1.796
peak=    3.242 closest distance to " OD1 ASN A 217 " =    1.659
peak=    3.241 closest distance to " N   THR A  52 " =    1.105
peak=    3.240 closest distance to " CB  ASN A 187 " =    1.285
peak=    3.239 closest distance to " CG  GLU A  37 " =    0.960
peak=    3.237 closest distance to " CB  GLU A  37 " =    0.756
peak=    3.237 closest distance to " CZ3 TRP A  92 " =    1.399
peak=    3.235 closest distance to " O   TYR A 116 " =    1.283
peak=    3.233 closest distance to " CA  MET A 105 " =    1.043
peak=    3.233 closest distance to " CA  GLY A 211 " =    1.412
peak=    3.233 closest distance to " O  BHOH Z 338 " =    2.250
peak=    3.232 closest distance to " CG1 ILE A 120 " =    0.996
peak=    3.229 closest distance to " CD BLYS A 290 " =    0.969
peak=    3.225 closest distance to " O   ASP A 191 " =    1.531
peak=    3.222 closest distance to " CB  LYS A 117 " =    1.193
peak=    3.215 closest distance to " O   HOH Z 393 " =    3.690
peak=    3.214 closest distance to " OD1 ASN A 301 " =    1.228
peak=    3.210 closest distance to " CA  ASP A 140 " =    1.458
peak=    3.209 closest distance to " CD2 TYR A 186 " =    1.050
peak=    3.208 closest distance to " CA  ARG A 156 " =    1.139
peak=    3.206 closest distance to " O   HOH Z 404 " =    2.357
peak=    3.204 closest distance to " N   ALA A 256 " =    1.039
peak=    3.204 closest distance to " O   HOH Z 353 " =    2.669
peak=    3.203 closest distance to " CA  ASN A 127 " =    1.199
peak=    3.201 closest distance to " O   HOH Z   1 " =    2.250
peak=    3.200 closest distance to " O   HOH Z 151 " =    1.616
peak=    3.198 closest distance to " CE3 TRP A 150 " =    1.119
peak=    3.198 closest distance to " CB  GLN A 103 " =    1.031
peak=    3.196 closest distance to " O   HOH Z 371 " =    2.689
peak=    3.195 closest distance to " O   HOH Z 207 " =    1.080
peak=    3.191 closest distance to " O   HOH Z 294 " =    1.559
peak=    3.191 closest distance to " CA  GLN A  88 " =    1.524
peak=    3.191 closest distance to " NH1 ARG A  14 " =    1.176
peak=    3.183 closest distance to " CB  ASN A 285 " =    0.905
peak=    3.182 closest distance to " O   HOH Z 116 " =    1.818
peak=    3.181 closest distance to " CD  GLN A  73 " =    1.166
peak=    3.177 closest distance to " O   HOH Z 408 " =    3.246
peak=    3.167 closest distance to " N   GLU A  44 " =    1.107
peak=    3.164 closest distance to " OG BSER A 134 " =    2.812
peak=    3.162 closest distance to " O   THR A 294 " =    1.681
peak=    3.161 closest distance to " N   PHE A 130 " =    1.215
peak=    3.157 closest distance to " O   HOH Z 299 " =    4.410
peak=    3.157 closest distance to " OG  SER A  62 " =    2.813
peak=    3.152 closest distance to " CB  THR A 235 " =    1.193
peak=    3.149 closest distance to " CA  GLN A  94 " =    0.754
peak=    3.142 closest distance to " O   HOH Z 343 " =    2.781
peak=    3.140 closest distance to " O   HOH Z 421 " =    2.511
peak=    3.126 closest distance to " CB  PHE A 283 " =    0.826
peak=    3.121 closest distance to " CB  TYR A 247 " =    1.014
peak=    3.114 closest distance to " O   HOH Z 147 " =    1.714
peak=    3.113 closest distance to " CB  ASN A 110 " =    1.195
peak=    3.102 closest distance to " CA  LEU A 282 " =    1.085
peak=    3.098 closest distance to " O   HOH Z 293 " =    2.080
peak=    3.095 closest distance to " O   HOH Z 180 " =    2.189
peak=    3.094 closest distance to " O   HOH Z 156 " =    2.559
peak=    3.094 closest distance to " CB  SER A 216 " =    0.925
peak=    3.093 closest distance to " O   PHE A 192 " =    1.394
