# Date 2008-01-16 Time 02:56:38 PST -0800 (1200480998.40 s)
#phil __OFF__

Command line arguments: "../1036.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 = 14492
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1036

-------------------------------------------------------------------------------
  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: (71.3037, 47.1647, 85.0941, 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: 3.33, per 1000 atoms: 1.18


================================== 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: (71.3037, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97125
Completeness in resolution range: 0.940648
Completeness with d_max=infinity: 0.937811

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9712

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: (71.3037, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97125
Completeness in resolution range: 0.940648
Completeness with d_max=infinity: 0.937811

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2189 [2188/2217]  1972   216   9.9%
  bin  2:  4.2189 -  3.3608 [2095/2114]  1884   211  10.1%
  bin  3:  3.3608 -  2.9396 [2073/2093]  1862   211  10.2%
  bin  4:  2.9396 -  2.6724 [2059/2084]  1862   197   9.6%
  bin  5:  2.6724 -  2.4818 [2049/2068]  1836   213  10.4%
  bin  6:  2.4818 -  2.3360 [2027/2073]  1829   198   9.8%
  bin  7:  2.3360 -  2.2194 [2014/2047]  1813   201  10.0%
  bin  8:  2.2194 -  2.1231 [2012/2048]  1810   202  10.0%
  bin  9:  2.1231 -  2.0415 [2010/2039]  1807   203  10.1%
  bin 10:  2.0415 -  1.9712 [1062/2042]   955   107  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1036/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 28
        2.42 -     3.04: 2187
        3.04 -     3.66: 4675
        3.66 -     4.28: 8990
        4.28 -     4.90: 12373
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.921 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.947 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.091 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28248 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_1036/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1036/model_refine_001.geo

CPU time processing inputs: 9.32


============================ 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 = 71.30375 47.16465 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4533   r_free= 0.4461   ksol= 0.00   Bsol= 0.00   scale= 0.809    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.253248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7060 0.99   1417  159 0.3766 0.3662      6.5558        6.52|
|  2:  4.7060 -  3.7542 0.99   1370  144 0.3564 0.3689      6.7082      6.7248|
|  3:  3.7542 -  3.2852 0.99   1336  158 0.4043 0.3757      6.6049      6.6328|
|  4:  3.2852 -  2.9874 0.99   1344  148 0.4314 0.4322      6.4708      6.4405|
|  5:  2.9874 -  2.7747 0.99   1311  147 0.4781 0.5000      6.3425      6.3778|
|  6:  2.7747 -  2.6120 0.98   1320  146 0.4774 0.4904      6.2444       6.197|
|  7:  2.6120 -  2.4818 0.99   1318  146 0.5034 0.4373      6.2474      6.1487|
|  8:  2.4818 -  2.3742 0.98   1293  139 0.5086 0.4977       6.148       6.189|
|  9:  2.3742 -  2.2831 0.98   1318  153 0.4988 0.4967      6.1078      6.0838|
| 10:  2.2831 -  2.2046 0.98   1283  139 0.4977 0.5287      6.0775      6.1064|
| 11:  2.2046 -  2.1358 0.99   1299  144 0.4989 0.4710      6.0224      6.0115|
| 12:  2.1358 -  2.0749 0.98   1282  144 0.5151 0.5542      5.9512      6.0048|
| 13:  2.0749 -  2.0204 0.95   1263  141 0.5255 0.4731      5.8778      5.8139|
| 14:  2.0204 -  1.9712 0.36    476   51 0.5363 0.5350      5.8391      5.7933|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7060  1417   159  0.73  31.64   0.81     0.75      61117.51|
|  2:  4.7060 -  3.7542  1370   144  0.74  31.57   0.90     0.80      86546.23|
|  3:  3.7542 -  3.2852  1336   158  0.65  39.98   0.85     0.76      94938.92|
|  4:  3.2852 -  2.9874  1344   148  0.56  47.03   0.82     0.66      88854.88|
|  5:  2.9874 -  2.7747  1311   147  0.47  54.52   0.75     0.56      75750.71|
|  6:  2.7747 -  2.6120  1320   146  0.45  55.72   0.76     0.53      64557.59|
|  7:  2.6120 -  2.4818  1318   146  0.47  54.13   0.75     0.53      55153.24|
|  8:  2.4818 -  2.3742  1293   139  0.46  55.52   0.72     0.54      50538.67|
|  9:  2.3742 -  2.2831  1318   153  0.44  56.95   0.75     0.52      46868.34|
| 10:  2.2831 -  2.2046  1283   139  0.40  59.94   0.76     0.47      46967.09|
| 11:  2.2046 -  2.1358  1299   144  0.34  64.75   0.79     0.41      45778.88|
| 12:  2.1358 -  2.0749  1282   144  0.28  69.16   0.75     0.35      45243.54|
| 13:  2.0749 -  2.0204  1263   141  0.29  68.29   0.73     0.37      37847.16|
| 14:  2.0204 -  1.9712   476    51  0.40  60.46   0.70     0.45      27950.69|
|alpha:            min =        0.35 max =            0.80 mean =         0.56|
|beta:             min =    27950.69 max =        94938.92 mean =     60952.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.90|
|phase err.(test): min =        0.00 max =           89.94 mean =        52.94|
|-----------------------------------------------------------------------------|

============================== 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 = 11.427349             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.527   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.916423              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.486   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1509 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2618 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3909 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5064 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6552 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7713 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.833 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.722 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4603   r_free= 0.4546   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.256269                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4453   r_free= 0.4362   ksol= 0.30   Bsol= 20.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.21,7.85,8.18,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.252333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.709537              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.859   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.872521              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.978   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4453      final r-factor (work) = 0.3495          |
| start r-factor (free) = 0.4362      final r-factor (free) = 0.3832          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.1973 = 9.71 * 0.50 * 6.2545 + 1.00 * 53.8333                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.9006 = 9.71 * 0.50 * 6.1315 + 1.00 * 0.1336                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3495      final r-factor (work) = 0.2978          |
| start r-factor (free) = 0.3832      final r-factor (free) = 0.3532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3642 = 0.87 * 1.00 * 6.1315 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2540 = 0.87 * 1.00 * 6.0058 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.59   11.68    None  None   None       |
|    all(noH): 2823   0      0.00    80.59   11.68    None  None   None       |
|    Sol.    : 438    0      0.00    80.59   28.81    None  None   None       |
|    Mac.    : 2385   0      0.00    78.32   8.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.059: 1491   |   5:    40.296 -  48.356:   69        |
|      1:     8.059 -  16.119:  698   |   6:    48.356 -  56.415:   32        |
|      2:    16.119 -  24.178:  263   |   7:    56.415 -  64.474:   20        |
|      3:    24.178 -  32.237:  146   |   8:    64.474 -  72.533:    7        |
|      4:    32.237 -  40.296:   95   |   9:    72.533 -  80.593:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2978 r_free = 0.3532             target_work(ml) = 5.970         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2973 r_free = 0.3536             target_work(ml) = 5.970         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2973   r_free= 0.3536   ksol= 0.30   Bsol= 20.00   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.21,7.85,8.18,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.969687                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2942   r_free= 0.3499   ksol= 0.32   Bsol= 46.70   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.80,4.38,5.40,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.970412                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.030853              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.714   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.424596              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.780  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2942      final r-factor (work) = 0.2080          |
| start r-factor (free) = 0.3499      final r-factor (free) = 0.2663          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2355 = 4.03 * 0.50 * 6.0047 + 1.00 * 0.1336                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8249 = 4.03 * 0.50 * 5.8345 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2080      final r-factor (work) = 0.1914          |
| start r-factor (free) = 0.2663      final r-factor (free) = 0.2447          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4911 = 0.42 * 1.00 * 5.8345 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4071 = 0.42 * 1.00 * 5.6438 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.78   12.10    None  None   None       |
|    all(noH): 2823   0      0.00    80.78   12.10    None  None   None       |
|    Sol.    : 438    0      1.46    80.78   33.17    None  None   None       |
|    Mac.    : 2385   0      0.00    78.58   8.23     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.078: 1549   |   5:    40.388 -  48.466:   89        |
|      1:     8.078 -  16.155:  666   |   6:    48.466 -  56.543:   46        |
|      2:    16.155 -  24.233:  190   |   7:    56.543 -  64.621:   24        |
|      3:    24.233 -  32.310:  107   |   8:    64.621 -  72.698:    6        |
|      4:    32.310 -  40.388:  144   |   9:    72.698 -  80.776:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1914 r_free = 0.2447             target_work(ml) = 5.602         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1913 r_free = 0.2447             target_work(ml) = 5.602         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1913   r_free= 0.2447   ksol= 0.32   Bsol= 46.70   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.80,4.38,5.40,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.601530                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1898   r_free= 0.2415   ksol= 0.32   Bsol= 46.70   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,2.95,3.62,0.00,0.00,0.00); trace/3= 3.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.601201                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.334169              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.104  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.701053              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.026  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1898      final r-factor (work) = 0.1464          |
| start r-factor (free) = 0.2415      final r-factor (free) = 0.1906          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6629 = 2.33 * 0.50 * 5.6524 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4724 = 2.33 * 0.50 * 5.4953 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1464      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.1906      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8632 = 0.70 * 1.00 * 5.4953 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7551 = 0.70 * 1.00 * 5.3382 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.27   12.75    None  None   None       |
|    all(noH): 2823   0      0.00    84.27   12.75    None  None   None       |
|    Sol.    : 438    0      1.27    82.58   36.57    None  None   None       |
|    Mac.    : 2385   0      0.00    84.27   8.37     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.427: 1608   |   5:    42.134 -  50.561:  117        |
|      1:     8.427 -  16.854:  603   |   6:    50.561 -  58.987:   63        |
|      2:    16.854 -  25.280:  188   |   7:    58.987 -  67.414:   25        |
|      3:    25.280 -  33.707:  101   |   8:    67.414 -  75.841:    9        |
|      4:    33.707 -  42.134:  105   |   9:    75.841 -  84.268:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1368 r_free = 0.1833             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1832             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1832   ksol= 0.32   Bsol= 46.70   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,2.95,3.62,0.00,0.00,0.00); trace/3= 3.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.318844                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1838   ksol= 0.33   Bsol= 46.70   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,2.55,3.04,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.320223                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.855034              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.049  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.571186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.477  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1838      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6817 = 2.86 * 0.50 * 5.3399 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5871 = 2.86 * 0.50 * 5.2669 + 1.00 * 0.0686                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2878 = 1.57 * 1.00 * 5.2669 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1848 = 1.57 * 1.00 * 5.2005 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.00   12.85    None  None   None       |
|    all(noH): 2823   0      0.00    93.00   12.85    None  None   None       |
|    Sol.    : 438    0      1.32    83.91   37.12    None  None   None       |
|    Mac.    : 2385   0      0.00    93.00   8.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.300: 1734   |   5:    46.501 -  55.801:   81        |
|      1:     9.300 -  18.600:  543   |   6:    55.801 -  65.101:   55        |
|      2:    18.600 -  27.900:  157   |   7:    65.101 -  74.401:   17        |
|      3:    27.900 -  37.201:  112   |   8:    74.401 -  83.701:    7        |
|      4:    37.201 -  46.501:  113   |   9:    83.701 -  93.001:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1174 r_free = 0.1652             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1173 r_free = 0.1651             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1651   ksol= 0.33   Bsol= 46.70   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,2.55,3.04,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197824                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1651   ksol= 0.33   Bsol= 46.70   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,2.60,3.03,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.197826                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.895743              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.710  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.391023              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.364  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9979 = 1.90 * 0.50 * 5.2004 + 1.00 * 0.0686                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9818 = 1.90 * 0.50 * 5.1947 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0449 = 0.39 * 1.00 * 5.1947 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0418 = 0.39 * 1.00 * 5.1912 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.17   12.60    None  None   None       |
|    all(noH): 2823   0      0.00    93.17   12.60    None  None   None       |
|    Sol.    : 438    0      1.31    83.38   36.25    None  None   None       |
|    Mac.    : 2385   0      0.00    93.17   8.26     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.317: 1754   |   5:    46.584 -  55.901:   82        |
|      1:     9.317 -  18.634:  546   |   6:    55.901 -  65.217:   49        |
|      2:    18.634 -  27.950:  146   |   7:    65.217 -  74.534:   15        |
|      3:    27.950 -  37.267:  114   |   8:    74.534 -  83.851:    7        |
|      4:    37.267 -  46.584:  107   |   9:    83.851 -  93.168:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1620             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1619             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1619   ksol= 0.33   Bsol= 46.70   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,2.60,3.03,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185366                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7060 0.99   1417  159 0.0973 0.1293      5.3701      5.5281|
|  2:  4.7060 -  3.7542 0.99   1370  144 0.0876 0.1117      5.4406      5.6425|
|  3:  3.7542 -  3.2852 0.99   1336  158 0.1084 0.1601      5.4912      5.8921|
|  4:  3.2852 -  2.9874 0.99   1344  148 0.1269 0.1566      5.4866      5.6015|
|  5:  2.9874 -  2.7747 0.99   1311  147 0.1380 0.1758      5.3667      5.5401|
|  6:  2.7747 -  2.6120 0.98   1320  146 0.1305 0.1992      5.2583      5.5164|
|  7:  2.6120 -  2.4818 0.99   1318  146 0.1290 0.1720      5.2069      5.4236|
|  8:  2.4818 -  2.3742 0.98   1293  139 0.1202 0.1733      5.0876      5.3285|
|  9:  2.3742 -  2.2831 0.98   1318  153 0.1238 0.1925      5.0691      5.3448|
| 10:  2.2831 -  2.2046 0.98   1283  139 0.1207 0.1738      5.0163      5.2539|
| 11:  2.2046 -  2.1358 0.99   1299  144 0.1204 0.1851      4.9864      5.3243|
| 12:  2.1358 -  2.0749 0.98   1282  144 0.1171 0.1739      4.9101       5.116|
| 13:  2.0749 -  2.0204 0.95   1263  141 0.1267 0.1828      4.8381      5.1003|
| 14:  2.0204 -  1.9712 0.36    476   51 0.1054 0.1748      4.6795      4.8936|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7060  1417   159  0.94   8.62   0.98     0.95       6917.85|
|  2:  4.7060 -  3.7542  1370   144  0.95   7.94   1.01     0.99       8851.89|
|  3:  3.7542 -  3.2852  1336   158  0.93  11.83   1.03     1.02      10876.44|
|  4:  3.2852 -  2.9874  1344   148  0.91  14.33   1.01     0.99      10990.98|
|  5:  2.9874 -  2.7747  1311   147  0.89  17.06   0.99     0.96       9104.71|
|  6:  2.7747 -  2.6120  1320   146  0.89  17.05   0.99     0.96       7799.96|
|  7:  2.6120 -  2.4818  1318   146  0.90  15.93   0.99     0.96       6682.27|
|  8:  2.4818 -  2.3742  1293   139  0.90  16.20   0.99     0.96       5627.07|
|  9:  2.3742 -  2.2831  1318   153  0.90  16.62   1.00     0.98       5447.51|
| 10:  2.2831 -  2.2046  1283   139  0.90  16.19   1.00     0.96       4873.71|
| 11:  2.2046 -  2.1358  1299   144  0.89  17.35   1.00     0.95       4799.64|
| 12:  2.1358 -  2.0749  1282   144  0.91  15.91   1.00     0.99       4250.91|
| 13:  2.0749 -  2.0204  1263   141  0.89  17.15   1.00     0.99       3617.64|
| 14:  2.0204 -  1.9712   476    51  0.90  16.47   0.99     0.95       2786.35|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2786.35 max =        10990.98 mean =      6838.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.80 mean =        14.75|
|phase err.(test): min =        0.00 max =           88.36 mean =        14.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1619   ksol= 0.33   Bsol= 49.43   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.13,0.31,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185375                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1619   ksol= 0.33   Bsol= 49.43   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.13,0.31,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185375                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7060 0.99   1417  159 0.0973 0.1293      5.3701      5.5281|
|  2:  4.7060 -  3.7542 0.99   1370  144 0.0876 0.1117      5.4406      5.6424|
|  3:  3.7542 -  3.2852 0.99   1336  158 0.1084 0.1601      5.4911      5.8919|
|  4:  3.2852 -  2.9874 0.99   1344  148 0.1269 0.1566      5.4866      5.6016|
|  5:  2.9874 -  2.7747 0.99   1311  147 0.1380 0.1759      5.3668      5.5402|
|  6:  2.7747 -  2.6120 0.98   1320  146 0.1305 0.1992      5.2583      5.5163|
|  7:  2.6120 -  2.4818 0.99   1318  146 0.1290 0.1720      5.2069      5.4235|
|  8:  2.4818 -  2.3742 0.98   1293  139 0.1202 0.1733      5.0875      5.3285|
|  9:  2.3742 -  2.2831 0.98   1318  153 0.1238 0.1925      5.0691      5.3447|
| 10:  2.2831 -  2.2046 0.98   1283  139 0.1207 0.1737      5.0163       5.254|
| 11:  2.2046 -  2.1358 0.99   1299  144 0.1204 0.1852      4.9865      5.3245|
| 12:  2.1358 -  2.0749 0.98   1282  144 0.1171 0.1739      4.9103       5.116|
| 13:  2.0749 -  2.0204 0.95   1263  141 0.1267 0.1829      4.8381      5.1005|
| 14:  2.0204 -  1.9712 0.36    476   51 0.1054 0.1748      4.6797      4.8935|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7060  1417   159  0.94   8.62   0.98     0.95       6917.17|
|  2:  4.7060 -  3.7542  1370   144  0.95   7.94   1.01     0.99       8850.26|
|  3:  3.7542 -  3.2852  1336   158  0.93  11.83   1.03     1.02      10872.86|
|  4:  3.2852 -  2.9874  1344   148  0.91  14.33   1.01     0.99      10992.01|
|  5:  2.9874 -  2.7747  1311   147  0.89  17.06   0.99     0.96       9105.08|
|  6:  2.7747 -  2.6120  1320   146  0.89  17.05   0.99     0.96       7800.65|
|  7:  2.6120 -  2.4818  1318   146  0.90  15.93   0.99     0.96       6681.56|
|  8:  2.4818 -  2.3742  1293   139  0.90  16.20   0.99     0.96       5626.21|
|  9:  2.3742 -  2.2831  1318   153  0.90  16.61   1.00     0.98       5446.73|
| 10:  2.2831 -  2.2046  1283   139  0.90  16.19   1.00     0.96       4873.82|
| 11:  2.2046 -  2.1358  1299   144  0.89  17.35   1.00     0.95       4800.02|
| 12:  2.1358 -  2.0749  1282   144  0.91  15.91   1.00     0.99       4252.56|
| 13:  2.0749 -  2.0204  1263   141  0.89  17.16   1.00     0.99       3618.40|
| 14:  2.0204 -  1.9712   476    51  0.90  16.47   0.99     0.95       2787.01|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2787.01 max =        10992.01 mean =      6838.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.80 mean =        14.75|
|phase err.(test): min =        0.00 max =           88.36 mean =        14.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.73    95.90   15.33    None  None   None       |
|    all(noH): 2823   0      2.73    95.90   15.33    None  None   None       |
|    Sol.    : 438    0      4.04    86.11   38.99    None  None   None       |
|    Mac.    : 2385   0      2.73    95.90   10.99    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:     2.731 -  12.048: 1754   |   5:    49.315 -  58.632:   82        |
|      1:    12.048 -  21.365:  546   |   6:    58.632 -  67.948:   49        |
|      2:    21.365 -  30.681:  146   |   7:    67.948 -  77.265:   15        |
|      3:    30.681 -  39.998:  114   |   8:    77.265 -  86.582:    7        |
|      4:    39.998 -  49.315:  107   |   9:    86.582 -  95.899:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.389 - 5.925
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 340
   mapped sites are within: 0.712 - 5.925