peak=    3.087 closest distance to " CB  ALA A 100 " =    1.352
peak=    3.086 closest distance to " O   MET A 105 " =    1.817
peak=    3.081 closest distance to " CE1 TYR A  30 " =    0.959
peak=    3.074 closest distance to " CB  ALA A 242 " =    0.896
peak=    3.064 closest distance to " O   TRP A 274 " =    1.789
peak=    3.060 closest distance to " O   HOH Z  21 " =    1.777
peak=    3.059 closest distance to " CB  ALA A 227 " =    1.092
peak=    3.051 closest distance to " CB  THR A  31 " =    1.431
peak=    3.047 closest distance to " NE2 GLN A  58 " =    4.593
peak=    3.046 closest distance to " CB  GLN A  58 " =    1.035
peak=    3.046 closest distance to " CB  ALA A 295 " =    1.548
peak=    3.044 closest distance to " CB  ARG A 219 " =    1.453
peak=    3.035 closest distance to " O   HOH Z 433 " =    4.332
peak=    3.024 closest distance to " O   HOH Z 109 " =    2.582
peak=    3.010 closest distance to " O   HOH Z 154 " =    1.822

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.864 - 5.628
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.864 - 5.628

peak=   -4.825 closest distance to " CG1 VAL A 296 " =    1.040
peak=   -4.667 closest distance to " CG2 VAL A 230 " =    0.864
peak=   -4.544 closest distance to " CD  GLN A  58 " =    1.039
peak=   -4.397 closest distance to " CA  ASP A 298 " =    1.068
peak=   -4.348 closest distance to " CD  ARG A  14 " =    3.339
peak=   -4.330 closest distance to " O   HOH Z 166 " =    1.425
peak=   -4.297 closest distance to " CG2BVAL A  41 " =    2.850
peak=   -4.289 closest distance to " CD2 LEU A 237 " =    2.668
peak=   -4.236 closest distance to " O   PRO A 198 " =    1.297
peak=   -4.230 closest distance to " CE3 TRP A 150 " =    2.362
peak=   -4.196 closest distance to " O   SER A 271 " =    2.119
peak=   -4.136 closest distance to " CB  ALA A 291 " =    2.513
peak=   -4.133 closest distance to " O   HOH Z 411 " =    5.496
peak=   -4.041 closest distance to " CE2 TYR A  30 " =    2.700
peak=   -3.996 closest distance to " CG2 ILE A  49 " =    2.864
peak=   -3.986 closest distance to " CG  ARG A 269 " =    2.334
peak=   -3.983 closest distance to " O   HOH Z  37 " =    1.905
peak=   -3.977 closest distance to " O   HOH Z 438 " =    2.989
peak=   -3.967 closest distance to " O   HOH Z 107 " =    0.865
peak=   -3.953 closest distance to " CB  PRO A 243 " =    2.795
peak=   -3.934 closest distance to " CD1 PHE A  59 " =    1.996
peak=   -3.930 closest distance to " O   HOH Z 193 " =    1.132
peak=   -3.912 closest distance to " ND2BASN A 224 " =    1.929
peak=   -3.903 closest distance to " CD2 TYR A 293 " =    2.034
peak=   -3.857 closest distance to " O   PRO A 163 " =    2.251
peak=   -3.832 closest distance to " C   HIS A 108 " =    1.125
peak=   -3.827 closest distance to " OG BSER A 134 " =    1.391
peak=   -3.820 closest distance to " O   HOH Z 351 " =    1.540
peak=   -3.816 closest distance to " CG  GLN A 103 " =    2.538
peak=   -3.805 closest distance to " NE  ARG A 138 " =    1.379
peak=   -3.790 closest distance to " CD  ARG A 156 " =    2.090
peak=   -3.782 closest distance to " O   HOH Z 231 " =    2.234
peak=   -3.781 closest distance to " O   HOH Z  10 " =    1.647
peak=   -3.779 closest distance to " O   GLY A  17 " =    1.195
peak=   -3.755 closest distance to " CG1 VAL A 112 " =    2.660
peak=   -3.750 closest distance to " CB  VAL A 230 " =    1.126
peak=   -3.741 closest distance to " CE2 PHE A  61 " =    2.637
peak=   -3.736 closest distance to " CE3 TRP A  70 " =    1.848
peak=   -3.729 closest distance to " O   HOH Z  19 " =    2.269
peak=   -3.729 closest distance to " O   HOH Z 340 " =    1.580
peak=   -3.728 closest distance to " CG  PRO A 243 " =    1.646
peak=   -3.720 closest distance to " CB  PHE A 192 " =    2.088
peak=   -3.709 closest distance to " CG2 VAL A 189 " =    2.080
peak=   -3.701 closest distance to " O   HOH Z 283 " =    2.458
peak=   -3.682 closest distance to " O   HOH Z 431 " =    2.316
peak=   -3.681 closest distance to " CB  ALA A  10 " =    2.216
peak=   -3.674 closest distance to " CD1 LEU A 101 " =    2.387
peak=   -3.668 closest distance to " OE1 GLN A 223 " =    2.245
peak=   -3.665 closest distance to " O   HOH Z 211 " =    1.254
peak=   -3.653 closest distance to " O   HOH Z  13 " =    1.766
peak=   -3.644 closest distance to " CG  GLU A  53 " =    1.507
peak=   -3.640 closest distance to " O   HOH Z  68 " =    1.704
peak=   -3.626 closest distance to " O   HOH Z  52 " =    1.919
peak=   -3.622 closest distance to " CG  GLU A 277 " =    1.318
peak=   -3.616 closest distance to " O   HOH Z 216 " =    1.067
peak=   -3.614 closest distance to " O   HOH Z 177 " =    1.956
peak=   -3.608 closest distance to " CE2 TRP A  70 " =    2.213
peak=   -3.608 closest distance to " CA  GLY A 241 " =    2.293
peak=   -3.604 closest distance to " OD1 ASN A 148 " =    1.361
peak=   -3.600 closest distance to " NE2 GLN A 194 " =    2.015
peak=   -3.599 closest distance to " CB  ALA A 161 " =    2.647
peak=   -3.588 closest distance to " CG  GLN A  11 " =    1.572
peak=   -3.587 closest distance to " O   HOH Z 119 " =    2.129
peak=   -3.582 closest distance to " O   HOH Z 394 " =    1.688
peak=   -3.575 closest distance to " O   HOH Z  11 " =    1.838
peak=   -3.557 closest distance to " O   HOH Z 131 " =    4.089
peak=   -3.555 closest distance to " O   VAL A  67 " =    2.816
peak=   -3.554 closest distance to " SG  CYS A 260 " =    2.223
peak=   -3.548 closest distance to " O   HOH Z 133 " =    1.024
peak=   -3.546 closest distance to " ND2 ASN A  45 " =    1.160
peak=   -3.529 closest distance to " O   HOH Z 128 " =    2.581
peak=   -3.525 closest distance to " N   ALA A  43 " =    2.661
peak=   -3.524 closest distance to " N   ALA A 226 " =    2.017
peak=   -3.522 closest distance to " CG  ARG A 138 " =    1.027
peak=   -3.521 closest distance to " O   HOH Z 388 " =    2.110
peak=   -3.520 closest distance to " NE  ARG A  66 " =    4.412
peak=   -3.520 closest distance to " OG  SER A  97 " =    2.316
peak=   -3.513 closest distance to " C   LEU A 143 " =    1.094
peak=   -3.512 closest distance to " CD  PRO A 243 " =    2.009
peak=   -3.511 closest distance to " O   HOH Z 251 " =    4.815
peak=   -3.509 closest distance to " CZ  TYR A 169 " =    1.799
peak=   -3.507 closest distance to " O   HOH Z 165 " =    1.978
peak=   -3.503 closest distance to " O   HOH Z 285 " =    1.912
peak=   -3.501 closest distance to " O   HOH Z 102 " =    1.733
peak=   -3.496 closest distance to " O   HOH Z 200 " =    1.512
peak=   -3.490 closest distance to " O   HOH Z 304 " =    1.451
peak=   -3.478 closest distance to " O   HOH Z 231 " =    2.042
peak=   -3.477 closest distance to " O   HOH Z 377 " =    2.119
peak=   -3.477 closest distance to " O   HOH Z   9 " =    2.096
peak=   -3.475 closest distance to " O   ARG A  24 " =    2.078
peak=   -3.456 closest distance to " O   HOH Z 407 " =    2.889
peak=   -3.451 closest distance to " O   HOH Z 111 " =    1.568
peak=   -3.424 closest distance to " O   HOH Z 166 " =    1.642
peak=   -3.422 closest distance to " CB  ARG A  79 " =    2.728