peak=   10.776 closest distance to " CB  VAL A 230 " =    1.457
peak=    8.216 closest distance to " CG2 VAL A 296 " =    1.211
peak=    6.110 closest distance to " CG  LEU A   5 " =    1.283
peak=    6.024 closest distance to " NH2 ARG A  56 " =    2.268
peak=    5.626 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.544 closest distance to " CD2 LEU A   5 " =    1.200
peak=    5.403 closest distance to " CG  PRO A  54 " =    1.299
peak=    5.198 closest distance to " CD1AILE A 234 " =    1.080
peak=    5.192 closest distance to " CB  PRO A  54 " =    0.926
peak=    4.975 closest distance to " CB  SER A  63 " =    1.354
peak=    4.950 closest distance to " CG  PRO A 198 " =    1.295
peak=    4.876 closest distance to " CG  LEU A 228 " =    1.251
peak=    4.778 closest distance to " CG  PRO A 213 " =    1.278
peak=    4.714 closest distance to " O   HOH Z 247 " =    1.400
peak=    4.690 closest distance to " CB  GLN A 183 " =    1.291
peak=    4.617 closest distance to " O   HOH Z 126 " =    1.928
peak=    4.573 closest distance to " O   HOH Z  37 " =    1.175
peak=    4.558 closest distance to " O   HOH Z  48 " =    1.607
peak=    4.546 closest distance to " OD1 ASN A  69 " =    2.616
peak=    4.539 closest distance to " CB  ARG A 275 " =    0.858
peak=    4.498 closest distance to " CD2 LEU A 228 " =    1.227
peak=    4.483 closest distance to " O   PRO A 198 " =    1.564
peak=    4.446 closest distance to " O   HOH Z 232 " =    2.239
peak=    4.444 closest distance to " CB  VAL A 230 " =    1.233
peak=    4.433 closest distance to " CG  PRO A 243 " =    1.143
peak=    4.411 closest distance to " NH1 ARG A 138 " =    1.069
peak=    4.405 closest distance to " NE2 GLN A  11 " =    1.075
peak=    4.392 closest distance to " CB  SER A   3 " =    1.443
peak=    4.391 closest distance to " CB  GLU A 128 " =    1.065
peak=    4.371 closest distance to " CB  ASN A 148 " =    1.335
peak=    4.357 closest distance to " CB  VAL A 296 " =    1.065
peak=    4.342 closest distance to " O   HOH Z 316 " =    2.926
peak=    4.326 closest distance to " O   HOH Z 295 " =    1.570
peak=    4.306 closest distance to " O   HOH Z 298 " =    1.712
peak=    4.306 closest distance to " O   HOH Z 278 " =    0.921
peak=    4.278 closest distance to " O   HOH Z 369 " =    1.980
peak=    4.271 closest distance to " O   HOH Z 368 " =    2.148
peak=    4.246 closest distance to " CB  TYR A 169 " =    0.834
peak=    4.231 closest distance to " O   HOH Z 427 " =    3.182
peak=    4.202 closest distance to " CA  ALA A  21 " =    1.214
peak=    4.199 closest distance to " O   HOH Z 236 " =    1.823
peak=    4.193 closest distance to " CB  GLU A 152 " =    1.157
peak=    4.178 closest distance to " O   HOH Z 403 " =    1.750
peak=    4.163 closest distance to " O   HOH Z 303 " =    2.071
peak=    4.159 closest distance to " O   HOH Z 272 " =    1.876
peak=    4.148 closest distance to " CB  TRP A 266 " =    0.971
peak=    4.116 closest distance to " O   HOH Z 112 " =    1.524
peak=    4.082 closest distance to " O   SER A  87 " =    2.338
peak=    4.078 closest distance to " O   HOH Z 280 " =    3.003
peak=    4.077 closest distance to " O   HOH Z 263 " =    1.609
peak=    4.074 closest distance to " CB  VAL A 202 " =    1.588
peak=    4.068 closest distance to " O   HOH Z  88 " =    3.296
peak=    4.055 closest distance to " O   HOH Z  54 " =    2.346
peak=    4.041 closest distance to " O   HOH Z 124 " =    1.310
peak=    4.029 closest distance to " CB  VAL A 265 " =    1.230
peak=    4.027 closest distance to " CA  ALA A  51 " =    1.051
peak=    4.013 closest distance to " CD1 LEU A 300 " =    1.199
peak=    3.990 closest distance to " CB  ASP A 124 " =    0.712
peak=    3.990 closest distance to " O   HOH Z 128 " =    2.152
peak=    3.976 closest distance to " OD2 ASP A 286 " =    2.880
peak=    3.971 closest distance to " O   HOH Z  97 " =    1.955
peak=    3.970 closest distance to " O   HOH Z 371 " =    3.235
peak=    3.963 closest distance to " O   HOH Z 193 " =    1.846
peak=    3.952 closest distance to " O   HOH Z 411 " =    3.611
peak=    3.950 closest distance to " O   HOH Z 142 " =    1.604
peak=    3.945 closest distance to " CD  ARG A 269 " =    0.973
peak=    3.944 closest distance to " CA  TYR A  30 " =    0.957
peak=    3.944 closest distance to " CG1BVAL A  72 " =    1.624
peak=    3.933 closest distance to " O   HOH Z 423 " =    1.734
peak=    3.920 closest distance to " ND2 ASN A 249 " =    1.934
peak=    3.919 closest distance to " NH1 ARG A  56 " =    0.989
peak=    3.917 closest distance to " O   HOH Z  15 " =    2.126
peak=    3.914 closest distance to " O   TRP A 274 " =    1.835
peak=    3.912 closest distance to " CG2 THR A 221 " =    0.965
peak=    3.907 closest distance to " O   HOH Z  80 " =    1.745
peak=    3.879 closest distance to " O   HOH Z  68 " =    1.623
peak=    3.874 closest distance to " CG1 ILE A  33 " =    1.361
peak=    3.863 closest distance to " CB  LEU A 143 " =    1.195
peak=    3.857 closest distance to " O   HOH Z 126 " =    1.509
peak=    3.849 closest distance to " CA  THR A 221 " =    0.922
peak=    3.841 closest distance to " CB  LEU A 228 " =    1.317
peak=    3.834 closest distance to " O   HOH Z  78 " =    1.740
peak=    3.811 closest distance to " O   HOH Z  49 " =    2.511
peak=    3.809 closest distance to " O   HOH Z 134 " =    1.460
peak=    3.804 closest distance to " CB  SER A 216 " =    0.834
peak=    3.802 closest distance to " O   HOH Z 234 " =    3.742
peak=    3.800 closest distance to " NH1AARG A 145 " =    1.035
peak=    3.799 closest distance to " O   HOH Z 344 " =    2.917
peak=    3.793 closest distance to " NH2 ARG A 156 " =    1.162
peak=    3.793 closest distance to " CD BLYS A 290 " =    1.064
peak=    3.787 closest distance to " CB  TRP A 179 " =    1.374
peak=    3.775 closest distance to " CA  LEU A 282 " =    1.091
peak=    3.772 closest distance to " CG  ARG A  66 " =    2.717
peak=    3.770 closest distance to " NH2BARG A 102 " =    0.908
peak=    3.752 closest distance to " O   HOH Z  20 " =    1.822
peak=    3.751 closest distance to " CD  ARG A 159 " =    0.809
peak=    3.744 closest distance to " O   HOH Z 193 " =    2.057
peak=    3.741 closest distance to " CD2 LEU A 255 " =    1.405
peak=    3.739 closest distance to " CB  GLU A 277 " =    3.647
peak=    3.737 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.726 closest distance to " O   MET A 105 " =    1.776
peak=    3.723 closest distance to " O   HOH Z  63 " =    2.069
peak=    3.720 closest distance to " O   HOH Z 163 " =    1.560
peak=    3.715 closest distance to " O   HOH Z 426 " =    1.512
peak=    3.704 closest distance to " CA  LYS A 117 " =    1.273
peak=    3.693 closest distance to " O   HOH Z  61 " =    1.585
peak=    3.689 closest distance to " O   HOH Z 193 " =    1.609
peak=    3.687 closest distance to " O   ALA A 158 " =    1.360
peak=    3.681 closest distance to " O   HOH Z 271 " =    2.564
peak=    3.678 closest distance to " CD  LYS A 166 " =    1.343
peak=    3.676 closest distance to " CA  ASP A 191 " =    0.763
peak=    3.671 closest distance to " CZ  PHE A 192 " =    1.021
peak=    3.659 closest distance to " CA  MET A  40 " =    1.104
peak=    3.648 closest distance to " CA  VAL A  41 " =    0.874
peak=    3.640 closest distance to " CG1 VAL A 153 " =    0.982
peak=    3.638 closest distance to " O   HOH Z 425 " =    1.392
peak=    3.631 closest distance to " CB  ARG A  79 " =    1.444
peak=    3.629 closest distance to " O   HOH Z 345 " =    3.425
peak=    3.625 closest distance to " CA  ALA A 295 " =    1.076
peak=    3.625 closest distance to " O   HOH Z 203 " =    1.735
peak=    3.614 closest distance to " O   HOH Z 108 " =    1.238
peak=    3.612 closest distance to " O   THR A  31 " =    1.554
peak=    3.611 closest distance to " NZ  LYS A 117 " =    3.279
peak=    3.602 closest distance to " CA  THR A 264 " =    0.772
peak=    3.600 closest distance to " CB  ALA A 291 " =    1.388
peak=    3.597 closest distance to " O   HOH Z 102 " =    1.302
peak=    3.593 closest distance to " CG  LEU A 167 " =    1.130
peak=    3.593 closest distance to " O   HOH Z 133 " =    2.388
peak=    3.592 closest distance to " O   HOH Z 214 " =    2.072
peak=    3.590 closest distance to " O   HOH Z 313 " =    1.891
peak=    3.584 closest distance to " O   HOH Z  93 " =    2.692
peak=    3.583 closest distance to " CA  GLN A 194 " =    1.161
peak=    3.582 closest distance to " O   HOH Z 281 " =    4.420
peak=    3.580 closest distance to " CA  SER A  87 " =    0.890
peak=    3.579 closest distance to " O   HOH Z 116 " =    1.794
peak=    3.577 closest distance to " OG BSER A 164 " =    2.198
peak=    3.576 closest distance to " O   HOH Z 271 " =    1.917
peak=    3.573 closest distance to " CA  ASP A 140 " =    1.232
peak=    3.567 closest distance to " O   HOH Z 374 " =    3.121
peak=    3.562 closest distance to " O   HOH Z 346 " =    1.541
peak=    3.556 closest distance to " N   ASN A  39 " =    1.205
peak=    3.549 closest distance to " ND2 ASN A 187 " =    1.585
peak=    3.540 closest distance to " O   HOH Z 227 " =    1.720
peak=    3.539 closest distance to " OG  SER A  22 " =    2.861
peak=    3.536 closest distance to " O   HOH Z 261 " =    1.846
peak=    3.530 closest distance to " O   HOH Z   9 " =    2.065
peak=    3.526 closest distance to " CB  ALA A   9 " =    1.550
peak=    3.525 closest distance to " O   ALA A   1 " =    1.525
peak=    3.524 closest distance to " O   HOH Z 189 " =    2.748
peak=    3.520 closest distance to " CG BARG A 102 " =    1.847
peak=    3.518 closest distance to " O   HOH Z 437 " =    2.149
peak=    3.518 closest distance to " O   HOH Z 332 " =    1.577
peak=    3.517 closest distance to " O   HOH Z 132 " =    2.662
peak=    3.517 closest distance to " O   HOH Z 329 " =    3.753
peak=    3.516 closest distance to " CB  ASN A  39 " =    0.887
peak=    3.509 closest distance to " CB  ALA A 161 " =    0.940
peak=    3.498 closest distance to " NH1 ARG A  14 " =    1.036
peak=    3.498 closest distance to " O   HOH Z  21 " =    1.680
peak=    3.494 closest distance to " O   HOH Z 273 " =    2.628
peak=    3.492 closest distance to " CB  ASP A 140 " =    0.807
peak=    3.480 closest distance to " CB  ALA A 248 " =    1.060
peak=    3.478 closest distance to " CA  ALA A 248 " =    1.215
peak=    3.477 closest distance to " CB  GLN A  88 " =    1.225
peak=    3.476 closest distance to " CA  ALA A 158 " =    1.126
peak=    3.474 closest distance to " O   HOH Z  58 " =    1.480
peak=    3.471 closest distance to " CA  VAL A 126 " =    1.018
peak=    3.471 closest distance to " O   HOH Z  63 " =    1.125
peak=    3.469 closest distance to " CB  LEU A 255 " =    0.888
peak=    3.469 closest distance to " O   HOH Z 145 " =    1.899
peak=    3.467 closest distance to " CB  SER A 212 " =    1.209
peak=    3.466 closest distance to " O   HOH Z 420 " =    2.061
peak=    3.463 closest distance to " O   HOH Z  48 " =    2.295
peak=    3.458 closest distance to " O   HOH Z 215 " =    1.526
peak=    3.457 closest distance to " C   SER A  32 " =    1.027
peak=    3.456 closest distance to " CZ  PHE A 218 " =    1.041
peak=    3.454 closest distance to " O   HOH Z 383 " =    2.172
peak=    3.452 closest distance to " CB  PRO A 198 " =    0.961
peak=    3.449 closest distance to " CB  ASN A 187 " =    1.159
peak=    3.442 closest distance to " O   HOH Z  44 " =    2.267
peak=    3.432 closest distance to " CE1 TYR A 186 " =    1.303
peak=    3.429 closest distance to " O   HOH Z 244 " =    1.679
peak=    3.427 closest distance to " OE1 GLN A  11 " =    1.716
peak=    3.424 closest distance to " CG2 VAL A 257 " =    0.907
peak=    3.417 closest distance to " ND1 HIS A  86 " =    1.674
peak=    3.416 closest distance to " CA  ASN A 215 " =    1.210
peak=    3.415 closest distance to " CB  SER A  62 " =    1.295
peak=    3.413 closest distance to " O   HOH Z  68 " =    1.868
peak=    3.413 closest distance to " CE1 HIS A 108 " =    1.178
peak=    3.412 closest distance to " O   HOH Z  54 " =    1.523
peak=    3.411 closest distance to " C   ALA A 299 " =    0.982
peak=    3.409 closest distance to " O   HOH Z 197 " =    2.836
peak=    3.408 closest distance to " O   HOH Z 209 " =    2.435
peak=    3.405 closest distance to " CB  MET A  47 " =    1.099
peak=    3.403 closest distance to " CG2 VAL A 174 " =    1.356
peak=    3.403 closest distance to " O   HOH Z 355 " =    1.795
peak=    3.402 closest distance to " O   HOH Z 327 " =    2.348
peak=    3.399 closest distance to " O   HOH Z 184 " =    1.352
peak=    3.396 closest distance to " O   GLN A 278 " =    1.327
peak=    3.396 closest distance to " O   HOH Z  43 " =    2.023
peak=    3.393 closest distance to " CD1 ILE A 106 " =    0.972
peak=    3.390 closest distance to " O   HOH Z 236 " =    1.646
peak=    3.388 closest distance to " O   HOH Z 135 " =    1.937
peak=    3.388 closest distance to " OD1 ASN A 217 " =    1.651
peak=    3.384 closest distance to " O   HOH Z 185 " =    1.773
peak=    3.382 closest distance to " O   HOH Z 271 " =    2.095
peak=    3.381 closest distance to " CB  MET A  40 " =    0.781
peak=    3.380 closest distance to " CG AARG A 275 " =    1.169
peak=    3.380 closest distance to " ND1 HIS A  81 " =    1.602
peak=    3.376 closest distance to " O   HOH Z 133 " =    1.769
peak=    3.372 closest distance to " O   ASP A 124 " =    1.087
peak=    3.371 closest distance to " CE  LYS A  76 " =    0.870
peak=    3.363 closest distance to " CB BVAL A  41 " =    1.206
peak=    3.355 closest distance to " CD1 LEU A   5 " =    1.382
peak=    3.350 closest distance to " CD2 HIS A  81 " =    1.136
peak=    3.347 closest distance to " CD  LYS A 119 " =    1.476
peak=    3.346 closest distance to " CB  ARG A 139 " =    0.858
peak=    3.338 closest distance to " O   HOH Z 180 " =    2.090
peak=    3.337 closest distance to " CA  THR A 246 " =    1.206
peak=    3.336 closest distance to " O   HOH Z   4 " =    1.760
peak=    3.332 closest distance to " NE2 GLN A  58 " =    5.789
peak=    3.331 closest distance to " CA  ASN A  74 " =    1.204
peak=    3.329 closest distance to " O   HOH Z 158 " =    2.963
peak=    3.322 closest distance to " CG2 THR A 220 " =    0.962
peak=    3.318 closest distance to " CB  GLU A 236 " =    1.173
peak=    3.316 closest distance to " CB  THR A 157 " =    1.070