peak=   -3.413 closest distance to " O   HOH Z 252 " =    3.666
peak=   -3.412 closest distance to " O   SER A 210 " =    1.767
peak=   -3.412 closest distance to " O   HOH Z 149 " =    2.091
peak=   -3.410 closest distance to " OG1 THR A  82 " =    1.485
peak=   -3.408 closest distance to " O   GLY A  75 " =    2.112
peak=   -3.392 closest distance to " O   TYR A 186 " =    1.710
peak=   -3.391 closest distance to " O   SER A 206 " =    1.427
peak=   -3.390 closest distance to " CG  ASP A 231 " =    0.916
peak=   -3.390 closest distance to " O   HOH Z   6 " =    1.723
peak=   -3.376 closest distance to " O   HOH Z 154 " =    1.381
peak=   -3.373 closest distance to " CG2 THR A 178 " =    2.416
peak=   -3.363 closest distance to " CB  ALA A 248 " =    2.252
peak=   -3.355 closest distance to " O   HOH Z 174 " =    2.041
peak=   -3.353 closest distance to " O   HOH Z 189 " =    2.173
peak=   -3.353 closest distance to " O   HOH Z 198 " =    1.887
peak=   -3.345 closest distance to " CG  GLN A  58 " =    1.276
peak=   -3.340 closest distance to " CG  TRP A 266 " =    1.825
peak=   -3.340 closest distance to " NH2 ARG A  66 " =    1.898
peak=   -3.339 closest distance to " CA  VAL A 197 " =    1.017
peak=   -3.333 closest distance to " O   PHE A 218 " =    1.525
peak=   -3.333 closest distance to " CZ3 TRP A 179 " =    1.230
peak=   -3.331 closest distance to " O   ALA A  34 " =    2.586
peak=   -3.329 closest distance to " C   ASP A 270 " =    1.130
peak=   -3.329 closest distance to " CA  ALA A   8 " =    1.494
peak=   -3.328 closest distance to " CD  GLN A  88 " =    0.959
peak=   -3.327 closest distance to " CG  MET A 105 " =    0.975
peak=   -3.319 closest distance to " NH2 ARG A 159 " =    2.393
peak=   -3.316 closest distance to " CG1 VAL A 112 " =    2.682
peak=   -3.314 closest distance to " CA  GLY A 203 " =    2.459
peak=   -3.309 closest distance to " OE1 GLN A  88 " =    0.927
peak=   -3.307 closest distance to " CG  LEU A   5 " =    1.645
peak=   -3.305 closest distance to " C   ALA A 158 " =    1.419
peak=   -3.301 closest distance to " O   HOH Z 359 " =    2.857
peak=   -3.293 closest distance to " O   HOH Z 185 " =    2.367
peak=   -3.289 closest distance to " OG1 THR A  82 " =    1.369
peak=   -3.289 closest distance to " CG  GLN A  55 " =    1.048
peak=   -3.282 closest distance to " O   HOH Z 423 " =    2.321
peak=   -3.280 closest distance to " C   ASN A 285 " =    2.385
peak=   -3.275 closest distance to " O   HOH Z 275 " =    1.846
peak=   -3.274 closest distance to " O   HOH Z 106 " =    1.827
peak=   -3.271 closest distance to " O   HOH Z 348 " =    2.313
peak=   -3.265 closest distance to " O   HOH Z 128 " =    1.190
peak=   -3.259 closest distance to " O   HOH Z 136 " =    2.587
peak=   -3.254 closest distance to " O   HOH Z 136 " =    1.436
peak=   -3.252 closest distance to " CA  ASN A 127 " =    1.058
peak=   -3.251 closest distance to " CD  GLN A 223 " =    1.368
peak=   -3.247 closest distance to " CD1 ILE A 263 " =    2.125
peak=   -3.246 closest distance to " O   HOH Z 329 " =    1.461
peak=   -3.245 closest distance to " OD2 ASP A 270 " =    1.087
peak=   -3.243 closest distance to " CG1BVAL A  72 " =    2.574
peak=   -3.242 closest distance to " CB  ASN A  45 " =    2.148
peak=   -3.240 closest distance to " N   ILE A 120 " =    1.000
peak=   -3.236 closest distance to " O   HOH Z 340 " =    2.027
peak=   -3.236 closest distance to " CG  ASP A  50 " =    2.337
peak=   -3.236 closest distance to " CB  ALA A 248 " =    2.139
peak=   -3.235 closest distance to " O   HOH Z 196 " =    1.951