peak=    3.315 closest distance to " CB  ASN A 142 " =    0.932
peak=    3.315 closest distance to " O   HOH Z 172 " =    3.934
peak=    3.313 closest distance to " O   HOH Z 394 " =    1.749
peak=    3.312 closest distance to " NZ  LYS A  48 " =    1.420
peak=    3.309 closest distance to " CB  SER A  28 " =    0.944
peak=    3.308 closest distance to " CA  ARG A  36 " =    1.118
peak=    3.306 closest distance to " CA  ILE A 106 " =    0.819
peak=    3.301 closest distance to " CG1 VAL A 174 " =    1.182
peak=    3.300 closest distance to " CB  TYR A  30 " =    1.451
peak=    3.296 closest distance to " O   HOH Z 216 " =    2.603
peak=    3.295 closest distance to " CB  ARG A 190 " =    1.754
peak=    3.294 closest distance to " O   HOH Z 227 " =    1.946
peak=    3.291 closest distance to " O   HOH Z 128 " =    1.981
peak=    3.288 closest distance to " O   HOH Z 109 " =    2.608
peak=    3.287 closest distance to " O   HOH Z 276 " =    1.220
peak=    3.284 closest distance to " O   HOH Z  48 " =    1.569
peak=    3.284 closest distance to " CG2 ILE A 120 " =    1.286
peak=    3.281 closest distance to " CB  LEU A 237 " =    0.948
peak=    3.281 closest distance to " O   ALA A 165 " =    1.386
peak=    3.279 closest distance to " O   HOH Z 155 " =    2.979
peak=    3.275 closest distance to " O   HOH Z 183 " =    1.391
peak=    3.271 closest distance to " O   HOH Z 114 " =    1.216
peak=    3.271 closest distance to " CG1 VAL A 296 " =    1.229
peak=    3.271 closest distance to " CD  GLU A 152 " =    0.903
peak=    3.270 closest distance to " CB  ASN A 148 " =    1.904
peak=    3.270 closest distance to " CA  ASN A 176 " =    1.117
peak=    3.269 closest distance to " O   HOH Z  48 " =    1.810
peak=    3.266 closest distance to " O   HOH Z 290 " =    1.132
peak=    3.263 closest distance to " O   HOH Z 171 " =    3.803
peak=    3.260 closest distance to " CB  SER A 141 " =    0.990
peak=    3.260 closest distance to " CG1 ILE A  49 " =    1.554
peak=    3.257 closest distance to " CG2AVAL A 121 " =    2.276
peak=    3.256 closest distance to " CA  GLY A 211 " =    1.230
peak=    3.254 closest distance to " O   HOH Z 410 " =    1.471
peak=    3.253 closest distance to " CA  GLY A 267 " =    0.954
peak=    3.253 closest distance to " CB  LYS A 117 " =    1.167
peak=    3.252 closest distance to " CA  ALA A 154 " =    1.164
peak=    3.251 closest distance to " N   ASN A 127 " =    1.218
peak=    3.248 closest distance to " N   SER A 135 " =    1.407
peak=    3.248 closest distance to " O   HOH Z 118 " =    1.514
peak=    3.244 closest distance to " O   HOH Z  40 " =    1.457
peak=    3.244 closest distance to " N   ARG A 156 " =    1.402
peak=    3.243 closest distance to " C   LYS A 290 " =    1.337
peak=    3.240 closest distance to " CB  LYS A 193 " =    1.190
peak=    3.240 closest distance to " O   HOH Z 374 " =    2.564
peak=    3.237 closest distance to " O   HOH Z 279 " =    2.258
peak=    3.236 closest distance to " O   HOH Z 147 " =    1.639
peak=    3.230 closest distance to " O   HOH Z  30 " =    1.140
peak=    3.226 closest distance to " OD2 ASP A 200 " =    1.358
peak=    3.225 closest distance to " CA  ALA A 160 " =    0.876
peak=    3.222 closest distance to " CB  ALA A 295 " =    1.309
peak=    3.213 closest distance to " O   ASN A 217 " =    1.277
peak=    3.212 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.209 closest distance to " O   HOH Z 260 " =    1.151
peak=    3.208 closest distance to " OE1 GLN A  58 " =    1.224
peak=    3.205 closest distance to " O   HOH Z 406 " =    1.575
peak=    3.205 closest distance to " OE1 GLU A   2 " =    2.165
peak=    3.204 closest distance to " CG  MET A 185 " =    1.036
peak=    3.200 closest distance to " CG  MET A 185 " =    1.276
peak=    3.194 closest distance to " CB  THR A  82 " =    1.294
peak=    3.193 closest distance to " CD1 LEU A 101 " =    1.151
peak=    3.191 closest distance to " N   VAL A 126 " =    1.292
peak=    3.191 closest distance to " O   HOH Z 353 " =    2.797
peak=    3.188 closest distance to " O   HOH Z 280 " =    2.445
peak=    3.187 closest distance to " CG1 ILE A 151 " =    1.144
peak=    3.183 closest distance to " O   PRO A 213 " =    1.533
peak=    3.183 closest distance to " O   HOH Z 213 " =    1.623
peak=    3.182 closest distance to " CB  GLN A  89 " =    1.084
peak=    3.180 closest distance to " OH  TYR A 214 " =    1.224
peak=    3.177 closest distance to " CA  GLU A 152 " =    0.811
peak=    3.174 closest distance to " CE2 TYR A 186 " =    0.939
peak=    3.168 closest distance to " NZ  LYS A  76 " =    1.330
peak=    3.168 closest distance to " O   HOH Z 391 " =    3.012
peak=    3.167 closest distance to " O   HOH Z 175 " =    3.574
peak=    3.166 closest distance to " CD  ARG A 138 " =    1.103
peak=    3.160 closest distance to " CB  GLU A  46 " =    1.067
peak=    3.156 closest distance to " O   HOH Z 302 " =    1.952
peak=    3.152 closest distance to " O   HOH Z 151 " =    2.070
peak=    3.147 closest distance to " O   HOH Z 420 " =    5.925
peak=    3.141 closest distance to " N   GLN A 278 " =    0.990
peak=    3.141 closest distance to " CD  ARG A 219 " =    1.013
peak=    3.139 closest distance to " O   HOH Z 422 " =    2.666
peak=    3.139 closest distance to " O   HOH Z  10 " =    1.838
peak=    3.138 closest distance to " NH2BARG A 145 " =    2.126
peak=    3.134 closest distance to " O   HOH Z 197 " =    1.882
peak=    3.134 closest distance to " OG1 THR A 246 " =    3.222
peak=    3.133 closest distance to " CA  LEU A 101 " =    1.648
peak=    3.132 closest distance to " O   GLN A  58 " =    1.706
peak=    3.132 closest distance to " OG  SER A 206 " =    1.252
peak=    3.130 closest distance to " CD2 TYR A 186 " =    1.013
peak=    3.126 closest distance to " OG1 THR A 279 " =    1.693
peak=    3.125 closest distance to " O   HOH Z 367 " =    3.540
peak=    3.122 closest distance to " CG2 VAL A 202 " =    1.200
peak=    3.121 closest distance to " O   HOH Z 368 " =    3.561
peak=    3.120 closest distance to " CG  MET A 188 " =    1.146
peak=    3.115 closest distance to " O   HOH Z 435 " =    1.995
peak=    3.114 closest distance to " NE  ARG A 156 " =    1.032
peak=    3.101 closest distance to " O   HOH Z 305 " =    3.537
peak=    3.100 closest distance to " O   HOH Z 357 " =    2.005
peak=    3.099 closest distance to " OD1 ASP A 286 " =    1.695
peak=    3.098 closest distance to " N   ALA A 256 " =    1.075
peak=    3.093 closest distance to " CB  VAL A 268 " =    0.871
peak=    3.089 closest distance to " O   HOH Z 301 " =    1.820
peak=    3.087 closest distance to " O   HOH Z  59 " =    2.317
peak=    3.080 closest distance to " CB  LEU A 261 " =    0.884
peak=    3.074 closest distance to " O   HOH Z 211 " =    2.530
peak=    3.071 closest distance to " O   THR A 220 " =    1.321
peak=    3.069 closest distance to " O   HOH Z 427 " =    3.143
peak=    3.066 closest distance to " CG2 THR A  82 " =    0.713
peak=    3.065 closest distance to " O   HOH Z 298 " =    2.454
peak=    3.055 closest distance to " O   HOH Z 425 " =    2.123
peak=    3.045 closest distance to " CB  PRO A 243 " =    1.198
peak=    3.004 closest distance to " C   GLY A  80 " =    1.132

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.510
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.780 - 5.510

peak=   -5.355 closest distance to " CG2 VAL A 230 " =    0.835
peak=   -4.338 closest distance to " O   HOH Z 266 " =    4.563
peak=   -4.216 closest distance to " O   HOH Z 231 " =    1.815
peak=   -4.192 closest distance to " CG  LEU A 101 " =    2.592
peak=   -4.173 closest distance to " O   ILE A 109 " =    2.669
peak=   -4.159 closest distance to " CD  ARG A 156 " =    2.012
peak=   -4.087 closest distance to " O   HOH Z 290 " =    1.101
peak=   -4.072 closest distance to " NH2 ARG A  66 " =    1.737
peak=   -4.002 closest distance to " OG ASER A 134 " =    1.307
peak=   -3.984 closest distance to " CD  GLN A  88 " =    2.310
peak=   -3.932 closest distance to " O   HOH Z 103 " =    1.895
peak=   -3.929 closest distance to " O   HOH Z  52 " =    1.659
peak=   -3.893 closest distance to " CE2 TYR A  30 " =    2.779
peak=   -3.856 closest distance to " O   HOH Z 166 " =    1.894
peak=   -3.830 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.823 closest distance to " O   SER A 271 " =    2.230
peak=   -3.821 closest distance to " O   HOH Z  43 " =    1.642
peak=   -3.817 closest distance to " OXT GLY A 302 " =    3.005
peak=   -3.816 closest distance to " CG  GLN A 223 " =    2.214
peak=   -3.809 closest distance to " O   HOH Z  19 " =    2.190
peak=   -3.807 closest distance to " O   HOH Z  92 " =    1.395
peak=   -3.805 closest distance to " O   HOH Z  13 " =    1.331
peak=   -3.800 closest distance to " O   HOH Z 388 " =    1.929
peak=   -3.798 closest distance to " CG1 VAL A 296 " =    1.389
peak=   -3.792 closest distance to " C   ALA A 158 " =    1.302
peak=   -3.790 closest distance to " CD2 LEU A 237 " =    2.649
peak=   -3.763 closest distance to " N   ALA A 226 " =    2.128
peak=   -3.760 closest distance to " CD1 LEU A 101 " =    2.859
peak=   -3.745 closest distance to " NH2AARG A 275 " =    5.270
peak=   -3.744 closest distance to " N   THR A 157 " =    1.553
peak=   -3.731 closest distance to " CG  TRP A 266 " =    1.779
peak=   -3.720 closest distance to " OG1 THR A   4 " =    1.955
peak=   -3.716 closest distance to " CD  LYS A 289 " =    2.547
peak=   -3.711 closest distance to " CD1 LEU A 228 " =    2.389
peak=   -3.707 closest distance to " O   PRO A 163 " =    1.996
peak=   -3.696 closest distance to " CG2 VAL A 112 " =    2.632
peak=   -3.686 closest distance to " O   HOH Z  17 " =    1.500
peak=   -3.685 closest distance to " O   HOH Z 275 " =    1.513
peak=   -3.677 closest distance to " SG  CYS A 254 " =    3.178
peak=   -3.677 closest distance to " O   HOH Z 351 " =    1.390
peak=   -3.658 closest distance to " CD1 PHE A  59 " =    1.843
peak=   -3.658 closest distance to " O   HOH Z 377 " =    1.818
peak=   -3.643 closest distance to " C   ASN A 285 " =    2.486
peak=   -3.642 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.621 closest distance to " C   ASN A 187 " =    1.791
peak=   -3.618 closest distance to " N   GLN A  58 " =    1.838
peak=   -3.612 closest distance to " CD2 LEU A 300 " =    2.841
peak=   -3.610 closest distance to " OE1 GLN A  88 " =    1.045
peak=   -3.610 closest distance to " CG  MET A 105 " =    0.943
peak=   -3.606 closest distance to " O   HOH Z 184 " =    1.521
peak=   -3.605 closest distance to " CD1 LEU A   5 " =    2.507
peak=   -3.602 closest distance to " O   HOH Z 389 " =    1.798
peak=   -3.592 closest distance to " O   HOH Z 292 " =    4.543
peak=   -3.584 closest distance to " OD1 ASN A 148 " =    1.593
peak=   -3.584 closest distance to " CD  ARG A 139 " =    1.652
peak=   -3.583 closest distance to " O   HOH Z 368 " =    1.694
peak=   -3.583 closest distance to " OG  SER A  97 " =    2.240
peak=   -3.578 closest distance to " CD  GLN A  88 " =    0.853
peak=   -3.575 closest distance to " CB  SER A 134 " =    1.849
peak=   -3.573 closest distance to " O   HOH Z 185 " =    2.344
peak=   -3.563 closest distance to " C   HIS A 108 " =    1.184
peak=   -3.561 closest distance to " O   ALA A 256 " =    1.636
peak=   -3.557 closest distance to " O   HOH Z 266 " =    4.613
peak=   -3.551 closest distance to " CZ3 TRP A 179 " =    1.210
peak=   -3.551 closest distance to " O   HOH Z 151 " =    1.415
peak=   -3.549 closest distance to " OG  SER A  87 " =    1.546
peak=   -3.547 closest distance to " CB  ALA A 248 " =    1.992
peak=   -3.541 closest distance to " O   HOH Z 241 " =    1.222
peak=   -3.541 closest distance to " CB  TYR A  15 " =    2.223
peak=   -3.533 closest distance to " O   HOH Z 243 " =    1.638
peak=   -3.530 closest distance to " CG  ASP A  50 " =    2.359
peak=   -3.523 closest distance to " CG  PHE A 283 " =    2.686
peak=   -3.512 closest distance to " CG2 VAL A 296 " =    1.626
peak=   -3.508 closest distance to " O   HOH Z 222 " =    1.280
peak=   -3.506 closest distance to " O   HOH Z 211 " =    1.535
peak=   -3.497 closest distance to " O   HOH Z 196 " =    2.400
peak=   -3.496 closest distance to " O   HOH Z 407 " =    3.184
peak=   -3.495 closest distance to " O   GLY A 211 " =    1.474
peak=   -3.493 closest distance to " O   HOH Z  10 " =    1.546
peak=   -3.489 closest distance to " O   HOH Z  38 " =    1.521
peak=   -3.477 closest distance to " O   VAL A  67 " =    2.543
peak=   -3.474 closest distance to " O   HOH Z 166 " =    1.551
peak=   -3.469 closest distance to " O   HOH Z 128 " =    2.444
peak=   -3.461 closest distance to " O   HOH Z 295 " =    1.375
peak=   -3.461 closest distance to " O   HOH Z 165 " =    2.023
peak=   -3.454 closest distance to " CG  GLU A  53 " =    1.575
peak=   -3.452 closest distance to " N   ALA A  43 " =    2.480
peak=   -3.446 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.443 closest distance to " CD2 TYR A 293 " =    2.088
peak=   -3.429 closest distance to " O   GLY A 196 " =    1.153
peak=   -3.414 closest distance to " O   HOH Z 311 " =    3.749
peak=   -3.413 closest distance to " O   HOH Z  11 " =    1.737
peak=   -3.411 closest distance to " CB  PRO A 243 " =    2.628
peak=   -3.408 closest distance to " CG  GLU A   2 " =    1.763
peak=   -3.401 closest distance to " O   HOH Z  71 " =    1.073
peak=   -3.401 closest distance to " CE  MET A 105 " =    2.110
peak=   -3.390 closest distance to " CA  GLY A 241 " =    2.966
peak=   -3.389 closest distance to " O   HOH Z 189 " =    2.194
peak=   -3.388 closest distance to " C   ALA A   8 " =    1.549
peak=   -3.387 closest distance to " O   HOH Z 353 " =    2.336
peak=   -3.387 closest distance to " CA  ASN A 127 " =    1.062
peak=   -3.382 closest distance to " CG  GLU A 277 " =    1.186
peak=   -3.376 closest distance to " CG2 ILE A 263 " =    2.450
peak=   -3.373 closest distance to " OG BSER A 134 " =    1.253
peak=   -3.373 closest distance to " O   HOH Z  97 " =    1.906