peak=   -3.230 closest distance to " ND2 ASN A  45 " =    2.230
peak=   -3.226 closest distance to " O   HOH Z 275 " =    1.553
peak=   -3.225 closest distance to " O   HOH Z 301 " =    2.462
peak=   -3.225 closest distance to " N   SER A 276 " =    1.459
peak=   -3.220 closest distance to " CE1 HIS A  86 " =    1.101
peak=   -3.214 closest distance to " CB  ALA A  43 " =    2.636
peak=   -3.209 closest distance to " CG2 VAL A 202 " =    2.709
peak=   -3.204 closest distance to " O   HOH Z  60 " =    2.023
peak=   -3.203 closest distance to " O   HOH Z 411 " =    1.726
peak=   -3.197 closest distance to " NH2 ARG A  79 " =    1.511
peak=   -3.196 closest distance to " CD  ARG A 139 " =    1.672
peak=   -3.186 closest distance to " CG1 VAL A  78 " =    2.511
peak=   -3.184 closest distance to " N   GLN A  77 " =    1.559
peak=   -3.181 closest distance to " O   HOH Z 148 " =    3.824
peak=   -3.177 closest distance to " O   HOH Z 191 " =    5.628
peak=   -3.173 closest distance to " CA  VAL A 296 " =    0.999
peak=   -3.169 closest distance to " O   SER A 276 " =    1.652
peak=   -3.165 closest distance to " NE2 GLN A 103 " =    1.766
peak=   -3.164 closest distance to " CG2 ILE A 263 " =    2.405
peak=   -3.163 closest distance to " CB  HIS A  86 " =    1.174
peak=   -3.154 closest distance to " O   GLU A  44 " =    1.853
peak=   -3.148 closest distance to " O   HOH Z 256 " =    1.422
peak=   -3.147 closest distance to " CD2 PHE A 225 " =    1.152
peak=   -3.147 closest distance to " O   VAL A 189 " =    2.593
peak=   -3.144 closest distance to " CA  TYR A  68 " =    3.037
peak=   -3.143 closest distance to " OXT GLY A 302 " =    3.323
peak=   -3.141 closest distance to " O   ARG A  56 " =    3.627
peak=   -3.140 closest distance to " SD  MET A  40 " =    1.935
peak=   -3.136 closest distance to " C   THR A 279 " =    1.205
peak=   -3.135 closest distance to " CG  LEU A   5 " =    1.001
peak=   -3.135 closest distance to " CD1 LEU A   5 " =    2.566
peak=   -3.131 closest distance to " CD2 LEU A 300 " =    2.615
peak=   -3.128 closest distance to " O   ASN A  45 " =    1.959
peak=   -3.123 closest distance to " CD2 HIS A 207 " =    2.425
peak=   -3.120 closest distance to " CA  GLY A 241 " =    3.198
peak=   -3.119 closest distance to " CH2 TRP A 150 " =    1.069
peak=   -3.116 closest distance to " O   HOH Z 171 " =    2.298
peak=   -3.111 closest distance to " CD1 ILE A 109 " =    2.892
peak=   -3.110 closest distance to " O   HOH Z 227 " =    1.323
peak=   -3.106 closest distance to " O   HOH Z 292 " =    1.810
peak=   -3.102 closest distance to " N   ASN A  60 " =    1.172
peak=   -3.101 closest distance to " CG  ASP A 132 " =    2.275
peak=   -3.093 closest distance to " O   HOH Z 137 " =    1.859
peak=   -3.092 closest distance to " O   HOH Z  64 " =    1.701
peak=   -3.088 closest distance to " O   HOH Z 392 " =    1.766
peak=   -3.088 closest distance to " O   HOH Z 395 " =    1.477
peak=   -3.087 closest distance to " O   GLN A 240 " =    2.503
peak=   -3.085 closest distance to " CA  GLY A 133 " =    2.335
peak=   -3.079 closest distance to " CB  TRP A  85 " =    2.528
peak=   -3.073 closest distance to " NH2AARG A 275 " =    5.133
peak=   -3.071 closest distance to " O   HOH Z 378 " =    1.684
peak=   -3.065 closest distance to " O   HOH Z  38 " =    1.357
peak=   -3.062 closest distance to " CB  ALA A 129 " =    2.482
peak=   -3.057 closest distance to " O   HOH Z  78 " =    1.865
peak=   -3.056 closest distance to " ND2 ASN A 249 " =    2.444
peak=   -3.027 closest distance to " O   HOH Z 145 " =    2.645
peak=   -3.007 closest distance to " CA  SER A  62 " =    2.575

================= 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    :  0.4873 0.4762   6.286477e+00   6.270471e+00
   1_bss:  0.4796 0.4657   6.278624e+00   6.263890e+00
   1_xyz:  0.3969 0.4173   6.172435e+00   6.195785e+00
   1_adp:  0.3523 0.4028   6.094258e+00   6.169519e+00
   1_occ:  0.3516 0.4034   6.093932e+00   6.170403e+00
   2_bss:  0.3487 0.3975   6.094839e+00   6.168779e+00
   2_xyz:  0.2750 0.3298   5.899826e+00   6.035520e+00
   2_adp:  0.2575 0.3067   5.848326e+00   5.986599e+00
   2_occ:  0.2571 0.3072   5.848040e+00   5.987527e+00
   3_bss:  0.2559 0.3069   5.849240e+00   5.987585e+00
   3_xyz:  0.1971 0.2389   5.614059e+00   5.780565e+00
   3_adp:  0.1825 0.2278   5.557384e+00   5.738489e+00
   3_occ:  0.1824 0.2279   5.557144e+00   5.738531e+00
   4_bss:  0.1823 0.2275   5.556665e+00   5.737031e+00
   4_xyz:  0.1452 0.1905   5.361207e+00   5.570208e+00
   4_adp:  0.1399 0.1830   5.327221e+00   5.535613e+00
   4_occ:  0.1397 0.1830   5.326904e+00   5.535927e+00
   5_bss:  0.1399 0.1835   5.328368e+00   5.536575e+00
   5_xyz:  0.1282 0.1706   5.254432e+00   5.469411e+00
   5_adp:  0.1247 0.1716   5.242597e+00   5.470005e+00
   5_occ:  0.1247 0.1716   5.242523e+00   5.470073e+00
   5_bss:  0.1246 0.1714   5.242591e+00   5.470184e+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:  0.309   9.451   6.383  10.083  11.056   0.000   0.000   0.000
   1_xyz:  0.309   9.451   6.383  10.083  11.056   0.000   0.000   0.000
   1_adp:  0.309   9.451   6.383  10.083  11.056   0.000   0.000   0.000
   1_occ:  0.309   9.451   6.383  10.083  11.056   0.000   0.000   0.000
   2_bss:  0.323  50.000   3.038   6.210   7.010   0.000   0.000   0.000
   2_xyz:  0.323  50.000   3.038   6.210   7.010   0.000   0.000   0.000
   2_adp:  0.323  50.000   3.038   6.210   7.010   0.000   0.000   0.000
   2_occ:  0.323  50.000   3.038   6.210   7.010   0.000   0.000   0.000
   3_bss:  0.307  50.001   1.750   3.800   4.539   0.000   0.000   0.000
   3_xyz:  0.307  50.001   1.750   3.800   4.539   0.000   0.000   0.000
   3_adp:  0.307  50.001   1.750   3.800   4.539   0.000   0.000   0.000
   3_occ:  0.307  50.001   1.750   3.800   4.539   0.000   0.000   0.000
   4_bss:  0.333  71.048   1.338   2.767   3.742   0.000   0.000   0.000
   4_xyz:  0.333  71.048   1.338   2.767   3.742   0.000   0.000   0.000
   4_adp:  0.333  71.048   1.338   2.767   3.742   0.000   0.000   0.000
   4_occ:  0.333  71.048   1.338   2.767   3.742   0.000   0.000   0.000
   5_bss:  0.336  71.048   1.280   2.300   3.468   0.000   0.000   0.000
   5_xyz:  0.336  71.048   1.280   2.300   3.468   0.000   0.000   0.000
   5_adp:  0.336  71.048   1.280   2.300   3.468   0.000   0.000   0.000
   5_occ:  0.336  71.048   1.280   2.300   3.468   0.000   0.000   0.000
   5_bss:  0.336  73.609  -0.942  -0.130   1.072   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.681 0.4367  0.4967    67999.877
   1_bss:  56.046 0.4440  0.6622    66957.225
   1_xyz:  47.410 0.5515  0.7996    49341.621
   1_adp:  44.449 0.5886  0.8997    45480.440
   1_occ:  44.558 0.5872  0.8969    45643.535
   2_bss:  44.238 0.5912  0.7965    45302.607
   2_xyz:  35.348 0.6969  0.9253    29915.656
   2_adp:  32.266 0.7329  0.9538    26044.913
   2_occ:  32.297 0.7326  0.9533    26087.875
   3_bss:  32.180 0.7340  0.8886    26042.684
   3_xyz:  24.045 0.8213  0.9627    15146.071
   3_adp:  22.456 0.8379  0.9678    13671.875
   3_occ:  22.455 0.8379  0.9678    13664.883
   4_bss:  22.390 0.8386  0.9436    13606.198