peak=   -3.367 closest distance to " CZ  TYR A 172 " =    1.719
peak=   -3.366 closest distance to " O   HOH Z  60 " =    2.103
peak=   -3.360 closest distance to " ND2 ASN A  45 " =    1.024
peak=   -3.357 closest distance to " NH2 ARG A  79 " =    1.943
peak=   -3.346 closest distance to " O   ALA A   7 " =    1.543
peak=   -3.340 closest distance to " O   HOH Z  98 " =    2.114
peak=   -3.335 closest distance to " NE2 GLN A  88 " =    0.951
peak=   -3.334 closest distance to " NE1 TRP A 266 " =    2.195
peak=   -3.329 closest distance to " CG1 VAL A 112 " =    2.644
peak=   -3.329 closest distance to " O   HOH Z 431 " =    1.686
peak=   -3.328 closest distance to " OG  SER A  26 " =    1.307
peak=   -3.328 closest distance to " CB  ASN A  39 " =    2.070
peak=   -3.316 closest distance to " CE2 PHE A 218 " =    2.630
peak=   -3.312 closest distance to " CE1 TYR A 169 " =    2.523
peak=   -3.308 closest distance to " N   PHE A  59 " =    2.262
peak=   -3.297 closest distance to " ND2 ASN A  60 " =    1.633
peak=   -3.296 closest distance to " CA  GLY A 203 " =    2.348
peak=   -3.294 closest distance to " O   HOH Z 234 " =    4.359
peak=   -3.291 closest distance to " N   SER A 276 " =    1.339
peak=   -3.290 closest distance to " CB  ALA A 227 " =    2.345
peak=   -3.289 closest distance to " CH2 TRP A 177 " =    2.181
peak=   -3.279 closest distance to " CE  MET A  93 " =    1.187
peak=   -3.279 closest distance to " CG1 VAL A 296 " =    1.261
peak=   -3.273 closest distance to " CB  PRO A 163 " =    2.679
peak=   -3.271 closest distance to " CA  GLY A  98 " =    2.121
peak=   -3.270 closest distance to " O   HOH Z 423 " =    2.209
peak=   -3.270 closest distance to " O   HOH Z 120 " =    4.211
peak=   -3.269 closest distance to " CE2 PHE A 283 " =    2.586
peak=   -3.268 closest distance to " CG2 VAL A 296 " =    0.915
peak=   -3.264 closest distance to " O   MET A  40 " =    2.746
peak=   -3.261 closest distance to " O   HOH Z 377 " =    1.396
peak=   -3.259 closest distance to " CD2 LEU A 167 " =    1.773
peak=   -3.258 closest distance to " O   HOH Z 437 " =    1.807
peak=   -3.250 closest distance to " O   HOH Z 308 " =    1.667
peak=   -3.249 closest distance to " CD1 TRP A 179 " =    1.050
peak=   -3.244 closest distance to " O   HOH Z 252 " =    4.118
peak=   -3.244 closest distance to " O   HOH Z 317 " =    2.376
peak=   -3.242 closest distance to " CE3 TRP A 150 " =    2.142
peak=   -3.238 closest distance to " O   GLY A 118 " =    2.134
peak=   -3.238 closest distance to " C   MET A 188 " =    1.597
peak=   -3.236 closest distance to " CB  TRP A  85 " =    2.468
peak=   -3.234 closest distance to " N   THR A 235 " =    1.231
peak=   -3.233 closest distance to " O   HOH Z 350 " =    1.874
peak=   -3.227 closest distance to " CG  LEU A 228 " =    1.004
peak=   -3.226 closest distance to " CB  CYS A 254 " =    2.232
peak=   -3.222 closest distance to " O   HOH Z 177 " =    1.545
peak=   -3.220 closest distance to " CZ  TYR A 169 " =    1.761
peak=   -3.214 closest distance to " O   HOH Z 232 " =    1.961
peak=   -3.210 closest distance to " OH  TYR A 169 " =    0.968
peak=   -3.209 closest distance to " CB  ALA A  43 " =    2.516
peak=   -3.208 closest distance to " CE3 TRP A  70 " =    1.765
peak=   -3.207 closest distance to " NH1 ARG A  56 " =    2.492
peak=   -3.207 closest distance to " OXT GLY A 302 " =    3.437
peak=   -3.206 closest distance to " CA  GLY A 133 " =    2.249
peak=   -3.200 closest distance to " CB  GLN A  55 " =    1.418
peak=   -3.198 closest distance to " CB  ALA A 114 " =    2.372
peak=   -3.198 closest distance to " O   LEU A 167 " =    1.463
peak=   -3.195 closest distance to " CG  LYS A 193 " =    2.408
peak=   -3.194 closest distance to " C   GLN A 240 " =    2.325
peak=   -3.190 closest distance to " CB  ALA A  10 " =    2.186
peak=   -3.188 closest distance to " O   ALA A 161 " =    1.614
peak=   -3.183 closest distance to " O   HOH Z 435 " =    2.709
peak=   -3.183 closest distance to " NZ  LYS A 119 " =    3.452
peak=   -3.180 closest distance to " OG  SER A  62 " =    1.578
peak=   -3.180 closest distance to " ND2 ASN A  60 " =    1.488
peak=   -3.179 closest distance to " OD1 ASN A 249 " =    1.205
peak=   -3.174 closest distance to " O   HOH Z 191 " =    5.510
peak=   -3.172 closest distance to " CE BMET A  47 " =    1.780
peak=   -3.170 closest distance to " O   HOH Z 423 " =    1.147
peak=   -3.169 closest distance to " O   HOH Z  98 " =    1.573
peak=   -3.166 closest distance to " OG  SER A 206 " =    1.792
peak=   -3.164 closest distance to " N   SER A 212 " =    1.869
peak=   -3.164 closest distance to " OD2 ASP A 171 " =    1.809
peak=   -3.164 closest distance to " NH2 ARG A 159 " =    2.358
peak=   -3.163 closest distance to " O   GLY A 203 " =    2.448
peak=   -3.163 closest distance to " CD2 LEU A 237 " =    2.775
peak=   -3.161 closest distance to " O   HOH Z 341 " =    1.225
peak=   -3.160 closest distance to " O   HOH Z 292 " =    2.957
peak=   -3.155 closest distance to " ND2 ASN A  45 " =    1.201
peak=   -3.149 closest distance to " O   PRO A 198 " =    1.283
peak=   -3.148 closest distance to " NH1 ARG A 195 " =    2.289
peak=   -3.148 closest distance to " O   HOH Z 396 " =    1.752
peak=   -3.132 closest distance to " CE  LYS A  76 " =    2.722
peak=   -3.128 closest distance to " O   GLU A  44 " =    1.522
peak=   -3.127 closest distance to " CB  SER A 245 " =    2.289
peak=   -3.124 closest distance to " CB  ALA A 291 " =    2.146
peak=   -3.119 closest distance to " O   GLY A  80 " =    2.459
peak=   -3.118 closest distance to " O   HOH Z 380 " =    4.816
peak=   -3.117 closest distance to " CG  LYS A 166 " =    2.120
peak=   -3.111 closest distance to " CB  ALA A 291 " =    2.310
peak=   -3.107 closest distance to " CG1 VAL A 197 " =    2.345
peak=   -3.105 closest distance to " CG  ARG A 269 " =    2.303
peak=   -3.089 closest distance to " CA  ARG A 139 " =    0.995
peak=   -3.088 closest distance to " O   HOH Z 231 " =    1.529
peak=   -3.083 closest distance to " O   HOH Z 179 " =    2.295
peak=   -3.080 closest distance to " O   HOH Z 136 " =    1.920
peak=   -3.079 closest distance to " CA  VAL A 232 " =    2.352
peak=   -3.074 closest distance to " CD1 ILE A 199 " =    2.611
peak=   -3.073 closest distance to " N   GLY A  23 " =    2.135
peak=   -3.070 closest distance to " CB  ASP A 132 " =    2.261
peak=   -3.064 closest distance to " N   ALA A 248 " =    1.659
peak=   -3.060 closest distance to " CD2 LEU A   5 " =    1.127
peak=   -3.056 closest distance to " O   HOH Z 430 " =    1.726
peak=   -3.052 closest distance to " O   HOH Z 417 " =    2.753
peak=   -3.038 closest distance to " CG  PRO A 163 " =    2.514
peak=   -3.036 closest distance to " O   HOH Z 322 " =    1.070
peak=   -3.009 closest distance to " CB  ASP A 286 " =    2.194