   4_xyz:  18.235 0.8782  0.9663     9391.925
   4_adp:  17.301 0.8871  0.9629     8802.866
   4_occ:  17.317 0.8870  0.9626     8804.307
   5_bss:  17.329 0.8869  0.9539     8836.351
   5_xyz:  15.708 0.9012  0.9608     7577.647
   5_adp:  15.714 0.9013  0.9515     7587.193
   5_occ:  15.712 0.9013  0.9514     7585.948
   5_bss:  15.714 0.9013  0.9587     7589.264
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4431e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4431e+01
   1_xyz:   1.727  0.014  0.109 18.133  0.007  4.112   1.4588e-01
   1_adp:   1.727  0.014  0.109 18.133  0.007  4.112   1.4588e-01
   1_occ:   1.727  0.014  0.109 18.133  0.007  4.112   1.4588e-01
   2_bss:   1.727  0.014  0.109 18.133  0.007  4.112   1.4588e-01
   2_xyz:   1.202  0.009  0.076 15.999  0.005  4.128   8.1325e-02
   2_adp:   1.202  0.009  0.076 15.999  0.005  4.128   8.1325e-02
   2_occ:   1.202  0.009  0.076 15.999  0.005  4.128   8.1325e-02
   3_bss:   1.202  0.009  0.076 15.999  0.005  4.128   8.1325e-02
   3_xyz:   1.040  0.007  0.074 15.585  0.004  4.129   6.3489e-02
   3_adp:   1.040  0.007  0.074 15.585  0.004  4.129   6.3489e-02
   3_occ:   1.040  0.007  0.074 15.585  0.004  4.129   6.3489e-02
   4_bss:   1.040  0.007  0.074 15.585  0.004  4.129   6.3489e-02
   4_xyz:   1.050  0.008  0.078 15.555  0.004  4.143   6.6419e-02
   4_adp:   1.050  0.008  0.078 15.555  0.004  4.143   6.6419e-02
   4_occ:   1.050  0.008  0.078 15.555  0.004  4.143   6.6419e-02
   5_bss:   1.050  0.008  0.078 15.555  0.004  4.143   6.6419e-02
   5_xyz:   1.067  0.008  0.082 15.383  0.003  4.116   6.7283e-02
   5_adp:   1.067  0.008  0.082 15.383  0.003  4.116   6.7283e-02
   5_occ:   1.067  0.008  0.082 15.383  0.003  4.116   6.7283e-02
   5_bss:   1.067  0.008  0.082 15.383  0.003  4.116   6.7283e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0568e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0568e+00
   1_xyz:  15.006  0.173  0.467 86.948  0.041  2.248   1.0880e-01
   1_adp:  15.006  0.173  0.467 86.948  0.041  2.248   1.0880e-01
   1_occ:  15.006  0.173  0.467 86.948  0.041  2.248   1.0880e-01
   2_bss:  15.006  0.173  0.467 86.948  0.041  2.248   1.0880e-01
   2_xyz:   9.113  0.070  0.282 84.253  0.027  2.119   7.7887e-02
   2_adp:   9.113  0.070  0.282 84.253  0.027  2.119   7.7887e-02
   2_occ:   9.113  0.070  0.282 84.253  0.027  2.119   7.7887e-02
   3_bss:   9.113  0.070  0.282 84.253  0.027  2.119   7.7887e-02
   3_xyz:   6.874  0.054  0.234 85.715  0.047  2.238   5.4189e-02
   3_adp:   6.874  0.054  0.234 85.715  0.047  2.238   5.4189e-02
   3_occ:   6.874  0.054  0.234 85.715  0.047  2.238   5.4189e-02
   4_bss:   6.874  0.054  0.234 85.715  0.047  2.238   5.4189e-02
   4_xyz:   8.427  0.051  0.338 82.044  0.036  2.249   4.5684e-02
   4_adp:   8.427  0.051  0.338 82.044  0.036  2.249   4.5684e-02
   4_occ:   8.427  0.051  0.338 82.044  0.036  2.249   4.5684e-02
   5_bss:   8.427  0.051  0.338 82.044  0.036  2.249   4.5684e-02
   5_xyz:   7.768  0.054  0.412 82.640  0.033  2.335   3.9416e-02
   5_adp:   7.768  0.054  0.412 82.640  0.033  2.335   3.9416e-02
   5_occ:   7.768  0.054  0.412 82.640  0.033  2.335   3.9416e-02
   5_bss:   7.768  0.054  0.412 82.640  0.033  2.335   3.9416e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  99.38   0.00  14.05  72.57   0.00  11.62  99.38   0.00  27.31
   1_occ:  99.38   0.00  14.05  72.57   0.00  11.62  99.38   0.00  27.31
   2_bss:  99.38   0.00  14.05  72.57   0.00  11.62  99.38   0.00  27.31
   2_xyz:  99.38   0.00  14.05  72.57   0.00  11.62  99.38   0.00  27.31
   2_adp: 102.34   0.00  13.30  67.79   0.00   9.94 102.34   0.00  31.55
   2_occ: 102.34   0.00  13.30  67.79   0.00   9.94 102.34   0.00  31.55
   3_bss: 102.34   0.00  13.30  67.79   0.00   9.94 102.34   0.00  31.55
   3_xyz: 102.34   0.00  13.30  67.79   0.00   9.94 102.34   0.00  31.55
   3_adp: 100.75   0.00  13.71  73.10   0.00   9.51 100.75   1.49  36.55
   3_occ: 100.75   0.00  13.71  73.10   0.00   9.51 100.75   1.49  36.55
   4_bss: 100.75   0.00  13.71  73.10   0.00   9.51 100.75   1.49  36.55
   4_xyz: 100.75   0.00  13.71  73.10   0.00   9.51 100.75   1.49  36.55
   4_adp:  96.89   0.00  13.39  75.34   0.00   9.05  96.89   1.64  36.99
   4_occ:  96.89   0.00  13.39  75.34   0.00   9.05  96.89   1.64  36.99
   5_bss:  96.89   0.00  13.39  75.34   0.00   9.05  96.89   1.64  36.99
   5_xyz:  96.89   0.00  13.39  75.34   0.00   9.05  96.89   1.64  36.99
   5_adp: 101.79   0.00  13.85  89.66   0.00   9.00 101.79   0.73  40.26
   5_occ: 101.79   0.00  13.85  89.66   0.00   9.00 101.79   0.73  40.26
   5_bss: 104.35   2.56  16.41  92.22   2.56  11.56 104.35   3.30  42.82
------------------------------------------------------------------------
 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:    1.267    0.018    0.413
   1_adp:    1.267    0.018    0.413
   1_occ:    1.267    0.018    0.413
   2_bss:    1.267    0.018    0.413
   2_xyz:    1.881    0.042    0.563
   2_adp:    1.881    0.042    0.563
   2_occ:    1.881    0.042    0.563
   3_bss:    1.881    0.042    0.563
   3_xyz:    1.753    0.051    0.642
   3_adp:    1.753    0.051    0.642
   3_occ:    1.753    0.051    0.642
   4_bss:    1.753    0.051    0.642
   4_xyz:    2.006    0.021    0.715
   4_adp:    2.006    0.021    0.715
   4_occ:    2.006    0.021    0.715
   5_bss:    2.006    0.021    0.715
   5_xyz:    2.104    0.074    0.748
   5_adp:    2.104    0.074    0.748
   5_occ:    2.104    0.074    0.748
   5_bss:    2.104    0.074    0.748
------------------------------------------------------------------------

CPU time actual refinement: 331.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_702/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_702/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_702/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_702/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_702/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.09 
  Macro-tasks:
    bulk solvent and scale       = 42.37  
    individual site refinement   = 134.87 
    weights calculation          = 32.09  
    collect and process          = 6.56   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 216.00 
  Micro-tasks:
    mask                            = 2.35   
    f_calc                          = 100.96 
    alpha_beta                      = 8.54   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.42 
    fmodel                         = 7.47   
    r_factors                      = 0.23   
    phase_errors                   = 10.53  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 242.91 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.704 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    638 calls, 100.60 s
gradients_fft:          583 calls,  98.54 s

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

# Date 2008-01-16 Time 02:13:41 PST -0800 (1200478421.19 s)
Start R-work = 0.4873, R-free = 0.4762 (no bulk solvent and anisotropic scale)
Final R-work = 0.1410, R-free = 0.1864 (no bulk solvent and anisotropic scale)

Start R-work = 0.4796, R-free = 0.4657
Final R-work = 0.1246, R-free = 0.1714