================= 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    :  0.4533 0.4461   6.253248e+00   6.243830e+00
   1_bss:  0.4453 0.4362   6.252333e+00   6.236287e+00
   1_xyz:  0.3495 0.3832   6.088411e+00   6.145550e+00
   1_adp:  0.2978 0.3532   5.970305e+00   6.086547e+00
   1_occ:  0.2973 0.3536   5.969687e+00   6.087129e+00
   2_bss:  0.2942 0.3499   5.970412e+00   6.084426e+00
   2_xyz:  0.2080 0.2663   5.681271e+00   5.863184e+00
   2_adp:  0.1914 0.2447   5.602164e+00   5.789087e+00
   2_occ:  0.1913 0.2447   5.601530e+00   5.788944e+00
   3_bss:  0.1898 0.2415   5.601201e+00   5.786387e+00
   3_xyz:  0.1464 0.1906   5.368384e+00   5.580256e+00
   3_adp:  0.1368 0.1833   5.318971e+00   5.539828e+00
   3_occ:  0.1368 0.1832   5.318844e+00   5.539948e+00
   4_bss:  0.1367 0.1838   5.320223e+00   5.541453e+00
   4_xyz:  0.1206 0.1667   5.211320e+00   5.446438e+00
   4_adp:  0.1174 0.1652   5.198018e+00   5.440520e+00
   4_occ:  0.1173 0.1651   5.197824e+00   5.440399e+00
   5_bss:  0.1173 0.1651   5.197826e+00   5.440400e+00
   5_xyz:  0.1159 0.1635   5.190227e+00   5.432563e+00
   5_adp:  0.1160 0.1620   5.185330e+00   5.422855e+00
   5_occ:  0.1160 0.1619   5.185366e+00   5.423133e+00
   5_bss:  0.1160 0.1619   5.185375e+00   5.423135e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   8.209   7.854   8.177   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.209   7.854   8.177   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.209   7.854   8.177   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.209   7.854   8.177   0.000   0.000   0.000
   2_bss:  0.317  46.701   4.802   4.377   5.400   0.000   0.000   0.000
   2_xyz:  0.317  46.701   4.802   4.377   5.400   0.000   0.000   0.000
   2_adp:  0.317  46.701   4.802   4.377   5.400   0.000   0.000   0.000
   2_occ:  0.317  46.701   4.802   4.377   5.400   0.000   0.000   0.000
   3_bss:  0.324  46.701   2.995   2.952   3.619   0.000   0.000   0.000
   3_xyz:  0.324  46.701   2.995   2.952   3.619   0.000   0.000   0.000
   3_adp:  0.324  46.701   2.995   2.952   3.619   0.000   0.000   0.000
   3_occ:  0.324  46.701   2.995   2.952   3.619   0.000   0.000   0.000
   4_bss:  0.326  46.702   2.549   2.548   3.044   0.000   0.000   0.000
   4_xyz:  0.326  46.702   2.549   2.548   3.044   0.000   0.000   0.000
   4_adp:  0.326  46.702   2.549   2.548   3.044   0.000   0.000   0.000
   4_occ:  0.326  46.702   2.549   2.548   3.044   0.000   0.000   0.000
   5_bss:  0.326  46.702   2.566   2.599   3.033   0.000   0.000   0.000
   5_xyz:  0.326  46.702   2.566   2.599   3.033   0.000   0.000   0.000
   5_adp:  0.326  46.702   2.566   2.599   3.033   0.000   0.000   0.000
   5_occ:  0.326  46.702   2.566   2.599   3.033   0.000   0.000   0.000
   5_bss:  0.326  49.433  -0.187  -0.125   0.313   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.906 0.4842  0.5571    60959.633
   1_bss:  53.535 0.4732  0.6812    58691.521
   1_xyz:  43.149 0.6027  0.8564    41605.463
   1_adp:  37.985 0.6654  0.9568    34163.619
   1_occ:  38.038 0.6648  0.9554    34253.996
   2_bss:  37.851 0.6670  0.8573    34033.240
   2_xyz:  27.019 0.7892  0.9791    18542.586
   2_adp:  23.918 0.8229  1.0087    15399.457
   2_occ:  23.913 0.8229  1.0087    15386.286
   3_bss:  23.818 0.8238  0.9501    15276.570
   3_xyz:  18.179 0.8788  0.9825     9477.907
   3_adp:  17.199 0.8882  0.9857     8763.255
   3_occ:  17.197 0.8882  0.9856     8760.921
   4_bss:  17.235 0.8879  0.9684     8824.706
   4_xyz:  15.269 0.9046  0.9771     7225.077
   4_adp:  15.136 0.9059  0.9747     7151.885
   4_occ:  15.131 0.9059  0.9747     7150.837
   5_bss:  15.131 0.9059  0.9753     7151.219
   5_xyz:  14.924 0.9077  0.9748     6970.897
   5_adp:  14.693 0.9097  0.9740     6837.548
   5_occ:  14.695 0.9097  0.9739     6839.625
   5_bss:  14.695 0.9097  0.9738     6839.382
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3833e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3833e+01
   1_xyz:   1.652  0.013  0.106 17.970  0.007  4.112   1.3361e-01
   1_adp:   1.652  0.013  0.106 17.970  0.007  4.112   1.3361e-01
   1_occ:   1.652  0.013  0.106 17.970  0.007  4.112   1.3361e-01
   2_bss:   1.652  0.013  0.106 17.970  0.007  4.112   1.3361e-01
   2_xyz:   1.007  0.007  0.070 15.925  0.005  4.128   6.5889e-02
   2_adp:   1.007  0.007  0.070 15.925  0.005  4.128   6.5889e-02
   2_occ:   1.007  0.007  0.070 15.925  0.005  4.128   6.5889e-02
   3_bss:   1.007  0.007  0.070 15.925  0.005  4.128   6.5889e-02
   3_xyz:   0.989  0.006  0.075 15.494  0.003  4.126   5.8892e-02
   3_adp:   0.989  0.006  0.075 15.494  0.003  4.126   5.8892e-02
   3_occ:   0.989  0.006  0.075 15.494  0.003  4.126   5.8892e-02
   4_bss:   0.989  0.006  0.075 15.494  0.003  4.126   5.8892e-02
   4_xyz:   1.075  0.008  0.084 15.848  0.004  4.133   6.8585e-02
   4_adp:   1.075  0.008  0.084 15.848  0.004  4.133   6.8585e-02
   4_occ:   1.075  0.008  0.084 15.848  0.004  4.133   6.8585e-02
   5_bss:   1.075  0.008  0.084 15.848  0.004  4.133   6.8585e-02
   5_xyz:   0.966  0.007  0.076 15.341  0.003  4.114   5.7866e-02
   5_adp:   0.966  0.007  0.076 15.341  0.003  4.114   5.7866e-02
   5_occ:   0.966  0.007  0.076 15.341  0.003  4.114   5.7866e-02
   5_bss:   0.966  0.007  0.076 15.341  0.003  4.114   5.7866e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9797e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9797e+00
   1_xyz:  14.539  0.161  0.476 84.834  0.050  2.246   9.8161e-02
   1_adp:  14.539  0.161  0.476 84.834  0.050  2.246   9.8161e-02
   1_occ:  14.539  0.161  0.476 84.834  0.050  2.246   9.8161e-02
   2_bss:  14.539  0.161  0.476 84.834  0.050  2.246   9.8161e-02
   2_xyz:   6.205  0.053  0.239 86.398  0.031  2.312   6.4906e-02
   2_adp:   6.205  0.053  0.239 86.398  0.031  2.312   6.4906e-02
   2_occ:   6.205  0.053  0.239 86.398  0.031  2.312   6.4906e-02
   3_bss:   6.205  0.053  0.239 86.398  0.031  2.312   6.4906e-02
   3_xyz:   7.540  0.049  0.361 86.580  0.037  2.404   4.1606e-02
   3_adp:   7.540  0.049  0.361 86.580  0.037  2.404   4.1606e-02
   3_occ:   7.540  0.049  0.361 86.580  0.037  2.404   4.1606e-02
   4_bss:   7.540  0.049  0.361 86.580  0.037  2.404   4.1606e-02
   4_xyz:   8.766  0.057  0.530 82.177  0.039  2.297   5.6814e-02
   4_adp:   8.766  0.057  0.530 82.177  0.039  2.297   5.6814e-02
   4_occ:   8.766  0.057  0.530 82.177  0.039  2.297   5.6814e-02
   5_bss:   8.766  0.057  0.530 82.177  0.039  2.297   5.6814e-02
   5_xyz:   7.691  0.041  0.456 83.058  0.036  2.385   3.6641e-02
   5_adp:   7.691  0.041  0.456 83.058  0.036  2.385   3.6641e-02
   5_occ:   7.691  0.041  0.456 83.058  0.036  2.385   3.6641e-02
   5_bss:   7.691  0.041  0.456 83.058  0.036  2.385   3.6641e-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:  80.59   0.00  11.68  78.32   0.00   8.53  80.59   0.00  28.81
   1_occ:  80.59   0.00  11.68  78.32   0.00   8.53  80.59   0.00  28.81
   2_bss:  80.59   0.00  11.68  78.32   0.00   8.53  80.59   0.00  28.81
   2_xyz:  80.59   0.00  11.68  78.32   0.00   8.53  80.59   0.00  28.81
   2_adp:  80.78   0.00  12.10  78.58   0.00   8.23  80.78   1.46  33.17
   2_occ:  80.78   0.00  12.10  78.58   0.00   8.23  80.78   1.46  33.17
   3_bss:  80.78   0.00  12.10  78.58   0.00   8.23  80.78   1.46  33.17
   3_xyz:  80.78   0.00  12.10  78.58   0.00   8.23  80.78   1.46  33.17
   3_adp:  84.27   0.00  12.75  84.27   0.00   8.37  82.58   1.27  36.57
   3_occ:  84.27   0.00  12.75  84.27   0.00   8.37  82.58   1.27  36.57
   4_bss:  84.27   0.00  12.75  84.27   0.00   8.37  82.58   1.27  36.57
   4_xyz:  84.27   0.00  12.75  84.27   0.00   8.37  82.58   1.27  36.57
   4_adp:  93.00   0.00  12.85  93.00   0.00   8.40  83.91   1.32  37.12
   4_occ:  93.00   0.00  12.85  93.00   0.00   8.40  83.91   1.32  37.12
   5_bss:  93.00   0.00  12.85  93.00   0.00   8.40  83.91   1.32  37.12
   5_xyz:  93.00   0.00  12.85  93.00   0.00   8.40  83.91   1.32  37.12
   5_adp:  93.17   0.00  12.60  93.17   0.00   8.26  83.38   1.31  36.25
   5_occ:  93.17   0.00  12.60  93.17   0.00   8.26  83.38   1.31  36.25
   5_bss:  95.90   2.73  15.33  95.90   2.73  10.99  86.11   4.04  38.99
------------------------------------------------------------------------
 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:    1.206    0.017    0.412
   1_adp:    1.206    0.017    0.412
   1_occ:    1.206    0.017    0.412
   2_bss:    1.206    0.017    0.412
   2_xyz:    1.521    0.036    0.534
   2_adp:    1.521    0.036    0.534
   2_occ:    1.521    0.036    0.534
   3_bss:    1.521    0.036    0.534
   3_xyz:    1.490    0.051    0.586
   3_adp:    1.490    0.051    0.586
   3_occ:    1.490    0.051    0.586
   4_bss:    1.490    0.051    0.586
   4_xyz:    1.635    0.048    0.624
   4_adp:    1.635    0.048    0.624
   4_occ:    1.635    0.048    0.624
   5_bss:    1.635    0.048    0.624
   5_xyz:    1.684    0.045    0.632
   5_adp:    1.684    0.045    0.632
   5_occ:    1.684    0.045    0.632
   5_bss:    1.684    0.045    0.632
------------------------------------------------------------------------

CPU time actual refinement: 343.94


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1036/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_1036/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1036/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1036/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1036/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.79 
  Macro-tasks:
    bulk solvent and scale       = 40.13  
    individual site refinement   = 146.43 
    weights calculation          = 32.75  
    collect and process          = 6.63   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 226.07 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 108.04 
    alpha_beta                      = 8.19   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 118.53 
    fmodel                         = 7.20   
    r_factors                      = 0.24   
    phase_errors                   = 10.72  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 256.19 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.794 micro seconds
Total CPU time: 5.96 minutes
from_scatterers_fft:    645 calls, 107.66 s
gradients_fft:          590 calls, 104.86 s

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

# Date 2008-01-16 Time 03:02:37 PST -0800 (1200481357.95 s)
Start R-work = 0.4533, R-free = 0.4461 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1782 (no bulk solvent and anisotropic scale)

Start R-work = 0.4453, R-free = 0.4362
Final R-work = 0.1160, R-free = 0.1619